Single Cell Research Group

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.

• Jean-Marie Volland: Assistant Professor, UC Santa Barbara
• Esther Singer: Director of Product and Market Development, Twist Bioscience
• Scott Clingenpeel: Industrial Hygienist, Berkeley Lab
• Devin Doud: Principal Scientist, Kintai Therapeutics, Cambridge, MA
• Jessica Jarett: Computational Biologist, AnimalBiome
• Asaf Levy: Assistant Professor, Hebrew University of Jerusalem, Israel
• Chris Rinke: Research Officer, Australian Centre for Ecogenomics
• Patrick Schwientek: Cofounder & CTO, Oralta

• 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).
• 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).
• Woyke T., Doud D. F. R., Schulz F. The trajectory of microbial single-cell sequencing. Nat Methods 14(11): 1045-1054 (2017).
• 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).
• 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).
• 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).
• Woyke T. & Rubin E.M. Evolution. Searching for new branches on the tree of life. Science. 346:698-9 (2014).
• 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).
• 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).
• 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).
• 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).
• 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).