ggKbase home page
Advanced Search
Search Help

Publications

Published data:
Closely related Lak megaphages replicate in the microbiomes of diverse animals
Crisci, Marco A., et al. “Closely related Lak megaphages replicate in the microbiomes of diverse animals.” iScience (2021): 102875.
Published data:
Borgs are giant extrachromosomal elements with the potential to augment methane oxidation
Basem Al-Shayeb, Marie C. Schoelmerich, Jacob West-Roberts, Luis E. Valentin-Alvarado, Rohan Sachdeva, Susan Mullen, Alexander Crits-Christoph, Michael J. Wilkins, Kenneth H. Williams, Jennifer A. Doudna, Jillian F. Banfield (2021). Borgs are giant extrachromosomal elements with the potential to augment methane oxidation. bioRxiv 2021.07.10.451761; doi: https://doi.org/10.1101/2021.07.10.451761
Published data:
Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems
Chen, L.-X. et al. (2019) “Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems.,” Frontiers in Microbiology, 10, p. 928. doi: 10.3389/fmicb.2019.00928.
Published data:
Megaphage infect Prevotella and variants are widespread in gut microbiomes
Audra E. Devoto, Joanne M. Santini, Matthew R. Olm, Karthik Anantharaman, Patrick Munk, Jenny Tung, Elizabeth A. Archie, Peter J. Turnbaugh, Kimberley D. Seed, Ran Blekhman, Frank M. Aarestrup, Brian C. Thomas and Jillian F. Banfield. “Megaphage infect Prevotella and variants are widespread in gut microbiomes”, submitted to bioRxiv
Published data:
Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle
Anantharaman, K., B. Hausmann, S. P. Jungbluth, R. S. Kantor, A. Lavy, L. A. Warren, M. S. Rappé, et al. 2018. Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle. The ISME Journal. https://doi.org/10.1038/s41396-018-0078-0.
Published data:
Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism
Probst A.J. and Banfield J.F. (2018). Homologous recombination and transposon propagation shapes the population structure of an organism from the deep subsurface with minimal metabolism. bioRxiv. doi: 10.1101/249516.
Published data:
Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome
Dudek, N.K., Sun, C.L., Burstein, D., Kantor, R.S., Aliaga Goltsman, D.S., Bik, E.M., Thomas, B.C., Banfield, J.F. and Relman, D.A. (2017) Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome. Current Biology, https://doi.org/10.1016/j.cub.2017.10.040
Published data:
Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics
Finstad KM, Probst AJ, Thomas BC, Andersen GL, Demergasso C, Echeverría A, Amundson RG and Banfield JF (2017) Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics. Front. Microbiol. 8:1435. doi: 10.3389/fmicb.2017.01435
Published data:
Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation
Kantor, R.S., Huddy, R.J., Iyer, R., Thomas, B.C., Brown, C.T., Anantharaman, K., Tringe, S., Hettich, R.L., Harrison, S.T.L., and Banfield, J.F. (2017). Genome-resolved meta-omics ties microbial dynamics to process performance in biotechnology for thiocyanate degradation. Environ. Sci. Technol.
Published data:
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
K. Anantharaman, C. T. Brown, L. A. Hug, I.Sharon, C. J. Castelle, A. J. Probst, B. C. Thomas, A. Singh, M. J. Wilkins, U. Karaoz, E. L. Brodie, K. H. Williams, S. S. Hubbard, and J. F. Banfield (2016). Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications 7, ncomms13219. doi:10.1038/ncomms13219
Published data:
Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations
Probst, A. J., Castelle, C. J., Singh, A., Brown, C. T., Anantharaman, K., Sharon, I., Hug, L. A., Burstein, D., Emerson, J. B., Thomas, B. C. and Banfield, J. F. (2016), Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations. Environ Microbiol., Epub ahead of print 7 July 2016 doi:10.1111/1462-2920.13362
Published data:
Genome-resolved metagenomic analysis reveals roles for candidate phyla and other microbial community members in biogeochemical transformations in oil reservoirs
Hu, P., Tom, L., Singh, A., Thomas, B.C., Baker, B.J., Piceno, Y.M., Andersen, G.L. and Banfield, J.F. (2016) Genome-resolved metagenomic analysis reveals roles for candidate phyla and other microbial community members in biogeochemical transformations in oil reservoirs. mBio, 7, :e01669-15. doi:10.1128/mBio.01669-15
Published data:
RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria
Wrighton, K.C., Castelle, C.J., Varaljay, V.A., Satagopan, S., Brown, C.T., Wilkins, M.J., Thomas, B.C., Sharon, I., Williams, K.H., Tabita, F.R., and Banfield, J.F. (2016) RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. ISME Journal, in press.
Published data:
Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unraveled with genome-resolved metagenomics
Kantor, R.S., van Zyl, A.W., van Hille, R.P., Thomas, B.C., Harrison, S.T.L., and Banfield, J.F. (2015). Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics. Environ Microbiol 17, 4929–4941.
Published data:
Unusual biology across a group comprising more than 15% of domain Bacteria
Brown, C.T., Hug, L.A., Thomas, B.C., Sharon, I., Castelle, C.J., Singh, A., Wilkins, M.J., Wrighton, K.C., Williams, K.H. and Banfield, J.F. (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208–211
Published data:
Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant
Brooks, B., Mueller, R. S., Young, J. C., Morowitz, M. J., Hettich, R. L., and Banfield, J. F. (2015). Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. Front. Microbiol. 6, 654. doi:10.3389/fmicb.2015.00654.
Published data:
Metagenomic analysis of a high CO2 subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
Emerson, J.B., Thomas, B.C., Alvarez, W. and Banfield, J.B. (2015) Metagenomic analysis of a high CO2 subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environmental Microbiology. DOI: 10.1111/1462-2920.12817
Published data:
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
Cindy J. Castelle, Kelly C. Wrighton, Brian C. Thomas, Laura A. Hug, Michael J. Wilkins, Kyle R. Frischkorn, Susannah Tringe, Kenneth H. Williams, Jillian F. Banfield. Current biology. 2015 Mar 16;25(6):690-701. doi: 10.1016/j.cub.2015.01.014. 15. Genomic expansion of Domain Archaea highlights roles for organisms from new phyla in anaerobic carbon
Published data:
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development
Raveh-Sadka, T., Thomas, B.C., Singh, A., Firek, B., Brooks, B., Castelle, C.J., Sharon, I., Baker, R., Good, M., Morowitz, M.J., and Banfield, J.F. (2015) Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife, eLife 2015;4:e05477
Published data:
Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms
Justice, N.B, Norman, A., Brown, C., Singh, A., Thomas, B.C and Banfield, J.F. (2015) Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics, 15, 1107-1124. doi:10.1186/1471-2164-15-1107
Published data:
Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
Brooks, B., Firek, B. A., