Microbial Pubs

All JGI Publications

2024

• Arthofer, Patrick et al. (2024) A giant virus infecting the amoeboflagellate Naegleria. Nature Communications 15(1), 3307. 10.1038/s41467-024-47308-2
• Arthofer, Patrick et al. (2024) A giant virus infecting the amoeboflagellate Naegleria. Nature Communications 15(1), 3307. 10.1038/s41467-024-47308-2
• Baltrus, David A. et al. (2024) Luteibacter mycovicinus sp. nov., a yellow-pigmented gammaproteobacterium found as an endohyphal symbiont of endophytic Ascomycota. International Journal of Systematic and Evolutionary Microbiology 74(5), 006240. 10.1099/ijsem.0.006240
• Baltrus, David A. et al. (2024) Luteibacter mycovicinus sp. nov., a yellow-pigmented gammaproteobacterium found as an endohyphal symbiont of endophytic Ascomycota. International Journal of Systematic and Evolutionary Microbiology 74(5), 006240. 10.1099/ijsem.0.006240
• Berner, Keely et al. (2024) Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T).. Microbiology Resource Announcements , e0051724. 10.1128/mra.00517-24
• Berner, Keely et al. (2024) Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615T) and Butyrivibrio fibrisolvens DSM 3071 (D1T).. Microbiology Resource Announcements , e0051724. 10.1128/mra.00517-24
• Bhat, Aditi et al. (2024) Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria. BMC Microbiology 24(1), 247. 10.1186/s12866-024-03391-5
• Bhat, Aditi et al. (2024) Horizontal gene transfer of the Mer operon is associated with large effects on the transcriptome and increased tolerance to mercury in nitrogen-fixing bacteria. BMC Microbiology 24(1), 247. 10.1186/s12866-024-03391-5
• Bowers, Robert M et al. (2024) scMicrobe PTA: near complete genomes from single bacterial cells. ISME Communications 4(1), ycae085. 10.1093/ismeco/ycae085
• Bowers, Robert M et al. (2024) scMicrobe PTA: near complete genomes from single bacterial cells. ISME Communications 4(1), ycae085. 10.1093/ismeco/ycae085
• Buscaglia, Marianne et al. (2024) Adaptation strategies of giant viruses to low-temperature marine ecosystems. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , wrae162. 10.1093/ismejo/wrae162
• Buscaglia, Marianne et al. (2024) Adaptation strategies of giant viruses to low-temperature marine ecosystems. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , wrae162. 10.1093/ismejo/wrae162
• Camargo, Antonio Pedro et al. (2024) Unveiling plasmid diversity in nature. Nature Reviews Microbiology 22(10), 597-597. 10.1038/s41579-024-01093-3
• Camargo, Antonio Pedro et al. (2024) Unveiling plasmid diversity in nature. Nature Reviews Microbiology 22(10), 597-597. 10.1038/s41579-024-01093-3
• Carhuaricra-Huaman, Dennis et al. (2024) Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host. PeerJ 12, e17206. 10.7717/peerj.17206
• Carhuaricra-Huaman, Dennis et al. (2024) Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths (Bradypus variegatus), the first from a non-human host. PeerJ 12, e17206. 10.7717/peerj.17206
• Chodkowski, John L. et al. (2024) Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems 9(4), e00064-24. 10.1128/msystems.00064-24
• Chodkowski, John L. et al. (2024) Bioactive exometabolites drive maintenance competition in simple bacterial communities. mSystems 9(4), e00064-24. 10.1128/msystems.00064-24
• Dieser, Markus et al. (2024) Seven genome sequences of airborne, bacterial isolates from Antarctica. Microbiology Resource Announcements 13(6), e01129-23. 10.1128/mra.01129-23
• Dieser, Markus et al. (2024) Seven genome sequences of airborne, bacterial isolates from Antarctica. Microbiology Resource Announcements 13(6), e01129-23. 10.1128/mra.01129-23
• Graham, Emily B. et al. (2024) A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nature Microbiology 9(7), 1873-1883. 10.1038/s41564-024-01686-x
• Graham, Emily B. et al. (2024) A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nature Microbiology 9(7), 1873-1883. 10.1038/s41564-024-01686-x
• Haghani, Nadia B. et al. (2024) Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection. Microbiology Spectrum 12(8), e00169-24. 10.1128/spectrum.00169-24
• Haghani, Nadia B. et al. (2024) Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection. Microbiology Spectrum 12(8), e00169-24. 10.1128/spectrum.00169-24
• Howard-Varona, Cristina et al. (2024) Environment-specific virocell metabolic reprogramming. The ISME Journal: Multidisciplinary Journal of Microbial Ecology , wrae055. 10.1093/ismejo/wrae055
• Jensen, Rasmus O. et al. (2024) Phylogenomics and genetic analysis of solvent-producing Clostridium species. Scientific Data 11(1), 432. 10.1038/s41597-024-03210-6
• Jensen, Rasmus O. et al. (2024) Phylogenomics and genetic analysis of solvent-producing Clostridium species. Scientific Data 11(1), 432. 10.1038/s41597-024-03210-6
• Jiao, Jian-Yu et al. (2024) Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. Microbiome 12(1), 123. 10.1186/s40168-024-01836-7
• Jiao, Jian-Yu et al. (2024) Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. Microbiome 12(1), 123. 10.1186/s40168-024-01836-7
• Kridler, Melanie R. et al. (2024) Draft genome sequences of Arthrobacter sp. AZCC_0090 and Mycobacterium sp. AZCC_0083 isolated from oligotrophic subsurface forest soil in the Santa Catalina mountains of Southern Arizona. Microbiology Resource Announcements 13(3), e01089-23. 10.1128/mra.01089-23
• Krinos, Arianna I. et al. (2024) Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake. Microbiome 12(1), 133. 10.1186/s40168-024-01831-y
• Krinos, Arianna I. et al. (2024) Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake. Microbiome 12(1), 133. 10.1186/s40168-024-01831-y
• Louie, Tiffany S et al. (2024) Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T. Letters in Applied Microbiology 77(4), ovae038. 10.1093/lambio/ovae038
• Louie, Tiffany S et al. (2024) Mo than meets the eye: genomic insights into molybdoenzyme diversity of Seleniivibrio woodruffii strain S4T. Letters in Applied Microbiology 77(4), ovae038. 10.1093/lambio/ovae038
• Marinos, Georgios et al. (2024) Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.. Microbiology Spectrum 12(2), e0114423. 10.1128/spectrum.01144-23
• Messyasz, Adriana et al. (2024) Genome analysis and description of Tunturibacter gen. nov. expands the diversity of Terriglobia in tundra soils. Environmental Microbiology 26(5), e16640. 10.1111/1462-2920.16640
• Messyasz, Adriana et al. (2024) Genome analysis and description of Tunturibacter gen. nov. expands the diversity of Terriglobia in tundra soils. Environmental Microbiology 26(5), e16640. 10.1111/1462-2920.16640
• Miliotis, Georgios et al. (2024) Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.. mBio 15(4), e00181-24. 10.1128/mbio.00181-24
• Miyada, Matthew G. et al. (2024) Fluorometric Analysis of Carrier-Protein-Dependent Biosynthesis through a Conformationally Sensitive Solvatochromic Pantetheinamide Probe. ACS Chemical Biology 19(7), 1416-1425. 10.1021/acschembio.4c00169
• Miyada, Matthew G. et al. (2024) Fluorometric Analysis of Carrier-Protein-Dependent Biosynthesis through a Conformationally Sensitive Solvatochromic Pantetheinamide Probe. ACS Chemical Biology 19(7), 1416-1425. 10.1021/acschembio.4c00169
• Pena, Michelle M et al. (2024) Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome Biology and Evolution 16(4), evae074. 10.1093/gbe/evae074
• Pena, Michelle M et al. (2024) Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome Biology and Evolution 16(4), evae074. 10.1093/gbe/evae074
• Pitot, Thomas M et al. (2024) Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes. ISME Communications 4(1), ycae048. 10.1093/ismeco/ycae048
• Pitot, Thomas M et al. (2024) Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes. ISME Communications 4(1), ycae048. 10.1093/ismeco/ycae048
• Romero, Miguel F et al. (2024) Novel Z-DNA binding domains in giant viruses. Journal of Biological Chemistry 300(8), 107504. 10.1016/j.jbc.2024.107504
• Romero, Miguel F et al. (2024) Novel Z-DNA binding domains in giant viruses. Journal of Biological Chemistry 300(8), 107504. 10.1016/j.jbc.2024.107504
• Schaible, George A. et al. (2024) Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells. PLOS Biology 22(7), e3002638. 10.1371/journal.pbio.3002638
• Schaible, George A. et al. (2024) Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells. PLOS Biology 22(7), e3002638. 10.1371/journal.pbio.3002638
• Sher, Andrew W et al. (2024) Dynamic nitrogen fixation in an aerobic endophyte of Populus. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrad012. 10.1093/ismejo/wrad012
• Sher, Andrew W et al. (2024) Dynamic nitrogen fixation in an aerobic endophyte of Populus. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 18(1), wrad012. 10.1093/ismejo/wrad012
• Smith, Heidi J. et al. (2024) Eight genome sequences of bacterial, environmental isolates from Canada Glacier, Antarctica. Microbiology Resource Announcements 13(8), e01130-23. 10.1128/mra.01130-23
• Smith, Heidi J. et al. (2024) Eight genome sequences of bacterial, environmental isolates from Canada Glacier, Antarctica. Microbiology Resource Announcements 13(8), e01130-23. 10.1128/mra.01130-23
• Soghomonian, Mark et al. (2024) Draft genome sequence of Nitrobacter vulgaris DSM 10236T. Microbiology Resource Announcements 13(8), e00305-24. 10.1128/mra.00305-24
• Soghomonian, Mark et al. (2024) Draft genome sequence of Nitrobacter vulgaris DSM 10236T. Microbiology Resource Announcements 13(8), e00305-24. 10.1128/mra.00305-24
• Wang, Yixu et al. (2024) Identification of synthetic consortia from a set of plant‐beneficial bacteria. Microbial Biotechnology 17(2), e14330. 10.1111/1751-7915.14330

2023

• (2023) Fast and accurate identification of plasmids and viruses in sequencing data using geNomad. Nature Biotechnology , 1-2. 10.1038/s41587-023-01982-7
• Anstett, Julia et al. (2023) A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Scientific Data 10(1), 332. 10.1038/s41597-023-02222-y
• Baltoumas, Fotis A et al. (2023) NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes. Nucleic Acids Research 52(D1), d502-d512. 10.1093/nar/gkad800
• Baltoumas, Fotis A et al. (2023) NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes. Nucleic Acids Research 52(D1), d502-d512. 10.1093/nar/gkad800
• Baltoumas, Fotis A et al. (2023) NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes. Nucleic Acids Research 52(D1), d502-d512. 10.1093/nar/gkad800
• Baltoumas, Fotis A. et al. (2023) Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters. Frontiers in Bioinformatics 3, 1157956. 10.3389/fbinf.2023.1157956
• Bhattacharjee, Ananda S. et al. (2023) Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids. ISME Communications 3(1), 10. 10.1038/s43705-022-00210-8
• Bowers, Robert M. et al. (2023) Gone with a trace: cataloguing the disappearing gut microbes. Nature Reviews Microbiology , 1-1. 10.1038/s41579-023-00968-1
• Bunbury, Freddy et al. (2023) Shedding light on spatial structure and dynamics in phototrophic biofilms. Current Opinion in Systems Biology 36, 100480. 10.1016/j.coisb.2023.100480
• Bunbury, Freddy et al. (2023) Shedding light on spatial structure and dynamics in phototrophic biofilms. Current Opinion in Systems Biology 36, 100480. 10.1016/j.coisb.2023.100480
• Bunbury, Freddy et al. (2023) Shedding light on spatial structure and dynamics in phototrophic biofilms. Current Opinion in Systems Biology 36, 100480. 10.1016/j.coisb.2023.100480
• Camargo, Antonio Pedro et al. (2023) Identification of mobile genetic elements with geNomad. Nature Biotechnology , 1-10. 10.1038/s41587-023-01953-y
• Camargo, Antonio Pedro et al. (2023) IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. Nucleic Acids Research 52(D1), d164-d173. 10.1093/nar/gkad964
• Camargo, Antonio Pedro et al. (2023) IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. Nucleic Acids Research 52(D1), d164-d173. 10.1093/nar/gkad964
• Camargo, Antonio Pedro et al. (2023) IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. Nucleic Acids Research 52(D1), d164-d173. 10.1093/nar/gkad964
• Chiu, Beverly K. et al. (2023) Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress. Frontiers in Microbiology 14, 1219779. 10.3389/fmicb.2023.1219779
• Džunková, Mária et al. (2023) Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium. Microbiome 11(1), 130. 10.1186/s40168-023-01560-8
• Eng, Ashley Y. et al. (2023) Thermal adaptation of soil microbial growth traits in response to chronic warming. Applied and Environmental Microbiology 89(11), e00825-23. 10.1128/aem.00825-23
• Eng, Ashley Y. et al. (2023) Thermal adaptation of soil microbial growth traits in response to chronic warming. Applied and Environmental Microbiology 89(11), e00825-23. 10.1128/aem.00825-23
• Eng, Ashley Y. et al. (2023) Thermal adaptation of soil microbial growth traits in response to chronic warming. Applied and Environmental Microbiology 89(11), e00825-23. 10.1128/aem.00825-23
• Esser, Sarah P. et al. (2023) A predicted CRISPR-mediated symbiosis between uncultivated archaea. Nature Microbiology 8(9), 1619-1633. 10.1038/s41564-023-01439-2
• Foreman, Christine M. et al. (2023) Seven genome sequences of bacterial, environmental isolates from Pony Lake, Antarctica. Microbiology Resource Announcements 13(1), e00744-23. 10.1128/mra.00744-23
• Ionescu, Danny et al. (2023) Genomic Mysteries of Giant Bacteria: Insights and Implications. Genome Biology and Evolution 15(9), evad163. 10.1093/gbe/evad163
• Jones, David T. et al. (2023) Solvent-Producing Clostridia Revisited. Microorganisms 11(9), 2253. 10.3390/microorganisms11092253
• Klonowska, Agnieszka et al. (2023) Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Frontiers in Microbiology 14, 1082107. 10.3389/fmicb.2023.1082107
• Madigan, Michael T. et al. (2023) Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis. Extremophiles 27(2), 19. 10.1007/s00792-023-01304-4
• Mayali, Xavier et al. (2023) Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. Nature Communications 14(1), 5642. 10.1038/s41467-023-41179-9
• Mechan-Llontop, Marco E. et al. (2023) Genome-sequenced bacterial collection from sorghum aerial root mucilage. Microbiology Resource Announcements 12(12), e00468-23. 10.1128/mra.00468-23
• Mechan-Llontop, Marco E. et al. (2023) Genome-sequenced bacterial collection from sorghum epicuticular wax. Microbiology Resource Announcements 12(12), e00484-23. 10.1128/mra.00484-23
• Morgan‐Lang, Connor et al. (2023) A Guide to Gene‐Centric Analysis Using TreeSAPP. Current Protocols 3(2), e671. 10.1002/cpz1.671
• Mukherjee, Supratim et al. (2023) Standardized naming of microbiome samples in Genomes OnLine Database.. Database 2023. 10.1093/database/baad001
• Mukherjee, Supratim et al. (2023) Bioinformatics Analysis Tools for Studying Microbiomes at the DOE Joint Genome Institute. Journal of the Indian Institute of Science , 1-19. 10.1007/s41745-023-00365-w
• Murali, Ranjani et al. (2023) Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea. PLOS Biology 21(9), e3002292. 10.1371/journal.pbio.3002292
• Nowinski, Brent et al. (2023) Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(6), 813-822. 10.1038/s41396-023-01390-4
• Olson, Daniel G. et al. (2023) Ethanol tolerance in engineered strains of Clostridium thermocellum. Biotechnology for Biofuels and Bioproducts 16(1), 137. 10.1186/s13068-023-02379-z
• Palmer, Marike et al. (2023) Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(7), 952-966. 10.1038/s41396-023-01405-0
• Pavlopoulos, Georgios A. et al. (2023) Unraveling the functional dark matter through global metagenomics. Nature 622(7983), 594-602. 10.1038/s41586-023-06583-7
• Pavlopoulos, Georgios A. et al. (2023) Unraveling the functional dark matter through global metagenomics. Nature 622(7983), 594-602. 10.1038/s41586-023-06583-7
• Pavlopoulos, Georgios A. et al. (2023) Unraveling the functional dark matter through global metagenomics. Nature 622(7983), 594-602. 10.1038/s41586-023-06583-7
• Qiu, Yilin et al. (2023) Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment. Microbiology Resource Announcements 12(2), e00759-22. 10.1128/mra.00759-22
• Riley, Lauren A. et al. (2023) Simple and Rapid Site-Specific Integration of Multiple Heterologous DNAs into the Escherichia coli Chromosome. Journal of Bacteriology 205(2), e00338-22. 10.1128/jb.00338-22
• Robertson, Raegan et al. (2023) Genome sequences of key bacterial symbionts of entomopathogenic nematodes: Xenorhabdus cabanillasii DSM17905, Xenorhabdus ehlersii DSM16337, Xenorhabdus japonica DSM16522, Xenorhabdus koppenhoeferii DSM18168, and Xenorhabdus mauleonii DSM17908. Microbiology Resource Announcements , e00548-23. 10.1128/mra.00548-23
• Roux, Simon et al. (2023) Updated Virophage Taxonomy and Distinction from Polinton-like Viruses. Biomolecules 13(2), 204. 10.3390/biom13020204
• Sannino, David R. et al. (2023) The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proceedings of the National Academy of Sciences of the United States of America 120(52), e2306160120. 10.1073/pnas.2306160120
• Seshadri, Rekha et al. (2023) Comparative Genomics Using the Integrated Microbial Genomes and Microbiomes (IMG/M) System: A Deinococcus Use Case. Journal of the Indian Institute of Science , 1-14. 10.1007/s41745-023-00368-7
• Seymour, Cale O. et al. (2023) Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nature Microbiology 8(4), 727-744. 10.1038/s41564-022-01319-1
• Shi, Zhou Jason et al. (2023) Maast: genotyping thousands of microbial strains efficiently. Genome Biology 24(1), 186. 10.1186/s13059-023-03030-8
• Toumi, Marwene et al. (2023) Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater.. International Journal of Systematic and Evolutionary Microbiology 73(12). 10.1099/ijsem.0.006205
• Toumi, Marwene et al. (2023) Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater.. International Journal of Systematic and Evolutionary Microbiology 73(12). 10.1099/ijsem.0.006205
• Toumi, Marwene et al. (2023) Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater.. International Journal of Systematic and Evolutionary Microbiology 73(12). 10.1099/ijsem.0.006205
• Volland, Jean-Marie et al. (2023) Small cells with big secrets. Nature Reviews Microbiology 21(7), 414-414. 10.1038/s41579-023-00903-4
• Woyke, Tanja et al. (2023) Cell by cell: population genetics in the wild. Nature Reviews Genetics 24(8), 490-490. 10.1038/s41576-023-00619-4
• Wu, Dongying et al. (2023) A tale of two codes. Nature Reviews Microbiology 21(8), 486-486. 10.1038/s41579-023-00921-2

2022

• Arthofer, Patrick et al. (2022) Defensive symbiosis against giant viruses in amoebae. Proceedings of the National Academy of Sciences of the United States of America 119(36), e2205856119. 10.1073/pnas.2205856119
• Batstone, Rebecca T. et al. (2022) Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont. Proceedings of the Royal Society B 289(1978), 20220477. 10.1098/rspb.2022.0477
• Batstone, Rebecca T. et al. (2022) Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 13(6), e01823-22. 10.1128/mbio.01823-22
• Bayer, Barbara et al. (2022) Complete Genome Sequences of Two Phylogenetically Distinct Nitrospina Strains Isolated from the Atlantic and Pacific Oceans. Microbiology Resource Announcements 11(5), e00100-22. 10.1128/mra.00100-22
• Bell, Emma et al. (2022) Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(6), 1583-1593. 10.1038/s41396-022-01207-w
• Bender, Kelly S. et al. (2022) Genomic Features of the Bundle-Forming Heliobacterium Heliophilum fasciatum. Microorganisms 10(5), 869. 10.3390/microorganisms10050869
• Bizic, Mina et al. (2022) Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 17(3), 340-353. 10.1038/s41396-022-01350-4
• Brown, Igor et al. (2022) High-Quality Draft Genome Sequence of Fischerella thermalis JSC-11, a Siderophilic Cyanobacterium with Bioremediation Potential. Microbiology Resource Announcements 11(11), e00761-22. 10.1128/mra.00761-22
• Camargo, Antonio Pedro et al. (2022) IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.. Nucleic Acids Research 51(D1), d733-d743. 10.1093/nar/gkac1037
• Chadwick, Grayson L. et al. (2022) Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLOS Biology 20(1), e3001508. 10.1371/journal.pbio.3001508
• Chaput, Gina et al. (2022) Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium. Microbiology Spectrum 10(3), e02346-21. 10.1128/spectrum.02346-21
• Chen, I-Min A et al. (2022) The IMG/M data management and analysis system v.7: content updates and new features.. Nucleic Acids Research 51(D1), d723-d732. 10.1093/nar/gkac976
• Chen, Song‐Can et al. (2022) Genome and proteome analyses show the gaseous alkane degrader Desulfosarcina sp. strain BuS5 as an extreme metabolic specialist. Environmental Microbiology 24(4), 1964-1976. 10.1111/1462-2920.15956
• Chevrette, Marc G. et al. (2022) Microbiome composition modulates secondary metabolism in a multispecies bacterial community. Proceedings of the National Academy of Sciences of the United States of America 119(42), e2212930119. 10.1073/pnas.2212930119
• Couceiro, Joana Fernandes et al. (2022) Genome Sequencing Suggests Diverse Secondary Metabolism in Coral-Associated Aquimarina megaterium. Microbiology Resource Announcements 11(11), e00620-22. 10.1128/mra.00620-22
• del Carmen Montero-Calasanz, Maria et al. (2022) Genotype–phenotype correlations within the Geodermatophilaceae. Frontiers in Microbiology 13, 975365. 10.3389/fmicb.2022.975365
• diCenzo, George C. et al. (2022) DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp.. mSystems 7(1), e01092-21. 10.1128/msystems.01092-21
• Dofher, Kalen et al. (2022) The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential. Frontiers in Bioengineering and Biotechnology 10, 932695. 10.3389/fbioe.2022.932695
• Doty, Sharon L. et al. (2022) Potential Biocontrol Activities of Populus Endophytes against Several Plant Pathogens Using Different Inhibitory Mechanisms. Pathogens 12(1), 13. 10.3390/pathogens12010013
• Eardly, Bertrand et al. (2022) The Genome of the Acid Soil-Adapted Strain Rhizobium favelukesii OR191 Encodes Determinants for Effective Symbiotic Interaction With Both an Inverted Repeat Lacking Clade and a Phaseoloid Legume Host. Frontiers in Microbiology 13, 735911. 10.3389/fmicb.2022.735911
• Epstein, Brendan et al. (2022) Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis. Molecular Ecology 32(14), 3798-3811. 10.1111/mec.16602
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• Howard-Varona, Cristina et al. (2022) Protist impacts on marine cyanovirocell metabolism. ISME Communications 2(1), 94. 10.1038/s43705-022-00169-6
• Keller-Costa, Tina et al. (2022) Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome. Microbiome 10(1), 151. 10.1186/s40168-022-01343-7
• Koch, Moritz et al. (2022) The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential. Frontiers in Bioengineering and Biotechnology 10, 932695. 10.3389/fbioe.2022.932695
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• Podowski, Justin C. et al. (2022) Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers. mBio 13(3), e02379-21. 10.1128/mbio.02379-21
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• Reichart, Nicholas J. et al. (2022) Metagenomes and Metagenome-Assembled Genomes from Substrate-Amended Hot Spring Sediment Incubations from Yellowstone National Park. Microbiology Resource Announcements 11(4), e01065-21. 10.1128/mra.01065-21
• Riley, Alex B. et al. (2022) Discordant population structure among rhizobium divided genomes and their legume hosts. Molecular Ecology 32(10), 2646-2659. 10.1111/mec.16704
• Rodríguez-Gijón, Alejandro et al. (2022) A Genomic Perspective Across Earth’s Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Frontiers in Microbiology 12, 761869. 10.3389/fmicb.2021.761869
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• Zhang, Yaoping et al. (2022) Transcriptomic Data Sets for Zymomonas mobilis 2032 during Fermentation of Ammonia Fiber Expansion (AFEX)-Pretreated Corn Stover and Switchgrass Hydrolysates. Microbiology Resource Announcements 11(9), e00564-22. 10.1128/mra.00564-22

2021

• Altae-Tran, Han et al. (2021) The widespread IS200/605 transposon family encodes diverse programmable RNA-guided endonucleases. Science 374(6563), 57-65. 10.1126/science.abj6856
• Altamia, M. A. et al. (2021) Wteredinibacter haidensis sp. Nov., teredinibacter purpureus sp. nov. and teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc bankia setacea (bivalvia: Teredinidae) and emended description of the genus teredinibacter. International Journal of Systematic and Evolutionary Microbiology 71(2), 1-11. 10.1099/ijsem.0.004627
• Andreani, Julien et al. (2021) Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54. Frontiers in Microbiology 12, 719703. 10.3389/fmicb.2021.719703
• Andreopoulos, William B et al. (2021) Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes. Nucleic Acids Research 50(3), gkab1115-. 10.1093/nar/gkab1115
• Banerjee, Deepanwita et al. (2021) Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress. Frontiers in Bioengineering and Biotechnology 9, 766674. 10.3389/fbioe.2021.766674
• Berg, M. et al. (2021) Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions. Isme Journal , 16. 10.1038/s41396-020-00870-1
• Boeuf, D. et al. (2021) Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage. Microbiome 9(1). 10.1186/s40168-021-01119-5
• Bowers, Robert M. et al. (2021) Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(5), 1337-1347. 10.1038/s41396-021-01178-4
• Brown, I. et al. (2021) High-quality draft genome sequence of the siderophilic and thermophilic leptolyngbyaceae cyanobacterium JSC-12. Microbiology Resource Announcements 10(25). 10.1128/MRA.00495-21
• Bruckbauer, S. T. et al. (2021) Experimental evolution of extremophile resistance to ionizing radiation. Trends in Genetics . 10.1016/j.tig.2021.04.011
• Carper, Dana L. et al. (2021) Cultivating the Bacterial Microbiota of Populus Roots. mSystems 6(3), e01306-20. 10.1128/msystems.01306-20
• Chai, Y. N. et al. (2021) High-resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities. Plant Cell and Environment 44(5), 1611-1626. 10.1111/pce.14004
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• Ciobanu, Doina et al. (2021) A single-cell genomics pipeline for environmental microbial eukaryotes. iScience 24(4), 102290. 10.1016/j.isci.2021.102290
• Couceiro, J. F. et al. (2021) The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos. Microbiology Resource Announcements 10(34). 10.1128/MRA.00320-21
• Eng, T. et al. (2021) Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor. Metabolic Engineering 66, 229-238. 10.1016/j.ymben.2021.04.015
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• Gao, C. et al. (2021) Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen. ISME Journal . 10.1038/s41396-021-01024-7
• Gavrilov, S. N. et al. (2021) Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium. Frontiers in Microbiology 11. 10.3389/fmicb.2020.597818
• Harris, C. R. et al. (2021) Draft genome sequence of Bordetella sp. strain FB-8, isolated from a former uranium mining area in Germany. Microbiology Resource Announcements 10(14). 10.1128/MRA.01035-19
• Hempel, Priscilla P. et al. (2021) RNA-Seq Reveals that Light and Darkness Are Different Stimuli in Freshwater Heterotrophic Actinobacteria. Frontiers in Microbiology 12, 739005. 10.3389/fmicb.2021.739005
• Hu, D. et al. (2021) Counting mRNA Copies in Intact Bacterial Cells by Fluctuation Localization Imaging-Based Fluorescence In Situ Hybridization (fliFISH). Methods in Molecular Biology 2246, 237-247. 10.1007/978-1-0716-1115-9_15
• Hurley, A. et al. (2021) Tiny Earth: A Big Idea for STEM Education and Antibiotic Discovery. Mbio 12(1), 7. 10.1128/mBio.03432-20
• Jones, L. B. et al. (2021) Draft genome sequences of switchgrass diazotrophs. Microbiology Resource Announcements 10(21). 10.1128/MRA.00284-21
• Kim, W. E. et al. (2021) Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics. ACS Chemical Biology 16(5), 813-819. 10.1021/acschembio.1c00157
• Lanahan, Anthony et al. (2021) A Single Nucleotide Change in the polC DNA Polymerase III in Clostridium thermocellum Is Sufficient To Create a Hypermutator Phenotype. Applied and Environmental Microbiology 88(1), e01531-21. 10.1128/aem.01531-21
• Linz, Alexandra M. et al. (2021) Aromatic Dimer Dehydrogenases from Novosphingobium aromaticivorans Reduce Monoaromatic Diketones. Applied and Environmental Microbiology 87(24), e01742-21. 10.1128/aem.01742-21
• Matson, Morgan M et al. (2021) Adaptive laboratory evolution for improved tolerance of isobutyl acetate in Escherichia coli. Metabolic Engineering 69, 50-58. 10.1016/j.ymben.2021.11.002
• Mavrodi, O. V. et al. (2021) Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. Frontiers in Microbiology 12. 10.3389/fmicb.2021.651282
• Mazzoli, Roberto et al. (2021) In vivo evolution of lactic acid hyper-tolerant Clostridium thermocellum. New Biotechnology 67, 12-22. 10.1016/j.nbt.2021.12.003
• McKay, Luke J. et al. (2021) Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane. The ISME Journal: Multidisciplinary Journal of Microbial Ecology 16(4), 915-926. 10.1038/s41396-021-01139-x
• Menes, R. J. et al. (2021) Frigoriflavimonas asaccharolytica gen. nov., sp. nov., a novel psychrophilic esterase and protease producing bacterium isolated from Antarctica. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology . 10.1007/s10482-021-01656-x
• Murphy, C. L. et al. (2021) Genomic analysis of the yet-uncultured binatota reveals broad methylotrophic, alkane-degradation, and pigment production capacities. mBio 12(3). 10.1128/mBio.00985-21
• Nielsen, D. A. et al. (2021) Aerobic bacteria and archaea tend to have larger and more versatile genomes. Oikos 130(4), 501-511. 10.1111/oik.07912
• Pons, Joan Carles et al. (2021) VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. Bioinformatics . 10.1093/bioinformatics/btab026
• Presley, G. N. et al. (2021) Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound. Metabolic Engineering 65, 1-10. 10.1016/j.ymben.2021.02.003
• Rahlff, J. et al. (2021) Lytic archaeal viruses infect abundant primary producers in Earth’s crust. Nature Communications 12(1). 10.1038/s41467-021-24803-4
• Roldán, D. M. et al. (2021) Hymenobacter caeli sp. Nov., an airborne bacterium isolated from king george island, antarctica. International Journal of Systematic and Evolutionary Microbiology 71(6). 10.1099/ijsem.0.004838
• Schiffer, Jodie A et al. (2021) Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide. PLOS Pathogens 17(12), e1010112. 10.1371/journal.ppat.1010112
• Singer, Esther et al. (2021) Impact of Harvest on Switchgrass Leaf Microbial Communities. Genes 13(1), 22. 10.3390/genes13010022
• Sun, J. et al. (2021) Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications 1(1), 30. 10.1038/s43705-021-00032-0
• Swift, C. L. et al. (2021) Cocultivation of anaerobic fungi with rumen bacteria establishes an antagonistic relationship. mBio 12(4). 10.1128/mBio.01442-21
• Wang, Q. et al. (2021) Escalation in the host-pathogen arms race: A host resistance response corresponds to a heightened bacterial virulence response. Plos Pathogens 17(1), 27. 10.1371/journal.ppat.1009175
• Weiner, Agnes K M et al. (2021) Examining the Relationship Between the Testate Amoeba Hyalosphenia papilio (Arcellinida, Amoebozoa) and its Associated Intracellular Microalgae Using Molecular and Microscopic Methods. Protist 173(1), 125853. 10.1016/j.protis.2021.125853
• Yayo, J. et al. (2021) Laboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and Fructose. Applied and Environmental Microbiology 87(9), 1-18. 10.1128/AEM.03017-20

2020

• Akob, D. M. et al. (2020) Mixotrophic Iron-Oxidizing Thiomonas Isolates from an Acid Mine Drainage-Affected Creek. Appl Environ Microbiol 86(24). 10.1128/AEM.01424-20
• Alteio, L. V. et al. (2020) Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil. mSystems 5(2). 10.1128/mSystems.00768-19
• Arroyo-Herrera, I. et al. (2020) Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. 3 Biotech 10(6), 242. 10.1007/s13205-020-02210-8
• Bayer, B. et al. (2020) Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. ISME J . 10.1038/s41396-020-00828-3
• Beri, D. et al. (2020) Development of a thermophilic coculture for corn fiber conversion to ethanol. Nat Commun 11(1), 1937. 10.1038/s41467-020-15704-z
• Chen, M. L. et al. (2020) Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. Front Microbiol 11, 376. 10.3389/fmicb.2020.00376
• Eichorst, S. A. et al. (2020) One Complete and Seven Draft Genome Sequences of Subdivision 1 and 3 Acidobacteria Isolated from Soil. Microbiol Resour Announc 9(5). 10.1128/MRA.01087-19
• Flores-Tinoco, C. E. et al. (2020) Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation. Mol Syst Biol 16(6), e9419. 10.15252/msb.20199419
• Haas, K. N. et al. (2020) Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa. Int J Syst Evol Microbiol 70(1), 23-34. 10.1099/ijsem.0.003698
• Hatmaker, E. A. et al. (2020) Methylome and Complete Genome Sequence of Parageobacillus toebii DSM 14590(T), a Thermophilic Bacterium. Microbiology Resource Announcements 9(25). 10.1128/MRA.00589-20
• Hordt, A. et al. (2020) Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 11, 468. 10.3389/fmicb.2020.00468
• Klonowska, A. et al. (2020) Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. BMC Genomics 21(1), 214. 10.1186/s12864-020-6623-z
• Kostlbacher, S. et al. (2020) Draft Genome Sequences of Chlamydiales Bacterium STE3 and Neochlamydia sp. Strain AcF84, Endosymbionts of Acanthamoeba spp. Microbiol Resour Announc 9(20). 10.1128/MRA.00220-20
• Koutrouli, M. et al. (2020) A Guide to Conquer the Biological Network Era Using Graph Theory. Frontiers in Bioengineering and Biotechnology 8. 10.3389/fbioe.2020.00034
• Koziaeva, V. V. et al. (2020) Biodiversity of Magnetotactic Bacteria in the Freshwater Lake Beloe Bordukovskoe, Russia. Microbiology 89(3), 348-358. 10.1134/S002626172003008x
• Laviad-Shitrit, S. et al. (2020) Draft genome of Rosenbergiella nectarea strain 8N4(T) provides insights into the potential role of this species in its plant host. PeerJ 8, e8822. 10.7717/peerj.8822
• Lee, K. S. et al. (2020) Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions. Nat Protoc . 10.1038/s41596-020-00427-8
• Madhaiyan, M. et al. (2020) Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants. Antonie Van Leeuwenhoek 113(11), 1617-1632. 10.1007/s10482-020-01468-5
• Madin, J. S. et al. (2020) A synthesis of bacterial and archaeal phenotypic trait data. Sci Data 7(1), 170. 10.1038/s41597-020-0497-4
• Metcalfe, K. S. et al. (2020) Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy. ISME J . 10.1038/s41396-020-00757-1
• Meyers, D. J. et al. (2020) Draft Genome Sequence of Yokenella regensburgei Strain WCD67, Isolated from the Boxelder Bug. Microbiol Resour Announc 9(15). 10.1128/MRA.00104-20
• Mobilian, C. et al. (2020) Differential effects of press vs. pulse seawater intrusion on microbial communities of a tidal freshwater marsh. Limnology and Oceanography Letters . 10.1002/lol2.10171
• Morrow, M. A. et al. (2020) Draft Genome Sequence of a Terrestrial Planctomycete, Singulisphaera sp. Strain GP187, Isolated from Forest Soil. Microbiol Resour Announc 9(50). 10.1128/MRA.00956-20
• Oshlag, J. Z. et al. (2020) Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris. Appl Environ Microbiol 86(3). 10.1128/AEM.01888-19
• Ouyang, Y. et al. (2020) Short-Term Nitrogen Fertilization Affects Microbial Community Composition and Nitrogen Mineralization Functions in an Agricultural Soil. Appl Environ Microbiol 86(5). 10.1128/AEM.02278-19
• Sabuda, M. C. et al. (2020) A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite. Environ Microbiol 22(6), 2329-2345. 10.1111/1462-2920.15006
• Saito, M. A. et al. (2020) Abundant nitrite-oxidizing metalloenzymes in the mesopelagic zone of the tropical Pacific Ocean. Nature Geoscience 13(5). 10.1038/s41561-020-0565-6
• Schulz, F. et al. (2020) Giant virus diversity and host interactions through global metagenomics. Nature 578(7795), 432-436. 10.1038/s41586-020-1957-x
• Seshadri, R. et al. (2020) A bacterial toolkit for plants. Nat Rev Microbiol 18(3), 124. 10.1038/s41579-020-0333-z
• Sheremet, A. et al. (2020) Ecological and genomic analyses of candidate phylum WPS-2 bacteria in an unvegetated soil. Environ Microbiol . 10.1111/1462-2920.15054
• Strepis, N. et al. (2020) Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. BMC Genomics 21(1). 10.1186/s12864-019-6410-x

