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Single Cells Group

Shedding light on the tree of life. Image credit: Zosia Rostomian, LBNL

Shedding light on the tree of life. Image credit: Zosia Rostomian, LBNL

Research in the Woyke laboratory focuses on the utility of single-cell methods to access genetic material of uncultivated taxa of interest.  One such effort is targeted at environmental cells that are from candidate phyla, major branches in the phylogenetic tree without cultivated representatives. The “Great Plate-Count Anomaly” first described by Stanley and Konopa in 1985, which highlights our skewed understanding of microbial metabolism towards a minority of cultivated bacteria, still persists to date. Phylogenetic diversity estimates show that the gap between cultivated and uncultivated Bacteria and Archaea has steadily been widening since 2005. This gap is also reflected in the strongly biased representation of sequenced genomes in the public domain, the bulk of which belong to only three phyla. The Woyke group uses single-cell sequencing as a means to begin filling this gap. A primary goal is to get insights into the coding potential of candidate phyla to decipher their possible roles in the environment, establish phylogenetic relationships and to provide valuable reference genomes in under-populated areas of the tree of life, as reference genomes are critical to serve as phylogenetic anchors for metagenomes studies.

While uncovering the metabolic potential of uncultivated lineages is of high value to establish models and hypotheses, experimental data is critical to further test such hypotheses. In particular during an era of ‘homology creep’, function prediction as purely based on annotation may not be sufficient. A more recent effort in the Woyke lab is therefore focused on the application of function-driven single-cell genomics. Here, single cells are characterized and selected as based on a specific functional trait or phenotype of interest, prior to and in conjunction with whole genome sequencing.

Research Team

Tanja Woyke, PI Robert Bowers,
Research Scientist		 Maria Dzunkova,
Postdoc		 Janey Lee,
Sr. Research Associate 
twoyke@lbl.gov
 rmbowers@lbl.gov mdzunkova@lbl.gov jlee2@lbl.gov
More about Tanja. Bob uses single-cell genomics and metagenomics to explore how microbes influence people and the environment. This includes studying the diversity, physiology and community ecology of microbes sampled from the natural environment. Maria identifies links between phages and their bacterial hosts by the “single-cell viral tagging” method Janey provides support for custom single-cell user projects and projects within the group.
Frederik Schulz
Frederik Schulz,
Research Scientist		 Esther Singer,
Research Scientist		 Tomas Tyml,
Postdoc		 Jean-Marie Volland Visiting Scientist
fschulz@lbl.gov esinger@lbl.gov ttyml@lbl.gov jvolland@lbl.gov
Frederik is a bioinformatician interested in microbial symbiosis, evolutionary microbiology and virology. He is exploring metagenomic and single-cell genomic data to find novel host-associated bacteria and viruses and applying state-of-the-art phylogenetic tools to place them in the tree of life. Esther studies plant microbiome interactions in field and lab combining omics tools, plant genetics and phenotyping, as well as soil geochemistry analyses. Tomas uses traditional cultivation methods along with microscopy and genomics for studying endosymbiotic associations within microbial eukaryotes. With his research, he hopes to broaden our understanding of the roles that these associations have played in the evolutionary history of life. Jean-Marie uses classic and cutting-edge imaging approaches in conjunction with sequencing technologies to investigate unusual life strategies and symbiotic interactions in uncultivated bacteria and small eukaryotes

Former Lab Members

Selected Publications

  1. Schulz F., Roux S., Paez-Espino D., Jungbluth S., Walsh D. A., Denef V. J., McMahon K. D., Konstantinidis K. T., Eloe-Fadrosh E. A., Kyrpides N. C., Woyke T. Giant virus diversity and host interactions through global metagenomics.” Nature 578(7795): 432-436 (2020).
  2. Seshadri R., Leahy S. C., Attwood G. T., Teh K. H., Lambie S. C., Cookson A. L., Eloe-Fadrosh E. A., Pavlopoulos G. A., Hadjithomas M., Varghese N. J., Paez-Espino D., Hungate project, collaborators Perry R., Henderson G., Creevey C. J., Terrapon N., Lapebie P., Drula E., Lombard V., Rubin E., Kyrpides N. C., Henrissat B., Woyke T., Ivanova N. N., Kelly W. J. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.” Nat Biotechnol 36(4): 359-367 (2018).
  3. Woyke T., Doud D. F. R., Schulz F. The trajectory of microbial single-cell sequencing. Nat Methods 14(11): 1045-1054 (2017).
  4. Schulz F., Yutin N., Ivanova N. N., Ortega D. R., Lee T. K., Vierheilig J., Daims H., Horn M., Wagner M., Jensen G. J., Kyrpides N. C., Koonin E. V., Woyke T. Giant viruses with an expanded complement of translation system components.” Science 356(6333): 82-85 (2017).
  5. Mukherjee S., Seshadri R., Varghese N. J., Eloe-Fadrosh E. A., Meier-Kolthoff J. P., Goker M., Coates R. C., Hadjithomas M., Pavlopoulos G. A., Paez-Espino D., Yoshikuni Y., Visel A., Whitman W. B., Garrity G. M., Eisen J. A., Hugenholtz P., Pati A., Ivanova N. N., Woyke T., Klenk H. P., Kyrpides N. C. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.” Nat Biotechnol 35(7): 676-683 (2017).
  6. Bowers R. M., Kyrpides N. C., Stepanauskas R., … Banfield J. F., Hugenholtz P., Woyke T. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 35(8): 725-731 (2017).
  7. Woyke T. & Rubin E.M. Evolution. Searching for new branches on the tree of life. Science. 346:698-9 (2014).
  8. Ivanova N.N., Schwientek P., Tripp H.J., Rinke C., Pati A., Huntemann M., Visel A., Woyke T., Kyrpides N.C. & Rubin E.M. Stop codon reassignments in the wild. Science 344, 909-13 (2014).
  9. Rinke C., Schwientek P., Sczyrba A., Ivanova N.N., Anderson I.J., Cheng J.F., Darling A., Malfatti S., Swan B.K., Gies E.A., Dodsworth J.A., Hedlund B.P., Tsiamis G., Sievert S.M., Liu W.T., Eisen J.A., Hallam S.J., Kyrpides N.C., Stepanauskas R., Rubin E.M., Hugenholtz P. & Woyke T. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-7 (2013).
  10. Hess M., Sczyrba A., Egan R., Kim T.W., Chokhawala H., Schroth G., Luo S., Clark D.S., Chen F., Zhang T., Mackie R.I., Pennacchio L.A., Tringe S.G., Visel A., Woyke T., Wang Z. & Rubin E.M. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463-7 (2011).
  11. Newton I.L., Woyke T., Auchtung T.A., Dilly G.F., Dutton R.J., Fisher M.C., Fontanez K.M., Lau E., Stewart F.J., Richardson P.M., Barry K.W., Saunders E., Detter J.C., Wu D., Eisen J.A. & Cavanaugh C.M. The Calyptogena magnifica chemoautotrophic symbiont genome. Science 315, 998-1000 (2007).
  12. Woyke T., Teeling H., Ivanova N.N., Huntemann M., Richter M., Gloeckner F.O., Boffelli D., Anderson I.J., Barry K.W., Shapiro H.J., Szeto E., Kyrpides N.C., Mussmann M., Amann R., Bergin C., Ruehland C., Rubin E.M. & Dubilier, N. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443, 950-5 (2006).