2019

• Albert, R. A. et al. (2019) Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 69(5), 1376-1383. 10.1099/ijsem.0.003319
• Avontuur, J. R. et al. (2019) Genome-informed Bradyrhizobium taxonomy: where to from here?. Syst Appl Microbiol . 10.1016/j.syapm.2019.03.006
• Berben, T. et al. (2019) Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria. Front Microbiol 10, 160. 10.3389/fmicb.2019.00160
• Berghuis, B. A. et al. (2019) Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proc Natl Acad Sci U S A 116(11), 5037-5044. 10.1073/pnas.1815631116
• Bruckbauer, S. T. et al. (2019) Experimental evolution of extreme resistance to ionizing radiation in Escherichia coli after 50 cycles of selection. J Bacteriol . 10.1128/JB.00784-18
• Brzoska, R. M. et al. (2019) Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium. Microbiol Resour Announc 8(14). 10.1128/MRA.01701-18
• Bushman, T. J. et al. (2019) Draft Genome Sequence of Mn(II)-Oxidizing Bacterium Oxalobacteraceae sp. Strain AB_14. Microbiol Resour Announc 8(43). 10.1128/MRA.01024-19
• Chaput, G. et al. (2019) Complete Genome Sequence of Serratia quinivorans Strain 124R, a Facultative Anaerobe Isolated on Organosolv Lignin as a Sole Carbon Source. Microbiol Resour Announc 8(18). 10.1128/MRA.00409-19
• Chen, I. A. et al. (2019) IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 47(D1), D666-D677. 10.1093/nar/gky901
• Cui, J. et al. (2019) Characterization of the Clostridium thermocellum AdhE, NfnAB, ferredoxin and Pfor proteins for their ability to support high titer ethanol production in Thermoanaerobacterium saccharolyticum. Metab Eng 51, 32-42. 10.1016/j.ymben.2018.09.006
• Davenport, E. J. et al. (2019) Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States). Frontiers in Microbiology 10. 10.3389/fmicb.2019.02081
• Doud, D. F. R. et al. (2019) Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME J . 10.1038/s41396-019-0557-y
• Duell, E. R. et al. (2019) Direct pathway cloning of the sodorifen biosynthetic gene cluster and recombinant generation of its product in E. coli. Microb Cell Fact 18(1), 32. 10.1186/s12934-019-1080-6
• Garcia-Lopez, M. et al. (2019) Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 10, 2083. 10.3389/fmicb.2019.02083
• Hausmann, B. et al. (2019) Long-Term Transcriptional Activity at Zero Growth of a Cosmopolitan Rare Biosphere Member. MBio 10(1). 10.1128/mBio.02189-18
• Izrael-Zivkovic, L. et al. (2019) High-quality draft genome sequence of Pseudomonas aeruginosa san ai, an environmental isolate resistant to heavy metals. Extremophiles 23(4), 399-405. 10.1007/s00792-019-01092-w
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• Langley, S. et al. (2019) Complete Genome Sequence of Agrobacterium sp. Strain 33MFTa1.1, Isolated from Thlaspi arvense Roots. Microbiol Resour Announc 8(37). 10.1128/MRA.00432-19
• Lee, L. L. et al. (2019) Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tapirins) from Extremely Thermophilic Caldicellulosiruptor Species. Appl Environ Microbiol 85(3). 10.1128/AEM.01983-18
• Luek, J. L. et al. (2019) Organic sulfur fingerprint indicates continued injection fluid signature 10 months after hydraulic fracturing. Environ Sci Process Impacts 21(2), 206-213. 10.1039/c8em00331a
• Matheus Carnevali, P. B. et al. (2019) Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. Nat Commun 10(1), 463. 10.1038/s41467-018-08246-y
• Mukherjee, S. et al. (2019) Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res 47(D1), D649-D659. 10.1093/nar/gky977
• Needham, D. M. et al. (2019) A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proc Natl Acad Sci U S A . 10.1073/pnas.1907517116
• Paez-Espino, D. et al. (2019) IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes. Nucleic Acids Res 47(D1), D678-D686. 10.1093/nar/gky1127
• Palevich, N. et al. (2019) Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities. Appl Environ Microbiol 86(1). 10.1128/AEM.01993-19
• Price, M. N. et al. (2019) Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. mSystems 4(1). 10.1128/mSystems.00297-18
• Ren, M. et al. (2019) Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J . 10.1038/s41396-019-0418-8
• Rochman, F. F. et al. (2019) Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. ISME J . 10.1038/s41396-019-0561-2
• Rojas-Rojas, F. U. et al. (2019) Draft Genome of Burkholderia cenocepacia TAtl-371, a Strain from the Burkholderia cepacia Complex Retains Antagonism in Different Carbon and Nitrogen Sources. Curr Microbiol . 10.1007/s00284-019-01657-0
• Roux, S. et al. (2019) Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes. Nat Microbiol . 10.1038/s41564-019-0510-x
• Sackett, J. D. et al. (2019) Four Draft Single-Cell Genome Sequences of Novel, Nearly Identical Kiritimatiellaeota Strains Isolated from the Continental Deep Subsurface. Microbiol Resour Announc 8(11). 10.1128/MRA.01249-18
• Sahib, M. R. et al. (2019) Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants. Microbiol Resour Announc 8(45). 10.1128/MRA.00927-19
• Spring, S. et al. (2019) Sulfate-Reducing Bacteria That Produce Exopolymers Thrive in the Calcifying Zone of a Hypersaline Cyanobacterial Mat. Front Microbiol 10, 862. 10.3389/fmicb.2019.00862
• Tian, L. et al. (2019) A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol. Scientific Reports 9. 10.1038/s41598-018-37979-5
• Tyml, T. et al. (2019) A single-cell genome perspective on studying intracellular associations in unicellular eukaryotes. Philos Trans R Soc Lond B Biol Sci 374(1786), 20190082. 10.1098/rstb.2019.0082
• Ul-Hasan, S. et al. (2019) Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California. PLoS One 14(2), e0212355. 10.1371/journal.pone.0212355
• Wiese, J. et al. (2019) Genome analysis of the marine bacterium Kiloniella laminariae and first insights into comparative genomics with related Kiloniella species. Arch Microbiol . 10.1007/s00203-019-01791-0
• Woyke, T. et al. (2019) Beyond the census of human gut dwellers. Nat Rev Microbiol 17(7), 401. 10.1038/s41579-019-0220-7
• Xia, Y. et al. (2019) Improved Draft Genome Sequence of Pseudomonas poae A2-S9, a Strain with Plant Growth-Promoting Activity. Microbiol Resour Announc 8(15). 10.1128/MRA.00275-19

2018

Biswas, R. et al. (2018) Complete Genome Sequence of Thermoanaerobacterium sp. Strain RBIITD, a Butyrate- and Butanol-Producing Thermophile. Genome Announc 6(2). 10.1128/genomeA.01411-17

• Cantillo, Angela et al. (2018) Genome Sequences of Actinobacteria from Extreme Environments in Colombia. Microbiology Resource Announcements 7(22), e01384-18. 10.1128/MRA.01384-18
• Carro, L. et al. (2018) Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 8(1), 525. 10.1038/s41598-017-17392-0
• Cheng, H. et al. (2018) The Biota Project: A Case Study of a Multimedia, Grassroots Approach to Scientific Communication for Engaging Diverse Audiences. Integr Comp Biol 58(6), 1294-1303. 10.1093/icb/icy091
• Chernikova, T. N. et al. (2018) Draft Genome Sequence of Monaibacterium marinum C7(T), Isolated from Seawater from the Menai Straits, Wales, United Kingdom. Genome Announc 6(5). 10.1128/genomeA.01444-17
• Eichorst, S. A. et al. (2018) Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol 20(3), 1041-1063. 10.1111/1462-2920.14043
• Fleming, E. J. et al. (2018) Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea. Appl Environ Microbiol . 10.1128/AEM.02239-17
• Ganesh, S. et al. (2018) Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. ISME J . 10.1038/s41396-018-0223-9
• Ganesh, S. et al. (2018) Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. Isme Journal 12(11), 2706-2722. 10.1038/s41396-018-0223-9
• Hesse, C. et al. (2018) Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol . 10.1111/1462-2920.14130
• Jarett, J. K. et al. (2018) Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis. Microbiome 6(1), 161. 10.1186/s40168-018-0539-8
• Lee, L. L. et al. (2018) Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis. Appl Environ Microbiol . 10.1128/AEM.02694-17
• Levy, A. et al. (2018) Elucidating Bacterial Gene Functions in the Plant Microbiome. Cell Host Microbe 24(4), 475-485. 10.1016/j.chom.2018.09.005
• Lopez, G. et al. (2018) Description of Alicyclobacillus montanus sp. nov., a mixotrophic bacterium isolated from acidic hot springs. Int J Syst Evol Microbiol . 10.1099/ijsem.0.002718
• Neumann, A. P. et al. (2018) The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential. mSphere 3(6). 10.1128/mSphere.00593-18
• Nouioui, I. et al. (2018) Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 9, 2007. 10.3389/fmicb.2018.02007
• Paver, S. F. et al. (2018) Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems. mSystems 3(6). 10.1128/mSystems.00232-18
• Pitt, A. et al. (2018) Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. Int J Syst Evol Microbiol 68(6), 1975-1985. 10.1099/ijsem.0.002777
• Pold, G. et al. (2018) Genome Sequence of Verrucomicrobium sp. Strain GAS474, a Novel Bacterium Isolated from Soil. Genome Announc 6(4). 10.1128/genomeA.01451-17
• Pold, G. et al. (2018) Draft Genome Sequences of Three Strains of a Novel Rhizobiales Species Isolated from Forest Soil. Genome Announc 6(5). 10.1128/genomeA.01452-17
• Price, M. N. et al. (2018) Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 557(7706), 503-509. 10.1038/s41586-018-0124-0
• Rodriguez, R. Lm et al. (2018) How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?. Appl Environ Microbiol 84(6). 10.1128/AEM.00014-18
• Scott, K. M. et al. (2018) Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol . 10.1111/1462-2920.14090
• Seshadri, R. et al. (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol . 10.1038/nbt.4110
• Singer, Esther et al. (2018) Plant compartment and genetic variation drive microbiome composition in switchgrass roots. Environmental Microbiology Reports . 10.1111/1758-2229.12727
• Skraban, J. et al. (2018) Draft genome sequence of Chryseobacterium limigenitum SUR2(T) (LMG 28734(T)) isolated from dehydrated sludge. Braz J Microbiol 49(1), 5-6. 10.1016/j.bjm.2017.03.009
• Tschitschko, B. et al. (2018) Genomic variation and biogeography of Antarctic haloarchaea. Microbiome 6(1), 113. 10.1186/s40168-018-0495-3
• Vigneron, A. et al. (2018) Beyond the tip of the iceberg; a new view of the diversity of sulfite- and sulfate-reducing microorganisms. ISME J . 10.1038/s41396-018-0155-4
• Warshan, D. et al. (2018) Genomic changes associated with the evolutionary transitions of Nostoc to a plant symbiont. Mol Biol Evol . 10.1093/molbev/msy029
• Wehking, J. et al. (2018) Community composition and seasonal changes of archaea in coarse and fine air particulate matter. Biogeosciences 15(13), 4205-4214. 10.5194/bg-15-4205-2018
• Woyke, Tanja et al. (2018) Entities inside one another – a matryoshka doll in biology?. Environmental Microbiology Reports 0(0). 10.1111/1758-2229.12716
• Zhou, E. M. et al. (2018) Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles 22(6), 983-991. 10.1007/s00792-018-1055-2
• Zhou, E. M. et al. (2018) Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles 22(6), 983-991. 10.1007/s00792-018-1055-2

2017

• Ahn, A. C. et al. (2017) Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio. PLoS One 12(3), e0173517. 10.1371/journal.pone.0173517
• Aserse, A. A. et al. (2017) Draft genome sequence of type strain HBR26T and description of Rhizobium aethiopicum sp. nov. Stand Genomic Sci 12, 14. 10.1186/s40793-017-0220-z
• Aserse, A. A. et al. (2017) Draft genome sequences of Bradyrhizobium shewense sp. nov. ERR11(T) and Bradyrhizobium yuanmingense CCBAU 10071(T). Stand Genomic Sci 12, 74. 10.1186/s40793-017-0283-x
• Baltrus, D. A. et al. (2017) Absence of genome reduction in diverse, facultative endohyphal bacteria. Microb Genom 3(2), e000101. 10.1099/mgen.0.000101
• Becraft, E. D. et al. (2017) Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 8, 2264. 10.3389/fmicb.2017.02264
• Beukes, C. W. et al. (2017) Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Front Microbiol 8, 1154. 10.3389/fmicb.2017.01154
• Bowers, R. M. et al. (2017) Sequencing of Genomes from Environmental Single Cells. Methods Mol Biol 1712, 97-111. 10.1007/978-1-4939-7514-3_8
• Browne, P. et al. (2017) Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments. ISME J 11(1), 87-99. 10.1038/ismej.2016.104
• Bushnell, B. et al. (2017) BBMerge – Accurate paired shotgun read merging via overlap. PLoS One 12(10), e0185056. 10.1371/journal.pone.0185056
• Chen, L. X. et al. (2017) Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota. ISME J . 10.1038/s41396-017-0002-z
• Choi, D. H. et al. (2017) Draft genome sequence of Marinobacterium rhizophilum CL-YJ9(T) (DSM 18822(T)), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica. Stand Genomic Sci 12, 65. 10.1186/s40793-017-0275-x
• Diaz-Cardenas, C. et al. (2017) Draft genome and description of Consotaella salsifontis gen. nov. sp. nov., a halophilic, free-living, nitrogen-fixing alphaproteobacterium isolated from an ancient terrestrial saline spring. Int J Syst Evol Microbiol . 10.1099/ijsem.0.002185
• Diaz-Cardenas, C. et al. (2017) Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565(T) an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring. Stand Genomic Sci 12, 86. 10.1186/s40793-017-0303-x
• Doud, D. F. R. et al. (2017) Novel approaches in function-driven single-cell genomics. FEMS Microbiol Rev . 10.1093/femsre/fux009
• Doud, D. F. R. et al. (2017) Novel approaches in function-driven single-cell genomics. FEMS Microbiol Rev . 10.1093/femsre/fux009
• Frindte, K. et al. (2017) Draft Genome Sequences of Two Gammaproteobacterial Methanotrophs Isolated from Rice Ecosystems. Genome Announc 5(33). 10.1128/genomeA.00526-17
• Garcia, S. L. et al. (2017) Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations. ISME J . 10.1038/s41396-017-0001-0
• Gutierrez, T. et al. (2017) Genome Sequence of Oceanicola sp. Strain MCTG156(1a), Isolated from a Scottish Coastal Phytoplankton Net Sample. Genome Announc 5(32). 10.1128/genomeA.00796-17
• Gutierrez, T. et al. (2017) Genome Sequence of Roseovarius sp. Strain MCTG156(2b) Isolated from a Phytoplankton Net Trawl on the Scottish West Coast. Genome Announc 5(35). 10.1128/genomeA.00837-17
• Hadjithomas, M. et al. (2017) IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes. Nucleic Acids Res 45(D1), D560-D565. 10.1093/nar/gkw1103
• Hahn, M. W. et al. (2017) Reclassification of a Polynucleobacter cosmopolitanus strain isolated from tropical Lake Victoria as Polynucleobacter victoriensis sp. nov. Int J Syst Evol Microbiol . 10.1099/ijsem.0.002421
• Harrington, L. B. et al. (2017) A thermostable Cas9 with increased lifetime in human plasma. Nat Commun 8(1), 1424. 10.1038/s41467-017-01408-4
• Hutt, L. P. et al. (2017) Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria. Stand Genomic Sci 12, 10. 10.1186/s40793-017-0229-3
• Jiao, J. Y. et al. (2017) Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds. Stand Genomic Sci 12, 21. 10.1186/s40793-017-0226-6
• Klonowska, A. et al. (2017) High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia. Stand Genomic Sci 12, 7. 10.1186/s40793-016-0212-4
• Kruse, T. et al. (2017) Comparative genomics of the genus Desulfitobacterium. FEMS Microbiol Ecol 93(12). 10.1093/femsec/fix135
• Kublanov, I. V. et al. (2017) Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Front Microbiol 8, 195. 10.3389/fmicb.2017.00195
• Laviad-Shitrit, S. et al. (2017) High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. Stand Genomic Sci 12, 31. 10.1186/s40793-017-0242-6
• Laviad-Shitrit, S. et al. (2017) High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. Stand Genomic Sci 12, 31. 10.1186/s40793-017-0242-6
• Matrosova, V. Y. et al. (2017) High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Stand Genomic Sci 12, 46. 10.1186/s40793-017-0258-y
• Melton, E. D. et al. (2017) Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile. Stand Genomic Sci 12, 57. 10.1186/s40793-017-0268-9
• Miroshnikov, K. K. et al. (2017) Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil. Genome Announc 5(24). 10.1128/genomeA.00504-17
• Miroshnikov, K. K. et al. (2017) Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil. Genome Announc 5(24). 10.1128/genomeA.00504-17
• Montero-Calasanz, M. D. C. et al. (2017) Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae. Front Microbiol 8, 2501. 10.3389/fmicb.2017.02501
• Montero-Calasanz, M. D. C. et al. (2017) Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae. Front Microbiol 8, 2501. 10.3389/fmicb.2017.02501
• Mukai, T. et al. (2017) RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea. MBio 8(3). 10.1128/mBio.00561-17
• Mukai, T. et al. (2017) RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea. MBio 8(3). 10.1128/mBio.00561-17
• Mukherjee, S. et al. (2017) Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. Nucleic Acids Res 45(D1), D446-D456. 10.1093/nar/gkw992
• Nouioui, I. et al. (2017) High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea. Stand Genomic Sci 12, 4. 10.1186/s40793-016-0216-0
• Osman, W. A. M. et al. (2017) High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. Stand Genomic Sci 12, 58. 10.1186/s40793-017-0270-2
• Pachiadaki, M. G. et al. (2017) Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358(6366), 1046-1051. 10.1126/science.aan8260
• Paez-Espino, D. et al. (2017) IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res 45(D1), D457-D465. 10.1093/nar/gkw1030
• Patil, Y. et al. (2017) High-quality-draft genome sequence of the fermenting bacterium Anaerobium acetethylicum type strain GluBS11T (DSM 29698). Stand Genomic Sci 12, 24. 10.1186/s40793-017-0236-4
• Pavlopoulos, G. A. et al. (2017) Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis. Adv Bioinformatics 2017, 1278932. 10.1155/2017/1278932
• Proenca, D. N. et al. (2017) Draft genome sequence of the cellulolytic endophyte Chitinophaga costaii A37T2T. Stand Genomic Sci 12, 53. 10.1186/s40793-017-0262-2
• Proenca, D. N. et al. (2017) Arboriscoccus pini gen. nov., sp. nov., an endophyte from a pine tree of the class Alphaproteobacteria, emended description of Geminicoccus roseus, and proposal of Geminicoccaceae fam. nov. Syst Appl Microbiol . 10.1016/j.syapm.2017.11.006
• Reeve, W. et al. (2017) High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76T, isolated from Glycine max (L.) Merr. Stand Genomic Sci 12, 26. 10.1186/s40793-017-0238-2
• Rice, M. C. et al. (2017) Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters. Genome Announc 5(11). 10.1128/genomeA.00011-17
• Rojas-Rojas, F. U. et al. (2017) Draft genome of Paraburkholderia caballeronis TNe-841(T), a free-living, nitrogen-fixing, tomato plant-associated bacterium. Stand Genomic Sci 12, 80. 10.1186/s40793-017-0294-7
• Silas, S. et al. (2017) On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires. MBio 8(4). 10.1128/mBio.00897-17
• Simon, L. et al. (2017) Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater. Antonie Van Leeuwenhoek . 10.1007/s10482-017-0891-x
• Simon, L. et al. (2017) Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater. Antonie Van Leeuwenhoek . 10.1007/s10482-017-0891-x
• Singer, E. et al. (2017) Capturing the genetic makeup of the active microbiome in situ. ISME J . 10.1038/ismej.2017.59
• Singer, E. et al. (2017) Capturing the genetic makeup of the active microbiome in situ. ISME J . 10.1038/ismej.2017.59
• Skraban, J. et al. (2017) Draft genome sequence of Chryseobacterium limigenitum SUR2T (LMG 28734T) isolated from dehydrated sludge. Braz J Microbiol . 10.1016/j.bjm.2017.03.009
• Susanti, D. et al. (2017) Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533T, a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia. Genome Announc 5(15). 10.1128/genomeA.00078-17
• Susanti, D. et al. (2017) Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533T, a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia. Genome Announc 5(15). 10.1128/genomeA.00078-17
• Tian, R. et al. (2017) Evolution of a multi-step phosphorelay signal transduction system in Ensifer: Recruitment of the sigma factor RpoN and a novel enhancer binding protein triggers acid-activated gene expression. Mol Microbiol . 10.1111/mmi.13592
• Twing, K. I. et al. (2017) Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH. Front Microbiol 8, 308. 10.3389/fmicb.2017.00308
• Vigneron, A. et al. (2017) Succession in the petroleum reservoir microbiome through an oil field production lifecycle. ISME J . 10.1038/ismej.2017.78
• Waite, D. W. et al. (2017) Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 8, 682. 10.3389/fmicb.2017.00682
• Waite, D. W. et al. (2017) Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 8, 682. 10.3389/fmicb.2017.00682
• Wang, L. et al. (2017) Interactions among triphenyltin degradation, phospholipid synthesis and membrane characteristics of Bacillus thuringiensis in the presence of d-malic acid. Chemosphere 169, 403-412. 10.1016/j.chemosphere.2016.10.140
• Warshan, D. et al. (2017) Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis. ISME J . 10.1038/ismej.2017.134
• Woyke, T. et al. (2017) The trajectory of microbial single-cell sequencing. Nat Methods 14(11), 1045-1054. 10.1038/nmeth.4469
• Woyke, T. et al. (2017) The trajectory of microbial single-cell sequencing. Nat Methods 14(11), 1045-1054. 10.1038/nmeth.4469
• Yassin, A. F. et al. (2017) Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence. PLoS One 12(12), e0188914. 10.1371/journal.pone.0188914
• Yi, W. et al. (2017) Triphenyltin degradation and proteomic response by an engineered Escherichia coli expressing cytochrome P450 enzyme. Ecotoxicol Environ Saf 137, 29-34. 10.1016/j.ecoenv.2016.11.012
• Zojer, M. et al. (2017) Variant profiling of evolving prokaryotic populations. PeerJ 5, e2997. 10.7717/peerj.2997

2016

• Aizenberg-Gershtein, Y. et al. (2016) High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods. Stand Genomic Sci 11, 4. 10.1186/s40793-015-0127-5
• Anderson, I. J. et al. (2016) Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34. Stand Genomic Sci 11(1), 70. 10.1186/s40793-016-0194-2
• Bashir, M. et al. (2016) Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Frontiers in Microbiology 7. 10.3389/fmicb.2016.01321
• Blow, M. J. et al. (2016) The Epigenomic Landscape of Prokaryotes. PLoS Genet 12(2), e1005854. 10.1371/journal.pgen.1005854
• Boden, R. et al. (2016) Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia. Stand Genomic Sci 11, 74. 10.1186/s40793-016-0188-0
• Bremges, A. et al. (2016) MeCorS: Metagenome-enabled error correction of single cell sequencing reads. Bioinformatics . 10.1093/bioinformatics/btw144
• Browne, P. et al. (2016) Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments. ISME J . 10.1038/ismej.2016.104
• Brumm, P. J. et al. (2016) Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost. Stand Genomic Sci 11, 33. 10.1186/s40793-016-0153-y
• Chen, I. M. et al. (2016) Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. BMC Genomics 17(1), 307. 10.1186/s12864-016-2629-y
• De Meyer, S. E. et al. (2016) Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes. Mol Plant Microbe Interact 29(8), 609-619. 10.1094/MPMI-05-16-0091-R
• Eiler, A. et al. (2016) Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. ISME J . 10.1038/ismej.2015.260
• Flynn, J. D. et al. (2016) Draft Genome Sequences of Gammaproteobacterial Methanotrophs Isolated from Marine Ecosystems. Genome Announc 4(1). 10.1128/genomeA.01629-15
• Fujimoto, Masanori et al. (2016) Spatiotemporal distribution of bacterioplankton functional groups along a freshwater estuary to pelagic gradient in Lake Michigan. Journal of Great Lakes Research -(-), -. 10.1016/j.jglr.2016.07.029
• Ganji, R. et al. (2016) High-Quality Draft Genome Sequence of Thermocrinis jamiesonii GBS1T Isolated from Great Boiling Spring, Nevada. Genome Announc 4(5). 10.1128/genomeA.01112-16
• Gehlot, H. S. et al. (2016) High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India. Stand Genomic Sci 11, 43. 10.1186/s40793-016-0157-7
• Ghodhbane-Gtari, F. et al. (2016) Permanent Draft Genome Sequence of Nocardia sp. BMG111209, an Actinobacterium Isolated from Nodules of Casuarina glauca. Genome Announc 4(4). 10.1128/genomeA.00770-16
• Ghodhbane-Gtari, F. et al. (2016) Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca. Genome Announc 4(4). 10.1128/genomeA.00799-16
• Goordial, J. et al. (2016) Cold adaptive traits revealed by comparative genomic analysis of the eurypsychrophile Rhodococcus sp. JG3 isolated from high elevation McMurdo Dry Valley permafrost, Antarctica. FEMS Microbiol Ecol . 10.1093/femsec/fiv154
• Goordial, J. et al. (2016) Improved High-Quality Draft Genome Sequence of the Eurypsychrophile Rhodotorula sp. JG1b, Isolated from Permafrost in the Hyperarid Upper-Elevation McMurdo Dry Valleys, Antarctica. Genome Announc 4(2). 10.1128/genomeA.00069-16
• Gregory, A. C. et al. (2016) Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics 17(1), 930. 10.1186/s12864-016-3286-x
• Gunsalus, R. P. et al. (2016) Complete genome sequence of Methanospirillum hungatei type strain JF1. Stand Genomic Sci 11, 2. 10.1186/s40793-015-0124-8
• Gutierrez, T. et al. (2016) Genome Sequence of Arenibacter algicola Strain TG409, a Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc 4(4). 10.1128/genomeA.00765-16
• Gutierrez, T. et al. (2016) Genome Sequence of Marinobacter sp. Strain MCTG268 Isolated from the Cosmopolitan Marine Diatom Skeletonema costatum. Genome Announc 4(5). 10.1128/genomeA.00937-16
• Hahnke, R. L. et al. (2016) Genome-Based Taxonomic Classification of Bacteroidetes. Front Microbiol 7, 2003. 10.3389/fmicb.2016.02003
• Hatzenpichler, R. et al. (2016) Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci U S A . 10.1073/pnas.1603757113
• Hirschman, L. et al. (2016) Crowdsourcing and curation: perspectives from biology and natural language processing. Database (Oxford) 2016. 10.1093/database/baw115
• Holmfeldt, K. et al. (2016) Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol . 10.1111/1462-2920.13392
• Holmfeldt, K. et al. (2016) Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol 18(11), 3949-3961. 10.1111/1462-2920.13392
• Hwang, C. et al. (2016) Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds. Genome Announc 4(6). 10.1128/genomeA.01226-16
• Kanukollu, S. et al. (2016) Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. Stand Genomic Sci 11, 25. 10.1186/s40793-016-0143-0
• Kappler, U. et al. (2016) Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing gamma-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). Stand Genomic Sci 11, 38. 10.1186/s40793-016-0162-x
• Kelly, W. J. et al. (2016) Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract. Sci Rep 6, 30768. 10.1038/srep30768
• Louca, S. et al. (2016) Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. Proc Natl Acad Sci U S A 113(40), E5925-E5933. 10.1073/pnas.1602897113
• Louie, T. S. et al. (2016) High-quality draft genome sequence of Sedimenticola selenatireducens strain AK4OH1T, a gammaproteobacterium isolated from estuarine sediment. Stand Genomic Sci 11, 66. 10.1186/s40793-016-0191-5
• Lux, M. et al. (2016) acdc – Automated Contamination Detection and Confidence estimation for single-cell genome data. BMC Bioinformatics 17(1), 543. 10.1186/s12859-016-1397-7
• Mefferd, C. C. et al. (2016) High-Quality Draft Genomes from Thermus caliditerrae YIM 77777 and T. tengchongensis YIM 77401, Isolates from Tengchong, China. Genome Announc 4(2). 10.1128/genomeA.00312-16
• Melton, E. D. et al. (2016) Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes. Stand Genomic Sci 11(1), 67. 10.1186/s40793-016-0184-4
• Nicholson, W. L. et al. (2016) An improved high-quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1(T). Stand Genomic Sci 11(1), 65. 10.1186/s40793-016-0193-3
• Nouioui, I. et al. (2016) Draft Genome Sequence of Frankia Strain G2, a Nitrogen-Fixing Actinobacterium Isolated from Casuarina equisetifolia and Able To Nodulate Actinorhizal Plants of the Order Rhamnales. Genome Announc 4(3). 10.1128/genomeA.00437-16
• Panschin, I. et al. (2016) Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005. Stand Genomic Sci 11, 37. 10.1186/s40793-016-0163-9
• Pena, A. et al. (2016) High quality draft genome sequences of Pseudomonas fulva DSM 17717(T), Pseudomonas parafulva DSM 17004(T) and Pseudomonas cremoricolorata DSM 17059(T) type strains. Stand Genomic Sci 11(1), 55. 10.1186/s40793-016-0178-2
• Rice, M. C. et al. (2016) Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. Stand Genomic Sci 11, 46. 10.1186/s40793-016-0168-4
• Rojas-Rojas, F. U. et al. (2016) Draft Genome Sequence of Heavy Metal-Resistant Cupriavidus alkaliphilus ASC-732T, Isolated from Agave Rhizosphere in the Northeast of Mexico. Genome Announc 4(5). 10.1128/genomeA.01013-16
• Salman, V. et al. (2016) Insights into the single cell draft genome of “Candidatus Achromatium palustre”. Stand Genomic Sci 11, 28. 10.1186/s40793-016-0146-x
• Singer, E. et al. (2016) High-resolution phylogenetic microbial community profiling. ISME J . 10.1038/ismej.2015.249
• Singer, E. et al. (2016) Next generation sequencing data of a defined microbial mock community. Sci Data 3, 160081. 10.1038/sdata.2016.81
• Strassert, J. F. et al. (2016) Genome analysis of ‘Candidatus Ancillula trichonymphae’, first representative of a deep-branching clade of Bifidobacteriales, strengthens evidence for convergent evolution in flagellate endosymbionts. Environ Microbiol Rep . 10.1111/1758-2229.12451
• Strepis, N. et al. (2016) Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses. Int J Syst Evol Microbiol . 10.1099/ijsem.0.001294
• Strepis, N. et al. (2016) Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses. Int J Syst Evol Microbiol 66(10), 3957-3963. 10.1099/ijsem.0.001294
• Susanti, D. et al. (2016) Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. Stand Genomic Sci 11, 3. 10.1186/s40793-015-0128-4
• Tashkandy, N. et al. (2016) High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T). Stand Genomic Sci 11, 42. 10.1186/s40793-016-0159-5
• Tsementzi, D. et al. (2016) SAR11 bacteria linked to ocean anoxia and nitrogen loss. Nature 536(7615), 179-83. 10.1038/nature19068
• Tsesmetzis, N. et al. (2016) MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources. Stand Genomic Sci 11, 78. 10.1186/s40793-016-0203-5
• Winkel, M. et al. (2016) Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions. Frontiers in Microbiology 7, 964. 10.3389/fmicb.2016.00964
• Woo, H. L. et al. (2016) Near-Complete Genome Sequence of Thalassospira sp. Strain KO164 Isolated from a Lignin-Enriched Marine Sediment Microcosm. Genome Announc 4(6). 10.1128/genomeA.01297-16
• Zhou, E. M. et al. (2016) High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway. Stand Genomic Sci 11, 20. 10.1186/s40793-016-0140-3

2015

• Ai, C. et al. (2015) Complete Genome Sequences of Evolved Arsenate-Resistant Metallosphaera sedula Strains. Genome Announc 3(5). 10.1128/genomeA.01142-15
• Alawi, M. et al. (2015) Genome Sequence of Methanosarcina soligelidi SMA-21, Isolated from Siberian Permafrost-Affected Soil. Genome Announc 3(2). 10.1128/genomeA.00270-15
• Alivisatos, A. P. et al. (2015) MICROBIOME. A unified initiative to harness Earth’s microbiomes. Science 350(6260), 507-8. 10.1126/science.aac8480
• Ardley, J. et al. (2015) High-quality permanent draft genome sequence of Ensifer medicae strain WSM244, a microsymbiont isolated from Medicago polymorpha growing in alkaline soil. Stand Genomic Sci 10, 126. 10.1186/s40793-015-0119-5
• Beck, D. A. et al. (2015) Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environ Microbiol 17(3), 547-54. 10.1111/1462-2920.12736
• Berben, T. et al. (2015) Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1(T), an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake. Stand Genomic Sci 10, 105. 10.1186/s40793-015-0097-7
• Berben, T. et al. (2015) Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T). Stand Genomic Sci 10, 85. 10.1186/s40793-015-0078-x
• Berben, T. et al. (2015) Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification. Stand Genomic Sci 10, 84. 10.1186/s40793-015-0080-3
• Berry, D. et al. (2015) Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci U S A 112(2), E194-203. 10.1073/pnas.1420406112
• Billings, A. F. et al. (2015) Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Stand Genomic Sci 10, 106. 10.1186/s40793-015-0100-3
• Boundy-Mills, K. et al. (2015) The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections. Appl Environ Microbiol 81(17), 5671-4. 10.1128/AEM.01176-15
• Bowers, R. M. et al. (2015) Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics 16(1), 856. 10.1186/s12864-015-2063-6
• Brauer, S. L. et al. (2015) Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments. Microbiology . 10.1099/mic.0.000117
• Brumm, P. J. et al. (2015) Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park. Stand Genomic Sci 10, 73. 10.1186/s40793-015-0031-z
• Cadillo-Quiroz, H. et al. (2015) Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland. Genome Announc 3(6). 10.1128/genomeA.01280-15
• Carr, S. A. et al. (2015) Abundant Atribacteria in deep marine sediment from the Adelie Basin, Antarctica. Front Microbiol 6, 872. 10.3389/fmicb.2015.00872
• Choi, D. H. et al. (2015) High-quality draft genome sequence of Gracilimonas tropica CL-CB462(T) (DSM 19535(T)), isolated from a Synechococcus culture. Stand Genomic Sci 10, 98. 10.1186/s40793-015-0088-8
• Cohen, M. F. et al. (2015) Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1. Genome Announc 3(3). 10.1128/genomeA.00646-15
• De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Mimosa asperata – nodulating Cupriavidus sp. strain AMP6. Stand Genomic Sci 10, 80. 10.1186/s40793-015-0074-1
• De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. Stand Genomic Sci 10, 79. 10.1186/s40793-015-0072-3
• De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413. Stand Genomic Sci 10, 31. 10.1186/s40793-015-0018-9
• De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Cupriavidus sp. strain UYPR2.512. Stand Genomic Sci 10, 13. 10.1186/1944-3277-10-13
• De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Lebeckia – nodulating Burkholderia dilworthii strain WSM3556(T). Stand Genomic Sci 10, 64. 10.1186/s40793-015-0048-3
• De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Mimosa asperata – nodulating Cupriavidus sp. strain AMP6. Stand Genomic Sci 10, 80. 10.1186/s40793-015-0074-1
• De Meyer, S. E. et al. (2015) High-quality permanent draft genome sequence of the Lebeckia ambigua-nodulating Burkholderia sp. strain WSM4176. Stand Genomic Sci 10, 79. 10.1186/s40793-015-0072-3
• Dedysh, S. N. et al. (2015) Draft Genome Sequence of Methyloferula stellata AR4, an Obligate Methanotroph Possessing Only a Soluble Methane Monooxygenase. Genome Announc 3(2). 10.1128/genomeA.01555-14
• Eichorst, S. A. et al. (2015) Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecol . 10.1093/femsec/fiv106
• Eshraghi, L. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 – an effective microsymbiont of an Indigofera sp. growing in Australia. Stand Genomic Sci 10, 87. 10.1186/s40793-015-0073-2
• Gao, X. Y. et al. (2015) Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China. Stand Genomic Sci 10, 1. 10.1186/1944-3277-10-1
• Gaudana, S. B. et al. (2015) Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase Ci uptake by cyanobacteria. Photosynth Res 126(1), 99-109. 10.1007/s11120-014-0059-8
• Gaudana, S. B. et al. (2015) Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase Ci uptake by cyanobacteria. Photosynth Res 126(1), 99-109. 10.1007/s11120-014-0059-8
• Goordial, J. et al. (2015) Improved-high-quality draft genome sequence of Rhodococcus sp. JG-3, a eurypsychrophilic Actinobacteria from Antarctic Dry Valley permafrost. Stand Genomic Sci 10, 61. 10.1186/s40793-015-0043-8
• Gutierrez, T. et al. (2015) Genome Sequence of Polycyclovorans algicola Strain TG408, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc 3(2). 10.1128/genomeA.00207-15
• Gutierrez, T. et al. (2015) Genome Sequence of Halomonas sp. Strain MCTG39a, a Hydrocarbon-Degrading and Exopolymeric Substance-Producing Bacterium. Genome Announc 3(4). 10.1128/genomeA.00793-15
• Gutierrez, T. et al. (2015) Genome Sequence of Porticoccus hydrocarbonoclasticus Strain MCTG13d, an Obligate Polycyclic Aromatic Hydrocarbon-Degrading Bacterium Associated with Marine Eukaryotic Phytoplankton. Genome Announc 3(3). 10.1128/genomeA.00672-15
• Hahnke, R. L. et al. (2015) High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes. Stand Genomic Sci 10, 46. 10.1186/s40793-015-0032-y
• Hamilton, R. et al. (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc 3(3). 10.1128/genomeA.00515-15
• Hedlund, B. P. et al. (2015) High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism. Genome Announc 3(6). 10.1128/genomeA.01410-15
• Hedlund, B. P. et al. (2015) Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr Opin Microbiol 25, 136-45. 10.1016/j.mib.2015.06.008
• Hedlund, B. P. et al. (2015) High-Quality Draft Genome Sequence of Kallotenue papyrolyticum JKG1T Reveals Broad Heterotrophic Capacity Focused on Carbohydrate and Amino Acid Metabolism. Genome Announc 3(6). 10.1128/genomeA.01410-15
• Hultman, J. et al. (2015) Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521(7551), 208-12. 10.1038/nature14238
• Huntemann, M. et al. (2015) The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci 10, 86. 10.1186/s40793-015-0077-y
• Hwang, C. et al. (2015) Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment. Genome Announc 3(1). 10.1128/genomeA.01449-14
• Kalyuzhnaya, M. G. et al. (2015) Draft genome sequences of gammaproteobacterial methanotrophs isolated from lake washington sediment. Genome Announc 3(2). 10.1128/genomeA.00103-15
• Kato, S. et al. (2015) Comparative Genomic Insights into Ecophysiology of Neutrophilic, Microaerophilic Iron Oxidizing Bacteria. Frontiers in Microbiology 6. ARTN 1265 10.3389/fmicb.2015.01265
• Kazakov, A. E. et al. (2015) sigma54-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics 16, 919. 10.1186/s12864-015-2176-y
• Kirby, J. et al. (2015) Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate. Appl Environ Microbiol 81(1), 130-8. 10.1128/AEM.02920-14
• Kotak, M. et al. (2015) Complete Genome Sequence of the Opitutaceae Bacterium Strain TAV5, a Potential Facultative Methylotroph of the Wood-Feeding Termite Reticulitermes flavipes. Genome Announc 3(2). 10.1128/genomeA.00060-15
• Labonte, J. M. et al. (2015) Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME J . 10.1038/ismej.2015.48
• Lau, S. C. et al. (2015) Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group. Stand Genomic Sci 10, 51. 10.1186/s40793-015-0050-9
• Laviad, S. et al. (2015) High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci 10, 21. 10.1186/s40793-015-0003-3
• Laviad, S. et al. (2015) High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci 10, 29. 10.1186/s40793-015-0010-4
• Lee, L. L. et al. (2015) Complete Genome Sequences of Caldicellulosiruptor sp. Strain Rt8.B8, Caldicellulosiruptor sp. Strain Wai35.B1, and “Thermoanaerobacter cellulolyticus”. Genome Announc 3(3). 10.1128/genomeA.00440-15
• Mazur, A. et al. (2015) High-quality permanent draft genome sequence of Rhizobium leguminosarum bv. viciae strain GB30; an effective microsymbiont of Pisum sativum growing in Poland. Stand Genomic Sci 10, 36. 10.1186/s40793-015-0029-6
• McCarthy, S. et al. (2015) Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives. Genome Announc 3(3). 10.1128/genomeA.00549-15
• McIlroy, S. J. et al. (2015) High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov. Stand Genomic Sci 10, 23. 10.1186/s40793-015-0013-1
• McTaggart, T. L. et al. (2015) Draft genome sequences of five new strains of methylophilaceae isolated from lake washington sediment. Genome Announc 3(1). 10.1128/genomeA.01511-14
• McTaggart, T. L. et al. (2015) Draft genomes of two strains of flavobacterium isolated from lake washington sediment. Genome Announc 3(1). 10.1128/genomeA.01597-14
• McTaggart, T. L. et al. (2015) Draft Genome of Pseudomonas sp. Strain 11/12A, Isolated from Lake Washington Sediment. Genome Announc 3(1). 10.1128/genomeA.01587-14
• McTaggart, T. L. et al. (2015) Draft Genome of Janthinobacterium sp. RA13 Isolated from Lake Washington Sediment. Genome Announc 3(1). 10.1128/genomeA.01588-14
• Medema, Marnix H. et al. (2015) Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol 11(9), 625-631. 10.1038/nchembio.1890
• Mhamdi, R. et al. (2015) High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris. Stand Genomic Sci 10, 34. 10.1186/s40793-015-0005-1
• Mukherjee, S. et al. (2015) Large-scale contamination of microbial isolate genomes by Illumina PhiX control. Stand Genomic Sci 10, 18. 10.1186/1944-3277-10-18
• Mukherjee, S. et al. (2015) High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India. Stand Genomic Sci 10, 8. 10.1186/1944-3277-10-8
• Nobu, M. K. et al. (2015) Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J . 10.1038/ismej.2014.256
• Nobu, M. K. et al. (2015) Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics. ISME J . 10.1038/ismej.2015.97
• Ntougias, S. et al. (2015) High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7(T), and emended description of the genus Halotalea. Stand Genomic Sci 10, 52. 10.1186/s40793-015-0052-7
• Petit, E. et al. (2015) Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PLoS One 10(6), e0118285. 10.1371/journal.pone.0118285
• Ramsay, B. D. et al. (2015) High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater. Genome Announc 3(2). 10.1128/genomeA.00092-15
• Ray, J. et al. (2015) Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site. Genome Announc 3(3). 10.1128/genomeA.00322-15
• Reeve, W. et al. (2015) A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey. Stand Genomic Sci 10, 14. 10.1186/1944-3277-10-14
• Reeve, W. et al. (2015) High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym. Stand Genomic Sci 10, 54. 10.1186/s40793-015-0049-2
• Rooney, E. A. et al. (2015) Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a. Genome Announc 3(4). 10.1128/genomeA.00797-15
• Roux, S. et al. (2015) Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 4. 10.7554/eLife.08490
• Sakamoto, M. et al. (2015) High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum. Stand Genomic Sci 10, 48. 10.1186/s40793-015-0045-6
• Schicklberger, M. et al. (2015) Draft Genome Sequence of Raoultella terrigena R1Gly, a Diazotrophic Endophyte. Genome Announc 3(3). 10.1128/genomeA.00607-15
• Seshadri, R. et al. (2015) Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria. Sci Rep 5, 16825. 10.1038/srep16825
• Sharp, C. E. et al. (2015) Draft Genome Sequence of the Moderately Halophilic Methanotroph Methylohalobius crimeensis Strain 10Ki. Genome Announc 3(3). 10.1128/genomeA.00644-15
• Shetty, A. R. et al. (2015) Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Stand Genomic Sci 10, 55. 10.1186/s40793-015-0041-x
• Singh, R. et al. (2015) Complete Genome Sequence of an Evolved Thermotoga maritima Isolate. Genome Announc 3(3). 10.1128/genomeA.00557-15
• Smalley, N. E. et al. (2015) Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of the new species Methyloversatilis discipulorum sp. nov. Int J Syst Evol Microbiol . 10.1099/ijs.0.000190
• Tennessen, K. et al. (2015) ProDeGe: a computational protocol for fully automated decontamination of genomes. ISME J . 10.1038/ismej.2015.100
• Tian, R. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. Ai1a-2; a microsymbiont of Andira inermis discovered in Costa Rica. Stand Genomic Sci 10, 33. 10.1186/s40793-015-0007-z
• Tian, R. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. Th.b2, a microsymbiont of Amphicarpaea bracteata collected in Johnson City, New York. Stand Genomic Sci 10, 24. 10.1186/s40793-015-0008-y
• Tian, R. et al. (2015) High-quality permanent draft genome sequence of Bradyrhizobium sp. Tv2a.2, a microsymbiont of Tachigali versicolor discovered in Barro Colorado Island of Panama. Stand Genomic Sci 10, 27. 10.1186/s40793-015-0006-0
• Tisa, L. S. et al. (2015) Draft Genome Sequence of Frankia sp. Strain DC12, an Atypical, Noninfective, Ineffective Isolate from Datisca cannabina. Genome Announc 3(4). 10.1128/genomeA.00889-15
• Tiwari, R. et al. (2015) Genome sequence of Bradyrhizobium sp. WSM1253; a microsymbiont of Ornithopus compressus from the Greek Island of Sifnos. Stand Genomic Sci 10, 113. 10.1186/s40793-015-0115-9
• Tremblay, J. et al. (2015) Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol 6, 771. 10.3389/fmicb.2015.00771
• Tripp, H. J. et al. (2015) Toward a standard in structural genome annotation for prokaryotes. Stand Genomic Sci 10, 45. 10.1186/s40793-015-0034-9
• Varghese, N. J. et al. (2015) Microbial species delineation using whole genome sequences. Nucleic Acids Res 43(14), 6761-71. 10.1093/nar/gkv657
• Walworth, N. et al. (2015) Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle. Proc Natl Acad Sci U S A 112(14), 4251-6. 10.1073/pnas.1422332112
• Whitman, W. B. et al. (2015) Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci 10, 26. 10.1186/s40793-015-0017-x
• Woyke, T. et al. (2015) Function-driven single-cell genomics. Microb Biotechnol 8(1), 38-9. 10.1111/1751-7915.12247
• Yassin, A. F. et al. (2015) High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)). Stand Genomic Sci 10, 50. 10.1186/s40793-015-0036-7
• Yates, R. et al. (2015) High-quality permanent draft genome sequence of Rhizobium sullae strain WSM1592; a Hedysarum coronarium microsymbiont from Sassari, Italy. Stand Genomic Sci 10, 44. 10.1186/s40793-015-0020-2
• Youssef, N. H. et al. (2015) In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum “Latescibacteria” (WS3). PLoS One 10(6), e0127499. 10.1371/journal.pone.0127499
• Yung, M. C. et al. (2015) Tn-seq of Caulobacter crescentus under uranium stress reveals genes essential for detoxification and stress tolerance. J Bacteriol . 10.1128/JB.00382-15

2014

• Ardley, J. et al. (2014) Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598. Stand Genomic Sci 9, 5. 10.1186/1944-3277-9-5
• Axen, S. D. et al. (2014) A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 10(10), e1003898. 10.1371/journal.pcbi.1003898
• Beck, D. A. et al. (2014) The expanded diversity of methylophilaceae from Lake Washington through cultivation and genomic sequencing of novel ecotypes. PLoS One 9(7), e102458. 10.1371/journal.pone.0102458
• Biddle, A. S. et al. (2014) The complete genome sequence of Clostridium indolis DSM 755(T.). Stand Genomic Sci 9(3), 1089-104. 10.4056/sigs.5281010
• Billis, K. et al. (2014) Comparative Transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 Provide Insights into Mechanisms of Stress Acclimation. PLoS One 9(10), e109738. 10.1371/journal.pone.0109738
• Breider, S. et al. (2014) Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Stand Genomic Sci 9(3), 687-703. 10.4056/sigs.3828824
• Campbell, A. G. et al. (2014) Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Environ Microbiol . 10.1111/1462-2920.12461
• Clingenpeel, S. et al. (2014) Effects of sample treatments on genome recovery via single-cell genomics. ISME J . 10.1038/ismej.2014.92
• Clingenpeel, S. et al. (2014) Reconstructing each cell’s genome within complex microbial communities-dream or reality?. Front Microbiol 5, 771. 10.3389/fmicb.2014.00771
• Dmytrenko, O. et al. (2014) The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. BMC Genomics 15(1), 924. 10.1186/1471-2164-15-924
• Durham, B. P. et al. (2014) Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand Genomic Sci 9(3), 632-45. 10.4056/sigs.4998989
• Erbilgin, O. et al. (2014) Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides. Applied and Environmental Microbiology 80(7), 2193-2205. Doi 10.1128/Aem.03887-13
• Field, D. et al. (2014) Genomic standards consortium projects. Stand Genomic Sci 9(3), 599-601. 10.4056/sigs.5559680
• Field, E. K. et al. (2014) Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount. ISME J . 10.1038/ismej.2014.183
• Gan, F. et al. (2014) Extensive remodeling of a cyanobacterial photosynthetic apparatus in far-red light. Science 345(6202), 1312-7. 10.1126/science.1256963
• Garau, G. et al. (2014) Genome sequence of Ensifer medicae Di28; an effective N2-fixing microsymbiont of Medicago murex and M. polymorpha. Stand Genomic Sci 9, 4. 10.1186/1944-3277-9-4
• Gaudana, S. B. et al. (2014) Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase C uptake by cyanobacteria. Photosynth Res . 10.1007/s11120-014-0059-8
• Ghylin, T. W. et al. (2014) Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. ISME J . 10.1038/ismej.2014.135
• Goker, M. et al. (2014) Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci 9(3), 1076-88. 10.4056/sigs.5138968
• Goker, M. et al. (2014) Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring. Stand Genomic Sci 9(3), 1105-17. 10.4056/sigs.3016383
• Hedlund, B. P. et al. (2014) Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles 18(5), 865-75. 10.1007/s00792-014-0664-7
• Heller, P. et al. (2014) ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank. Bioinformatics . 10.1093/bioinformatics/btu417
• Ivanova, N. N. et al. (2014) Stop codon reassignments in the wild. Science 344(6186), 909-13. 10.1126/science.1250691
• Kamke, J. et al. (2014) The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One 9(1), e87353. 10.1371/journal.pone.0087353
• Kelly, S. et al. (2014) Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037. Stand Genomic Sci 9, 7. 10.1186/1944-3277-9-7
• Kelly, S. et al. (2014) Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A. Stand Genomic Sci 9, 6. 10.1186/1944-3277-9-6
• Kouvelis, V. N. et al. (2014) Finished Genome of Zymomonas mobilis subsp. mobilis Strain CP4, an Applied Ethanol Producer. Genome Announc 2(1). 10.1128/genomeA.00845-13
• Kruse, T. et al. (2014) Genomic, proteomic and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. J Bacteriol . 10.1128/JB.02370-14
• Kuever, J. et al. (2014) Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci 9(3), 821-39. 10.4056/sigs.5209235
• Kyrpides, N. C. et al. (2014) Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 12(8), e1001920. 10.1371/journal.pbio.1001920
• Kyrpides, N. C. et al. (2014) Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Stand Genomic Sci 9(3), 1278-84. 10.4056/sigs.5068949
• Lassila, J. K. et al. (2014) Assembly of robust bacterial microcompartment shells using building blocks from an organelle of unknown function. J Mol Biol 426(11), 2217-28. 10.1016/j.jmb.2014.02.025
• Leverenz, R. L. et al. (2014) Structural and functional modularity of the orange carotenoid protein: distinct roles for the N- and C-terminal domains in cyanobacterial photoprotection. Plant Cell 26(1), 426-37. 10.1105/tpc.113.118588
• Mason, O. U. et al. (2014) Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill. Front Microbiol 5, 332. 10.3389/fmicb.2014.00332
• Meier-Kolthoff, J.P. et al. (2014) Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 9, 2. 10.1186/1944-3277-9-2
• Moulin, L. et al. (2014) Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species. Stand Genomic Sci 9(3), 763-74. 10.4056/sigs.4861021
• Mukherjee, S. et al. (2014) Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans. PLoS One 9(1), e86731. 10.1371/journal.pone.0086731
• Nandasena, K. et al. (2014) Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)). Stand Genomic Sci 9(3), 462-72. 10.4056/sigs.4458283
• Ntougias, S. et al. (2014) High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway. Stand Genomic Sci 9(3), 783-93. 10.4056/sigs.5088950
• O’Connor, R. M. et al. (2014) Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk. Proc Natl Acad Sci U S A 111(47), E5096-104. 10.1073/pnas.1413110111
• Pedersen, K. et al. (2014) Complete Genome Sequence of the Subsurface, Mesophilic Sulfate-Reducing Bacterium Desulfovibrio aespoeensis Aspo-2. Genome Announc 2(3). 10.1128/genomeA.00509-14
• Piao, H. et al. (2014) Identification of novel biomass-degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation. Biotechnol Bioeng 111(8), 1550-65. 10.1002/bit.25250
• Ramirez, M. S. et al. (2014) Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates. Genome Announc 2(3). 10.1128/genomeA.00558-14
• Reeve, W. et al. (2014) Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.). Stand Genomic Sci 9(3), 540-50. 10.4056/sigs.4548266
• Reeve, W. et al. (2014) Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128. Stand Genomic Sci 9(3), 602-13. 10.4056/sigs.4929626
• Reeve, W. et al. (2014) Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece. Stand Genomic Sci 9(3), 514-26. 10.4056/sigs.4938652
• Reeve, W. et al. (2014) Genome sequence of Microvirga lupini strain LUT6(T), a novel Lupinus alphaproteobacterial microsymbiont from Texas. Stand Genomic Sci 9(3), 1159-67. 10.4056/sigs.5249382
• Reeve, W. et al. (2014) Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan. Stand Genomic Sci 9(3), 473-83. 10.4056/sigs.4828625
• Riedel, T. et al. (2014) Genome sequence of the Wenxinia marina type strain (DSM 24838(T)), a representative of the Roseobacter group isolated from oilfield sediments. Stand Genomic Sci 9(3), 855-65. 10.4056/sigs.5601028
• Riedel, T. et al. (2014) Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094(T)), a moderately halophilic member of the Roseobacter clade. Stand Genomic Sci 9(3), 1333-45. 10.4056/sigs.4909790
• Rinke, C. et al. (2014) Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nat Protoc 9(5), 1038-48. 10.1038/nprot.2014.067
• Roux, S. et al. (2014) Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. Elife 3, e03125. 10.7554/eLife.03125
• Scheuner, C. et al. (2014) Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci 9, 10. 10.1186/1944-3277-9-10
• Shi, W. et al. (2014) Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res . 10.1101/gr.168245.113
• Shilova, I. N. et al. (2014) A microarray for assessing transcription from pelagic marine microbial taxa. ISME J . 10.1038/ismej.2014.1
• Swan, B. K. et al. (2014) Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres. PLoS One 9(4), e95380. 10.1371/journal.pone.0095380
• Terpolilli, J. et al. (2014) Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum. Stand Genomic Sci 9(3), 527-39. 10.4056/sigs.4988693
• Thiel, T. et al. (2014) Complete genome sequence of Anabaena variabilis ATCC 29413. Stand Genomic Sci 9(3), 562-73. 10.4056/sigs.3899418
• Thrash, J.C. et al. (2014) Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J . 10.1038/ismej.2013.243
• Vishnivetskaya, T. A. et al. (2014) Draft genome sequences of 10 strains of the genus exiguobacterium. Genome Announc 2(5). 10.1128/genomeA.01058-14
• Visser, M. et al. (2014) Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. Stand Genomic Sci 9(3), 655-75. 10.4056/sigs.4718645
• Walker, R. et al. (2014) Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia. Stand Genomic Sci 9(3), 551-61. 10.4056/sigs.5008793
• Walker, R. et al. (2014) Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia. Stand Genomic Sci 9(3), 1168-80. 10.4056/sigs.5018795
• Willems, A. et al. (2014) Genome sequence of Burkholderia mimosarum strain LMG 23256(T), a Mimosa pigra microsymbiont from Anso, Taiwan. Stand Genomic Sci 9(3), 484-94. 10.4056/sigs.4848627
• Williams, T. J. et al. (2014) Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J . 10.1038/ismej.2014.18
• Wilson, J. G. et al. (2014) Draft Genome Sequence of Enterobacter cloacae Strain JD6301. Genome Announc 2(3). 10.1128/genomeA.00381-14
• Wilson, M. C. et al. (2014) An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506(7486), 58-62. 10.1038/nature12959
• Woo, H.L. et al. (2014) Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Stand Genomic Sci 9, 19. 10.1186/1944-3277-9-19
• Woyke, T. et al. (2014) Evolution. Searching for new branches on the tree of life. Science 346(6210), 698-9. 10.1126/science.1258871
• Wright, J. J. et al. (2014) Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle. ISME J 8(2), 455-68. 10.1038/ismej.2013.152
• Yamamoto, K. et al. (2014) Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge. Genome Announc 2(5). 10.1128/genomeA.00876-14
• Yamamoto, K. et al. (2014) Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor. Genome Announc 2(5). 10.1128/genomeA.00870-14
• Youssef, N. H. et al. (2014) Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’. ISME J . 10.1038/ismej.2014.141
• Zhou, Y. et al. (2014) High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China. Stand Genomic Sci 9(3), 1020-30. 10.4056/sigs.5449586
• Ziemert, N. et al. (2014) Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci U S A 111(12), E1130-9. 10.1073/pnas.1324161111
• Reeve, W. et al. (2014 ) Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B. Stand Genomic Sci 9, 3. 10.1186/1944-3277-9-3

2013

• Anderson, I. et al. (2013) Genome sequence of Frateuria aurantia type strain (Kondo 67(T)), a xanthomonade isolated from Lilium auratium Lindl. Stand Genomic Sci 9(1), 83-92. 10.4056/sigs.4338002
• Aylward, F. O. et al. (2013) Complete Genome of Serratia sp. Strain FGI 94, a Strain Associated with Leaf-Cutter Ant Fungus Gardens. Genome Announc 1(2), e0023912. 10.1128/genomeA.00239-12
• Buddruhs, N. et al. (2013) Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the Roseobacter clade. Stand Genomic Sci 9(1), 128-41. 10.4056/sigs.4297965
• Clingenpeel, S. et al. (2013) Yellowstone lake nanoarchaeota. Front Microbiol 4, 274. 10.3389/fmicb.2013.00274
• Davis, J. R. et al. (2013) Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete. Genome Announc 1(4). 10.1128/genomeA.00416-13
• Deole, R. et al. (2013) An extremely halophilic proteobacterium combines a highly acidic proteome with a low cytoplasmic potassium content. J Biol Chem 288(1), 581-8. 10.1074/jbc.M112.420505
• Dogs, M. et al. (2013) Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 9(1), 142-159. 10.4056/sigs.4287962
• Dogs, M. et al. (2013) Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Stand Genomic Sci 9(2), 334-350. 10.4056/sigs.4448212
• Elkins, J. G. et al. (2013) Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T. Genome Announc 1(2), e0016213. 10.1128/genomeA.00162-13
• Galardini, M. et al. (2013) Permanent draft genome sequences of the symbiotic nitrogen fixing Ensifer meliloti strains BO21CC and AK58. Stand Genomic Sci 9(2), 325-33. 10.4056/sigs.3797438
• Garcia, S. L. et al. (2013) Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. Isme Journal 7(1), 137-147. DOI 10.1038/ismej.2012.86
• Han, J. I. et al. (2013) Genome of the Root-Associated Plant Growth-Promoting Bacterium Variovorax paradoxus Strain EPS. Genome Announc 1(5). 10.1128/genomeA.00843-13
• Hirsch, A. M. et al. (2013) Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina equisetifolia Root Nodules. Genome Announc 1(5). 10.1128/genomeA.00759-13
• Kamke, J. et al. (2013) Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J 7(12), 2287-300. 10.1038/ismej.2013.111
• Kazakov, A. E. et al. (2013) New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol 195(19), 4466-75. 10.1128/JB.00679-13
• Khanna, N. et al. (2013) Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production. Stand Genomic Sci 9(2), 359-69. 10.4056/sigs.4348035
• Kruse, Thomas et al. (2013) Complete genome sequence of Dehalobacter restrictus PER-K23 T. Stand Genomic Sci 8(3). 10.4056/sigs.3787426
• Liolos, K. et al. (2013) Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Stand Genomic Sci 8(2), 165-76. 10.4056/sigs.3607108
• Mavromatis, K. et al. (2013) Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Stand Genomic Sci 8(1), 47-57. 10.4056/sigs.3547050
• Mavromatis, K. et al. (2013) Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Stand Genomic Sci 8(1), 26-36. 10.4056/sigs.3527032
• Meier-Kolthoff, J. P. et al. (2013) Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)). Stand Genomic Sci 9(1), 28-41. 10.4056/sigs.4207886
• Mishra, A. K. et al. (2013) Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. Stand Genomic Sci 9(1), 205-19. 10.4056/sigs.4378121
• Nakatsu, C. H. et al. (2013) Complete genome sequence of Arthrobacter sp. strain FB24. Stand Genomic Sci 9(1), 106-16. 10.4056/sigs.4438185
• Neupane, S. et al. (2013) Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4. Stand Genomic Sci 8(3), 441-9. 10.4056/sigs.4027757
• Nouioui, I. et al. (2013) Draft Genome Sequence of Frankia sp. Strain BMG5.12, a Nitrogen-Fixing Actinobacterium Isolated from Tunisian Soils. Genome Announc 1(4). 10.1128/genomeA.00468-13
• Nurk, S. et al. (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20(10), 714-37. 10.1089/cmb.2013.0084
• Palaniappan, K. et al. (2013) Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio. Stand Genomic Sci 9(1), 57-70. 10.4056/sigs.4237901
• Pena-Montenegro, T. D. et al. (2013) Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31. Stand Genomic Sci 9(1), 42-56. 10.4056/sigs.4227894
• Rajeev, L. et al. (2013) Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J . 10.1038/ismej.2013.83
• Rawat, S. R. et al. (2013) Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil. Stand Genomic Sci 9(1), 71-82. 10.4056/sigs.4328031
• Rawat, S. R. et al. (2013) Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil. Stand Genomic Sci 9(1), 71-82. 10.4056/sigs.4328031
• Reeve, W. et al. (2013) Genome sequence of the Lebeckia ambigua-nodulating “Burkholderia sprentiae” strain WSM5005. Standards in Genomic Sciences 9(2), 385-394. 10.4056/Sigs.4558268
• Reeve, W. et al. (2013) Genome sequence of the Ornithopus/Lupinus-nodulating Bradyrhizobium sp. strain WSM471. Stand Genomic Sci 9(2), 254-63. 10.4056/sigs.4498256
• Reeve, W. et al. (2013) Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI943. Stand Genomic Sci 9(2), 232-42. 10.4056/sigs.4478252
• Reeve, W. et al. (2013) Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain SRDI565. Stand Genomic Sci 9(2), 220-31. 10.4056/sigs.4468250
• Reeve, W. et al. (2013) Genome sequence of the Trifolium rueppellianum -nodulating Rhizobium leguminosarum bv. trifolii strain WSM2012. Stand Genomic Sci 9(2), 283-93. 10.4056/sigs.4528262
• Reeve, W. et al. (2013) Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.). Stand Genomic Sci 9(2), 294-303. 10.4056/sigs.4538264
• Reeve, W. et al. (2013) Complete genome sequence of Mesorhizobium australicum type strain (WSM2073(T)). Stand Genomic Sci 9(2), 410-9. 10.4056/sigs.4568282
• Reeve, W. et al. (2013) Genome sequence of the South American clover-nodulating Rhizobium leguminosarum bv. trifolii strain WSM597. Stand Genomic Sci 9(2), 264-72. 10.4056/sigs.4508258
• Reeve, W. et al. (2013) Genome sequence of the lupin-nodulating Bradyrhizobium sp. strain WSM1417. Stand Genomic Sci 9(2), 273-82. 10.4056/sigs.4518260
• Reeve, W. et al. (2013) Genome sequence of the clover-nodulating Rhizobium leguminosarum bv. trifolii strain TA1. Stand Genomic Sci 9(2), 243-253. 10.4056/sigs.4488254
• Riedel, T. et al. (2013) Genome sequence of the Leisingera aquimarina type strain (DSM 24565(T)), a member of the marine Roseobacter clade rich in extrachromosomal elements. Stand Genomic Sci 8(3), 389-402. 10.4056/sigs.3858183
• Riedel, T. et al. (2013) Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member of the Roseobacter clade isolated from sea sand. Stand Genomic Sci 9(1), 117-127. 10.4056/sigs.4258318
• Rinke, C. et al. (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459), 431-7. 10.1038/nature12352
• Smith, H. et al. (2013) Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium. Genome Announc 1(6). 10.1128/genomeA.00960-13
• Stackebrandt, E. et al. (2013) Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Stand Genomic Sci 8(1), 15-25. 10.4056/sigs.3507020
• Swan, B. K. et al. (2013) Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc Natl Acad Sci U S A 110(28), 11463-8. 10.1073/pnas.1304246110
• Tak, N. et al. (2013) Genome sequence of Ensifer sp TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert. Standards in Genomic Sciences 9(2), 304-314. 10.4056/Sigs.4598281
• Terpolilli, J. et al. (2013) Genome sequence of Ensifer medicae strain WSM1369; an effective microsymbiont of the annual legume Medicago sphaerocarpos. Stand Genomic Sci 9(2), 420-430. 10.4056/sigs.4838624
• Terpolilli, J. et al. (2013) Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17. Standards in Genomic Sciences 9(2), 315-324. 10.4056/Sigs.4608286
• van de Vossenberg, J. et al. (2013) The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol 15(5), 1275-89. 10.1111/j.1462-2920.2012.02774.x
• Vesth, T. et al. (2013) Veillonella, Firmicutes: Microbes disguised as Gram negatives. Stand Genomic Sci 9(2), 431-48. 10.4056/sigs.2981345
• Wall, L. G. et al. (2013) Draft Genome Sequence of Frankia sp. Strain BCU110501, a Nitrogen-Fixing Actinobacterium Isolated from Nodules of Discaria trinevis. Genome Announc 1(4). 10.1128/genomeA.00503-13
• Wu, D. et al. (2013) Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One 8(10), e77033. 10.1371/journal.pone.0077033
• Zaremba-Niedzwiedzka, K. et al. (2013) Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biol 14(11), R130. 10.1186/gb-2013-14-11-r130
• Zarzycki, J. et al. (2013) The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases. BMC Struct Biol 13, 28. 10.1186/1472-6807-13-28

2012

• Abt, B. et al. (2012) Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci 6(2), 194-209. 10.4056/sigs.2796069
• Anderson, I. et al. (2012) Genomics of aerobic cellulose utilization systems in actinobacteria. PLoS One 7(6), e39331. 10.1371/journal.pone.0039331
• Anderson, I. et al. (2012) Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand Genomic Sci 6(3), 1-13. 10.4056/sigs.2736042
• Anderson, I. et al. (2012) Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). Stand Genomic Sci 6(2), 174-84. 10.4056/sigs.2746047
• Anderson, I. et al. (2012) Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Stand Genomic Sci 6(2), 155-64. 10.4056/sigs.2665915
• Anderson, I. et al. (2012) Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)). Stand Genomic Sci 6(1), 31-42. 10.4056/sigs.2505605
• Anderson, I. et al. (2012) Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Stand Genomic Sci 7(2), 210-20. 10.4056/sigs.3117229
• Beckloff, N. et al. (2012) Bacterial genome annotation. Methods Mol Biol 881, 471-503. 10.1007/978-1-61779-827-6_16
• Challacombe, J. et al. (2012) Mobile genetic elements in the bacterial phylum Acidobacteria. Mob Genet Elements 2(4), 179-183. 10.4161/mge.21943
• Chow, V. et al. (2012) Complete genome sequence of Paenibacillus sp. strain JDR-2. Stand Genomic Sci 6(1), 1-10. 10.4056/sigs.2374349
• Copeland, A. et al. (2012) Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Sciences 6(1), 21-30. Doi 10.4056/Sigs.2435521
• Copeland, A. et al. (2012) Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). Stand Genomic Sci 6(2), 240-50. 10.4056/sigs.2756060
• Copeland, A. et al. (2012) Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Stand Genomic Sci 6(2), 145-54. 10.4056/sigs.2475579
• Davis, J. R. et al. (2012) Genome sequence of Amycolatopsis sp. strain ATCC 39116, a plant biomass-degrading actinomycete. J Bacteriol 194(9), 2396-7. 10.1128/JB.00186-12
• Desiniotis, A. et al. (2012) Complete genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis centrotype ATCC 29191. J Bacteriol 194(21), 5966-7. 10.1128/JB.01398-12
• Dichosa, A. E. et al. (2012) Artificial polyploidy improves bacterial single cell genome recovery. PLoS One 7(5), e37387. 10.1371/journal.pone.0037387
• Eichorst, S. A. et al. (2012) Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing. Applied and Environmental Microbiology 78(7), 2316-2327. Doi 10.1128/Aem.07313-11
• Fodor, A. A. et al. (2012) The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing. Plos One 7(7). ARTN e41294 DOI 10.1371/journal.pone.0041294
• Goker, M. et al. (2012) Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Stand Genomic Sci 6(2), 230-9. 10.4056/sigs.2726028
• Han, C. et al. (2012) Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Stand Genomic Sci 6(1), 94-103. 10.4056/sigs.2456004
• Huntemann, M. et al. (2012) Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Stand Genomic Sci 6(2), 185-93. 10.4056/sigs.2786069
• Isanapong, J. et al. (2012) High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. J Bacteriol 194(10), 2744-5. 10.1128/JB.00264-12
• Izquierdo, J. A. et al. (2012) Complete Genome Sequence of Clostridium clariflavum DSM 19732. Stand Genomic Sci 6(1), 104-15. 10.4056/sigs.2535732
• Jiang, K. et al. (2012) Complete genome sequence of Thauera aminoaromatica strain MZ1T. Stand Genomic Sci 6(3), 325-35. 10.4056/sigs.2696029
• Kamke, J. et al. (2012) Exploring symbioses by single-cell genomics. Biol Bull 223(1), 30-43.
• Kappler, U. et al. (2012) Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)). Stand Genomic Sci 7(1), 44-58. 10.4056/sigs.3006378
• Khudyakov, J. I. et al. (2012) Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proc Natl Acad Sci U S A 109(32), E2173-82. 10.1073/pnas.1112750109
• Kimelman, A. et al. (2012) A vast collection of microbial genes that are toxic to bacteria. Genome Research 22(4), 802-809. DOI 10.1101/gr.133850.111
• Kinney, J. N. et al. (2012) Elucidating essential role of conserved carboxysomal protein CcmN reveals common feature of bacterial microcompartment assembly. J Biol Chem 287(21), 17729-36. 10.1074/jbc.M112.355305
• Klenk, H. P. et al. (2012) Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)). Stand Genomic Sci 6(2), 220-9. 10.4056/sigs.2635833
• Klenk, H. P. et al. (2012) Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T)). Stand Genomic Sci 6(2), 265-75. 10.4056/sigs.2655905
• Kostka, J. E. et al. (2012) Genome sequences for six Rhodanobacter strains, isolated from soils and the terrestrial subsurface, with variable denitrification capabilities. J Bacteriol 194(16), 4461-2. 10.1128/JB.00871-12
• Liolios, K. et al. (2012) The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Stand Genomic Sci 6(3), 438-47. 10.4056/sigs.2675953
• Lucas-Elio, P. et al. (2012) Complete genome sequence of Marinomonas posidonica type strain (IVIA-Po-181(T)). Stand Genomic Sci 7(1), 31-43. 10.4056/sigs.2976373
• Lucas-Elio, P. et al. (2012) Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1(T)). Stand Genomic Sci 6(1), 63-73. 10.4056/sigs.2545743
• Lucas, S. et al. (2012) Complete genome sequence of the thermophilic, piezophilic, heterotrophic bacterium Marinitoga piezophila KA3. J Bacteriol 194(21), 5974-5. 10.1128/JB.01430-12
• Markowitz, V. M. et al. (2012) IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res 40(Database issue), D115-22. 10.1093/nar/gkr1044
• Martinez-Garcia, M. et al. (2012) Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS One 7(4), e35314. 10.1371/journal.pone.0035314
• Martinez, R. J. et al. (2012) Complete genome sequence of Rahnella sp. strain Y9602, a gammaproteobacterium isolate from metal- and radionuclide-contaminated soil. J Bacteriol 194(8), 2113-4. 10.1128/JB.00095-12
• Martinez, R. J. et al. (2012) Complete genome sequence of Rahnella aquatilis CIP 78.65. J Bacteriol 194(11), 3020-1. 10.1128/JB.00380-12
• Marx, C. J. et al. (2012) Complete genome sequences of six strains of the genus Methylobacterium. J Bacteriol 194(17), 4746-8. 10.1128/JB.01009-12
• Mason, O. U. et al. (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J 6(9), 1715-27. 10.1038/ismej.2012.59
• Mavromatis, K. et al. (2012) Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1). Stand Genomic Sci 6(2), 210-9. 10.4056/sigs.2816096
• Mead, D. A. et al. (2012) Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park. Stand Genomic Sci 6(3), 381-400. 10.4056/sigs.2605792
• Meincke, L. et al. (2012) Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)). Stand Genomic Sci 6(1), 74-83. 10.4056/sigs.2395367
• Monier, A. et al. (2012) Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges. Environmental Microbiology 14(1), 162-176. DOI 10.1111/j.1462-2920.2011.02576.x
• Neupane, S. et al. (2012) Complete genome sequence of Serratia plymuthica strain AS12. Stand Genomic Sci 6(2), 165-73. 10.4056/sigs.2705996
• Neupane, S. et al. (2012) Complete genome sequence of the plant-associated Serratia plymuthica strain AS13. Stand Genomic Sci 7(1), 22-30. 10.4056/sigs.2966299
• Neupane, S. et al. (2012) Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9. Stand Genomic Sci 6(1), 54-62. 10.4056/sigs.2595762
• Pagani, I. et al. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 40(D1), D571-D579. Doi 10.1093/Nar/Gkr1100
• Park, J. I. et al. (2012) A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One 7(5), e37010. 10.1371/journal.pone.0037010
• Pester, M. et al. (2012) Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. J Bacteriol 194(22), 6300-1. 10.1128/JB.01392-12
• Queiroux, C. et al. (2012) A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules. Bmc Microbiology 12. Artn 74 Doi 10.1186/1471-2180-12-74
• Rawat, S. R. et al. (2012) Complete genome sequence of Terriglobus saanensis type strain SP1PR4(T), an Acidobacteria from tundra soil. Standards in Genomic Sciences 7(1), 59-69. Doi 10.4056/Sigs.3036810
• Riedel, T. et al. (2012) Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Stand Genomic Sci 7(1), 107-19. 10.4056/sigs.3216895
• Riedel, T. et al. (2012) Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Stand Genomic Sci 7(1), 120-30. 10.4056/sigs.3296896
• Roberts, E. W. et al. (2012) Isolation and Characterization of the Prochlorococcus Carboxysome Reveal the Presence of the Novel Shell Protein CsoS1D. Journal of Bacteriology 194(4), 787-795. Doi 10.1128/Jb.06444-11
• Sessitsch, A. et al. (2012) Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis. Molecular Plant-Microbe Interactions 25(1), 28-36. Doi 10.1094/Mpmi-08-11-0204
• Siddaramappa, S. et al. (2012) A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics 13, 165. 10.1186/1471-2164-13-165
• Siddaramappa, S. et al. (2012) Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to “Dehalococcoides” strains. Stand Genomic Sci 6(2), 251-64. 10.4056/sigs.2806097
• Spring, S. et al. (2012) Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)). Stand Genomic Sci 7(2), 304-19. 10.4056/sigs.3226659
• Susanti, D. et al. (2012) Complete genome sequence of Desulfurococcus fermentans, a hyperthermophilic cellulolytic crenarchaeon isolated from a freshwater hot spring in Kamchatka, Russia. J Bacteriol 194(20), 5703-4. 10.1128/JB.01314-12
• Vandera, E. et al. (2012) Heterologous expression and characterization of two 1-hydroxy-2-naphthoic acid dioxygenases from Arthrobacter phenanthrenivorans. Appl Environ Microbiol 78(3), 621-7. 10.1128/AEM.07137-11
• Wilson, A. et al. (2012) The essential role of the N-terminal domain of the orange carotenoid protein in cyanobacterial photoprotection: importance of a positive charge for phycobilisome binding. Plant Cell 24(5), 1972-83. 10.1105/tpc.112.096909
• Zeytun, A. et al. (2012) Complete genome sequence of Francisella philomiragia ATCC 25017. J Bacteriol 194(12), 3266. 10.1128/JB.00413-12
• Zhaxybayeva, O. et al. (2012) Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date. Genome Biol Evol 4(8), 700-8. 10.1093/gbe/evs059

2011

• Abt, B. et al. (2011) Complete genome sequence of Cellulophaga algicola type strain (IC166). Stand Genomic Sci 4(1), 72-80. 10.4056/sigs.1543845
• Abt, B. et al. (2011) Complete genome sequence of Leadbetterella byssophila type strain (4M15). Stand Genomic Sci 4(1), 2-12. 10.4056/sigs.1413518
• Anderson, I. et al. (2011) Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A). Stand Genomic Sci 4(3), 381-92. 10.4056/sigs.2014648
• Anderson, I. et al. (2011) Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes. Plos One 6(5). ARTN e20237 DOI 10.1371/journal.pone.0020237
• Anderson, I. et al. (2011) Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1). Stand Genomic Sci 4(3), 322-30. 10.4056/sigs.1844518
• Blumer-Schuette, S. E. et al. (2011) Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensensis, and Caldicellulosiruptor lactoaceticus. Journal of Bacteriology 193(6), 1483-1484. Doi 10.1128/Jb.01515-10
• Brown, S. D. et al. (2011) Complete Genome Sequence of the Haloalkaliphilic, Hydrogen-Producing Bacterium Halanaerobium hydrogeniformans. Journal of Bacteriology 193(14), 3682-3683. Doi 10.1128/Jb.05209-11
• Brown, S. D. et al. (2011) Genome sequence of the mercury-methylating strain Desulfovibrio desulfuricans ND132. J Bacteriol 193(8), 2078-9. 10.1128/JB.00170-11
• Campbell, M. A. et al. (2011) Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world’s oceans: calls to validate the names ‘Nitrosococcus halophilus’ and ‘Nitrosomonas mobilis’. Fems Microbiology Ecology 76(1), 39-48. DOI 10.1111/j.1574-6941.2010.01027.x
• Chain, P. S. G. et al. (2011) Genome of Ochrobactrum anthropi ATCC 49188(T), a Versatile Opportunistic Pathogen and Symbiont of Several Eukaryotic Hosts. Journal of Bacteriology 193(16), 4274-4275. Doi 10.1128/Jb.05335-11
• Challacombe, J. F. et al. (2011) Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076. PLoS One 6(9), e24882. 10.1371/journal.pone.0024882
• Chang, Y. J. et al. (2011) Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci 5(1), 97-111. 10.4056/sigs.2114901
• Chertkov, O. et al. (2011) Complete genome sequence of Thermomonospora curvata type strain (B9). Stand Genomic Sci 4(1), 13-22. 10.4056/sigs.1453580
• Coleman, N. V. et al. (2011) Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp Strain JS614. Journal of Bacteriology 193(13), 3399-3400. Doi 10.1128/Jb.05109-11
• Daligault, H. et al. (2011) Complete genome sequence of Haliscomenobacter hydrossis type strain (O-T). Standards in Genomic Sciences 4(3), 352-360. Doi 10.4056/Sigs.1964579
• Dover, N. et al. (2011) Novel Structural Elements within the Nonproteolytic Clostridium botulinum Type F Toxin Gene Cluster. Applied and Environmental Microbiology 77(5), 1904-1906. Doi 10.1128/Aem.02422-10
• Duhaime, M. B. et al. (2011) Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard. Stand Genomic Sci 4(2), 271-85. 10.4056/sigs.621069
• Feinberg, L. et al. (2011) Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. J Bacteriol 193(11), 2906-7. 10.1128/JB.00322-11
• Field, D. et al. (2011) The Genomic Standards Consortium. PLoS Biol 9(6), e1001088. 10.1371/journal.pbio.1001088
• Frese, S. A. et al. (2011) The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri. Plos Genetics 7(2). ARTN e1001314 DOI 10.1371/journal.pgen.1001314
• Galardini, M. et al. (2011) Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti. Bmc Genomics 12. Artn 235 Doi 10.1186/1471-2164-12-235
• Gerasimova, A. et al. (2011) Comparative Genomics of the Dormancy Regulons in Mycobacteria. Journal of Bacteriology 193(14), 3446-3452. Doi 10.1128/Jb.00179-11
• Gibbons, H. S. et al. (2011) Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant. PLoS One 6(3), e17836. 10.1371/journal.pone.0017836
• Goker, M. et al. (2011) Complete genome sequence of Isosphaera pallida type strain (IS1B(T)). Standards in Genomic Sciences 4(1), 63-71. Doi 10.4056/Sigs.1533840
• Goker, M. et al. (2011) Complete genome sequence of Odoribacter splanchnicus type strain (1651/6(T)). Standards in Genomic Sciences 4(2), 200-209. Doi 10.4056/Sigs.1714269
• Goker, M. et al. (2011) Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2(T)). Standards in Genomic Sciences 4(3), 393-401. Doi 10.4056/Sigs.2064705
• Gronow, S. et al. (2011) Complete genome sequence of Bacteroides salanitronis type strain (BL78). Stand Genomic Sci 4(2), 191-9. 10.4056/sigs.1704212
• Gronow, S. et al. (2011) Complete genome sequence of Paludibacter propionicigenes type strain (WB4). Stand Genomic Sci 4(1), 36-44. 10.4056/sigs.1503846
• Grubbs, K. J. et al. (2011) Genome sequence of Streptomyces griseus strain XylebKG-1, an ambrosia beetle-associated actinomycete. J Bacteriol 193(11), 2890-1. 10.1128/JB.00330-11
• Han, C. et al. (2011) Complete genome sequence of Treponema succinifaciens type strain (6091). Stand Genomic Sci 4(3), 361-70. 10.4056/sigs.1984594
• Han, C. et al. (2011) Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR). Stand Genomic Sci 4(3), 371-80. 10.4056/sigs.2004684
• Hauser, L. J. et al. (2011) Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20. J Bacteriol 193(16), 4268-9. 10.1128/JB.05400-11
• Huntemann, M. et al. (2011) Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). Stand Genomic Sci 4(3), 303-11. 10.4056/sigs.1814460
• Ivanova, N. et al. (2011) Complete genome sequence of Truepera radiovictrix type strain (RQ-24). Stand Genomic Sci 4(1), 91-9. 10.4056/sigs.1563919
• Ivanova, N. et al. (2011) Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL). Stand Genomic Sci 4(3), 312-21. 10.4056/sigs.1824509
• Kalamorz, F. et al. (2011) Draft genome sequence of the thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1. J Bacteriol 193(16), 4290-1. 10.1128/JB.05035-11
• Kallimanis, A. et al. (2011) Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3). Stand Genomic Sci 4(2), 123-30. 10.4056/sigs.1393494
• Kant, R. et al. (2011) Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium. J Bacteriol 193(11), 2902-3. 10.1128/JB.00295-11
• Kant, R. et al. (2011) Genome sequence of “Pedosphaera parvula” Ellin514, an aerobic Verrucomicrobial isolate from pasture soil. J Bacteriol 193(11), 2900-1. 10.1128/JB.00299-11
• Kerfeld, C. A. et al. (2011) Using BLAST to Teach “E-value-tionary” Concepts. Plos Biology 9(2). ARTN e1001014 DOI 10.1371/journal.pbio.1001014
• Kinney, J. N. et al. (2011) Comparative analysis of carboxysome shell proteins. Photosynth Res 109(1-3), 21-32. 10.1007/s11120-011-9624-6
• Klenk, H. P. et al. (2011) Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2(T)) and reclassification in the new genus, Kyrpidia gen. nov as Kyrpidia tusciae comb. nov and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Standards in Genomic Sciences 5(1), 121-134. Doi 10.4056/Sigs.2144922
• Klippel, B. et al. (2011) Complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, polysaccharide-degrading members of the family Flavobacteriaceae. J Bacteriol 193(17), 4545-6. 10.1128/JB.05518-11
• Klippel, B. et al. (2011) Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5. J Bacteriol 193(17), 4547-8. 10.1128/JB.05468-11
• Kouvelis, V. N. et al. (2011) Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192. J Bacteriol 193(18), 5049-50. 10.1128/JB.05273-11
• Lang, E. et al. (2011) Complete genome sequence of Weeksella virosa type strain (9751). Stand Genomic Sci 4(1), 81-90. 10.4056/sigs.1603927
• Lapidus, A. et al. (2011) Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae. J Bacteriol 193(15), 3757-64. 10.1128/JB.00404-11
• Liu, S. et al. (2011) Complete genome sequence of Lactobacillus buchneri NRRL B-30929, a novel strain from a commercial ethanol plant. J Bacteriol 193(15), 4019-20. 10.1128/JB.05180-11
• Mavromatis, K. et al. (2011) Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). Stand Genomic Sci 4(2), 144-53. 10.4056/sigs.1553862
• Miller, D. A. et al. (2011) Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum. Journal of Bacteriology 193(9), 2357-2358. Doi 10.1128/Jb.00239-11
• Morrison, N. et al. (2011) Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets. Standards in Genomic Sciences 4(2), 286-292. Doi 10.4056/Sigs.1344279
• Munk, A. C. et al. (2011) Complete genome sequence of Rhodospirillum rubrum type strain (S1(T)). Standards in Genomic Sciences 4(3), 293-302. Doi 10.4056/Sigs.1804360
• Munk, A. C. et al. (2011) Complete genome sequence of Tsukamurella paurometabola type strain (no. 33(T)). Standards in Genomic Sciences 4(3), 342-351. Doi 10.4056/Sigs.1894556
• Muyzer, G. et al. (2011) Complete genome sequence of “Thioalkalivibrio sulfidophilus” HL-EbGr7. Stand Genomic Sci 4(1), 23-35. 10.4056/sigs.1483693
• Nawabi, P. et al. (2011) Engineering Escherichia coli for biodiesel production utilizing a bacterial fatty acid methyltransferase. Appl Environ Microbiol 77(22), 8052-61. 10.1128/AEM.05046-11
• Oosterkamp, M. J. et al. (2011) Genome sequences of Alicycliphilus denitrificans strains BC and K601T. J Bacteriol 193(18), 5028-9. 10.1128/JB.00365-11
• Pagani, I. et al. (2011) Complete genome sequence of Marivirga tractuosa type strain (H-43). Stand Genomic Sci 4(2), 154-62. 10.4056/sigs.1623941
• Pagani, I. et al. (2011) Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). Stand Genomic Sci 4(1), 100-10. 10.4056/sigs.1613929
• Pappas, K. M. et al. (2011) Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. J Bacteriol 193(18), 5051-2. 10.1128/JB.05395-11
• Pati, A. et al. (2011) Complete genome sequence of Cellulophaga lytica type strain (LIM-21). Stand Genomic Sci 4(2), 221-32. 10.4056/sigs.1774329
• Pati, A. et al. (2011) Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). Stand Genomic Sci 4(1), 45-53. 10.4056/sigs.1513795
• Pati, A. et al. (2011) Complete genome sequence of Oceanithermus profundus type strain (506). Stand Genomic Sci 4(2), 210-20. 10.4056/sigs.1734292
• Pitluck, S. et al. (2011) Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). Stand Genomic Sci 4(1), 54-62. 10.4056/sigs.1523807
• Pukall, R. et al. (2011) Complete genome sequence of Deinococcus maricopensis type strain (LB-34). Stand Genomic Sci 4(2), 163-72. 10.4056/sigs.1633949
• Rodionov, D. A. et al. (2011) Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics 12 Suppl 1, S3. 10.1186/1471-2164-12-S1-S3
• Sales, C. M. et al. (2011) Genome sequence of the 1,4-dioxane-degrading Pseudonocardia dioxanivorans strain CB1190. J Bacteriol 193(17), 4549-50. 10.1128/JB.00415-11
• Siddaramappa, S. et al. (2011) Common Ancestry and Novel Genetic Traits of Francisella novicida-Like Isolates from North America and Australia as Revealed by Comparative Genomic Analyses. Applied and Environmental Microbiology 77(15), 5110-5122. Doi 10.1128/Aem.00337-11
• Sikorski, J. et al. (2011) Complete genome sequence of Mahella australiensis type strain (50-1 BON). Stand Genomic Sci 4(3), 331-41. 10.4056/sigs.1864526
• Singer, E. et al. (2011) Genomic potential of Marinobacter aquaeolei, a biogeochemical “opportunitroph”. Appl Environ Microbiol 77(8), 2763-71. 10.1128/AEM.01866-10
• Starkenburg, S. R. et al. (2011) Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide. J Bacteriol 193(17), 4569-70. 10.1128/JB.05138-11
• Stein, L. Y. et al. (2011) Genome sequence of the methanotrophic alphaproteobacterium Methylocystis sp. strain Rockwell (ATCC 49242). J Bacteriol 193(10), 2668-9. 10.1128/JB.00278-11
• Suen, G. et al. (2011) The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS One 6(4), e18814. 10.1371/journal.pone.0018814
• Suen, G. et al. (2011) Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7. Journal of Bacteriology 193(19), 5574-5575. Doi 10.1128/Jb.05621-11
• Suwa, Y. et al. (2011) Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia. J Bacteriol 193(18), 5047-8. 10.1128/JB.05521-11
• Svenning, M. M. et al. (2011) Genome sequence of the Arctic methanotroph Methylobacter tundripaludum SV96. J Bacteriol 193(22), 6418-9. 10.1128/JB.05380-11
• Swithers, K. S. et al. (2011) Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North Sea. J Bacteriol 193(19), 5566-7. 10.1128/JB.05828-11
• Tang, K. H. et al. (2011) Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. BMC Genomics 12, 334. 10.1186/1471-2164-12-334
• van Passel, M. W. et al. (2011) Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems. J Bacteriol 193(9), 2367-8. 10.1128/JB.00228-11
• van Passel, M. W. et al. (2011) Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastrointestinal tract. J Bacteriol 193(9), 2373-4. 10.1128/JB.00271-11
• van Passel, M. W. J. et al. (2011) The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes. Plos One 6(3). ARTN e16876 DOI 10.1371/journal.pone.0016876
• Vishnivetskaya, T. A. et al. (2011) Complete genome sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b. J Bacteriol 193(11), 2880-1. 10.1128/JB.00303-11
• Weilharter, A. et al. (2011) Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. J Bacteriol 193(13), 3383-4. 10.1128/JB.05055-11
• Wirth, R. et al. (2011) Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Stand Genomic Sci 4(2), 173-82. 10.4056/sigs.1644004
• Woyke, T. et al. (2011) Decontamination of MDA Reagents for Single Cell Whole Genome Amplification. Plos One 6(10). ARTN e26161 DOI 10.1371/journal.pone.0026161
• Zeytun, A. et al. (2011) Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). Stand Genomic Sci 4(2), 131-43. 10.4056/sigs.1463589
• Zhang, T. et al. (2011) Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Green Chemistry 13(8), 2083-2090. Doi 10.1039/C1gc15193b
• Zhao, B. et al. (2011) Complete genome sequence of the anaerobic, halophilic alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF. J Bacteriol 193(15), 4023-4. 10.1128/JB.05157-11

2010

• Ayala-del-Rio, H. L. et al. (2010) The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl Environ Microbiol 76(7), 2304-12. 10.1128/AEM.02101-09
• Copeland, A. et al. (2010) Complete genome sequence of Atopobium parvulum type strain (IPP 1246(T)) (vol 1, pg 166, 2009). Standards in Genomic Sciences 2(3), 361-362. Doi 10.4056/Sigs.992408
• Foster, B. et al. (2010) Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07). Stand Genomic Sci 2(1), 1-8. 10.4056/sigs.571102
• Glavina Del Rio, T. et al. (2010) Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). Stand Genomic Sci 2(1), 87-95. 10.4056/sigs.661199
• Grim, C. J. et al. (2010) Genome sequence of hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and comparative genomics with V. cholerae. J Bacteriol 192(13), 3524-33. 10.1128/JB.00040-10
• Gronow, S. et al. (2010) Complete genome sequence of Veillonella parvula type strain (Te3). Stand Genomic Sci 2(1), 57-65. 10.4056/sigs.521107
• Hirschman, L. et al. (2010) Meeting Report: “Metagenomics, Metadata and Meta-analysis” (M3) Workshop at the Pacific Symposium on Biocomputing 2010. Stand Genomic Sci 2(3), 357-60. 10.4056/sigs.802738
• Hyatt, D. et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119. 10.1186/1471-2105-11-119
• Ivanova, N. et al. (2010) Complete genome sequence of Haliangium ochraceum type strain (SMP-2). Stand Genomic Sci 2(1), 96-106. 10.4056/sigs.69.1277
• Ivanova, N. et al. (2010) Complete genome sequence of Gordonia bronchialis type strain (3410). Stand Genomic Sci 2(1), 19-28. 10.4056/sigs.611106
• Ivanova, N. et al. (2010) Complete genome sequence of Geodermatophilus obscurus type strain (G-20). Stand Genomic Sci 2(2), 158-67. 10.4056/sigs.711311
• Kiss, H. et al. (2010) Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1). Stand Genomic Sci 3(2), 153-62. 10.4056/sigs.1153107
• Liolios, K. et al. (2010) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research 38, D346-D354. Doi 10.1093/Nar/Gkp848
• Lykidis, A. et al. (2010) The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader. Plos One 5(3). Artn E9729 Doi 10.1371/Journal.Pone.0009729
• Markowitz, V. M. et al. (2010) The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Research 38, D382-D390. Doi 10.1093/Nar/Gkp887
• Mavromatis, K. et al. (2010) Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA(T)). Standards in Genomic Sciences 2(1), 9-18. Doi 10.4056/Sigs.591104
• Nalbantoglu, U. et al. (2010) Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp tularensis A1 and Schu S4. Plos One 5(2). Artn E9007 Doi 10.1371/Journal.Pone.0009007
• Nolan, M. et al. (2010) Complete genome sequence of Streptosporangium roseum type strain (NI 9100). Stand Genomic Sci 2(1), 29-37. 10.4056/sigs.631049
• Pati, A. et al. (2010) Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci 2(1), 49-56. 10.4056/sigs.601105
• Reeve, W. et al. (2010) Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genomic Sci 2(1), 77-86. 10.4056/sigs.43526
• Reeve, W. et al. (2010) Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers. Stand Genomic Sci 2(3), 347-56. 10.4056/sigs.852027
• Saunders, E. et al. (2010) Complete genome sequence of Haloterrigena turkmenica type strain (4k). Stand Genomic Sci 2(1), 107-16. 10.4056/sigs.681272
• Spring, S. et al. (2010) Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)). Stand Genomic Sci 2(1), 38-48. 10.4056/sigs.581048
• Spring, S. et al. (2010) Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Stand Genomic Sci 2(3), 245-59. 10.4056/sigs.821804
• Wagner-Dobler, I. et al. (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker’s guide to life in the sea. Isme Journal 4(1), 61-77. DOI 10.1038/ismej.2009.94
• Young, M. et al. (2010) Genome Sequence of the Fleming Strain of Micrococcus luteus, a Simple Free-Living Actinobacterium. Journal of Bacteriology 192(3), 841-860. Doi 10.1128/Jb.01254-09

2009

• Aklujkar, M. et al. (2009) The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens. BMC Microbiol 9, 109. 10.1186/1471-2180-9-109
• Allen, M. A. et al. (2009) The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation. ISME J 3(9), 1012-35. 10.1038/ismej.2009.45
• Anderson, I. et al. (2009) Complete genome sequence of Halorhabdus utahensis type strain (AX-2). Stand Genomic Sci 1(3), 218-25. 10.4056/sigs.31864
• Anderson, I. et al. (2009) Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One 4(6), e5797. 10.1371/journal.pone.0005797
• Anderson, I. J. et al. (2009) Complete genome sequence of Methanocorpusculum labreanum type strain Z. Stand Genomic Sci 1(2), 197-203. 10.4056/sigs.35575
• Anderson, I. J. et al. (2009) Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1. Stand Genomic Sci 1(2), 189-96. 10.4056/sigs.32535
• Anderson, I. J. et al. (2009) Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1. Stand Genomic Sci 1(2), 183-8. 10.4056/sigs.30527
• Barabote, R. D. et al. (2009) Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Research 19(6), 1033-1043. DOI 10.1101/gr.084848.108
• Chain, P. S. et al. (2009) Genomics. Genome project standards in a new era of sequencing. Science 326(5950), 236-7. 10.1126/science.1180614
• Chovatia, M. et al. (2009) Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883(T)). Standards in Genomic Sciences 1(3), 254-261. Doi 10.4056/Sigs.40645
• Chun, J. et al. (2009) Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proceedings of the National Academy of Sciences of the United States of America 106(36), 15442-15447. DOI 10.1073/pnas.0907787106
• Clum, A. et al. (2009) Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Standards in Genomic Sciences 1(1), 38-45. Doi 10.4056/Sigs.1463
• Clum, A. et al. (2009) Complete genome sequence of Pirellula staleyi type strain (ATCC 27377(T)). Standards in Genomic Sciences 1(3), 308-316. Doi 10.4056/Sigs.51657
• Copeland, A. et al. (2009) Complete genome sequence of Catenulispora acidiphila type strain (ID 139908(T)). Standards in Genomic Sciences 1(2), 119-125. Doi 10.4056/Sigs.17259
• Copeland, A. et al. (2009) Complete genome sequence of Desulfomicrobium baculatum type strain (X). Stand Genomic Sci 1(1), 29-37. 10.4056/sigs.13134
• Foster, J. T. et al. (2009) Whole-genome-based phylogeny and divergence of the genus Brucella. J Bacteriol 191(8), 2864-70. 10.1128/JB.01581-08
• Han, C. et al. (2009) Complete genome sequence of Kangiella koreensis type strain (SW-125). Stand Genomic Sci 1(3), 226-33. 10.4056/sigs.36635
• Han, C. et al. (2009) Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci 1(1), 54-62. 10.4056/sigs.22138
• Herlemann, D. P. et al. (2009) Genomic analysis of “Elusimicrobium minutum,” the first cultivated representative of the phylum “Elusimicrobia” (formerly termite group 1). Appl Environ Microbiol 75(9), 2841-9. 10.1128/AEM.02698-08
• Hooper, S. D. et al. (2009) Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Nucleic Acids Research 37(7), 2096-2104. Doi 10.1093/Nar/Gkp075
• Hooper, S. D. et al. (2009) Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biology 10(4). Artn R45 Doi 10.1186/Gb-2009-10-4-R45
• Hugenholtz, P. et al. (2009) Focus: Synergistetes. Environ Microbiol 11(6), 1327-9. 10.1111/j.1462-2920.2009.01949.x
• Hugenholtz, P. et al. (2009) A changing of the guard. Environ Microbiol 11(3), 551-3. 10.1111/j.1462-2920.2009.01888.x
• Ivanova, N. et al. (2009) Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b(T)). Standards in Genomic Sciences 1(2), 126-132. Doi 10.4056/Sigs.1854
• Ivanova, N. et al. (2009) Complete genome sequence of Sanguibacter keddieii type strain (ST-74). Stand Genomic Sci 1(2), 110-8. 10.4056/sigs.16197
• Kataeva, I. A. et al. (2009) Genome Sequence of the Anaerobic, Thermophilic, and Cellulolytic Bacterium “Anaerocellum thermophilum” DSM 6725. Journal of Bacteriology 191(11), 3760-3761. Doi 10.1128/Jb.00256-09
• Kouvelis, V. N. et al. (2009) Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. J Bacteriol 191(22), 7140-1. 10.1128/JB.01084-09
• Kyrpides, N. C. et al. (2009) Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nat Biotechnol 27(7), 627-32. 10.1038/nbt.1552
• Labutti, K. et al. (2009) Complete genome sequence of Anaerococcus prevotii type strain (PC1). Stand Genomic Sci 1(2), 159-65. 10.4056/sigs.24194
• Land, M. et al. (2009) Complete genome sequence of Actinosynnema mirum type strain (101(T)). Standards in Genomic Sciences 1(1), 46-53. Doi 10.4056/Sigs.21137
• Land, M. et al. (2009) Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122). Stand Genomic Sci 1(1), 21-8. 10.4056/sigs.1162
• Lang, E. et al. (2009) Complete genome sequence of Dyadobacter fermentans type strain (NS114). Stand Genomic Sci 1(2), 133-40. 10.4056/sigs.19262
• Lapidus, A. et al. (2009) Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). Stand Genomic Sci 1(1), 3-11. 10.4056/sigs.492
• Lauro, F. M. et al. (2009) The genomic basis of trophic strategy in marine bacteria. Proceedings of the National Academy of Sciences of the United States of America 106(37), 15527-15533. DOI 10.1073/pnas.0903507106
• Malfatti, S. et al. (2009) Complete genome sequence of Halogeometricum borinquense type strain (PR3(T)). Standards in Genomic Sciences 1(2), 150-158. Doi 10.4056/23264
• Markowitz, V. M. et al. (2009) IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25(17), 2271-8. 10.1093/bioinformatics/btp393
• Mavromatis, K. et al. (2009) Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. PLoS One 4(11), e7979. 10.1371/journal.pone.0007979
• Mavromatis, K. et al. (2009) Genome Analysis of the Anaerobic Thermohalophilic Bacterium Halothermothrix orenii. Plos One 4(1). Artn E4192 Doi 10.1371/Journal.Pone.0004192
• Mavromatis, K. et al. (2009) The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Standards in Genomic Sciences 1(1), 63-67. Doi 10.4056/Sigs.632
• Mavrommatis, K. et al. (2009) Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845). Stand Genomic Sci 1(2), 101-9. 10.4056/sigs.15195
• Mavrommatis, K. et al. (2009) Complete genome sequence of Cryptobacterium curtum type strain (12-3). Stand Genomic Sci 1(2), 93-100. 10.4056/sigs.12260
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2008

• Anderson, I. et al. (2008) Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. Journal of Bacteriology 190(8), 2957-2965. Doi 10.1128/Jb.01949-07
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2007

• Markowitz, V. M. et al. (2007) Microbial genome data resources. Curr Opin Biotechnol 18(3), 267-72. 10.1016/j.copbio.2007.04.005
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• Yamada, T. et al. (2007) Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. Isme Journal 1(3), 246-255. Doi 10.1038/Ismej.2007.28

2006

• Markowitz, V. M. et al. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Research 34, D344-D348. Doi 10.1093/Nar/Gkj024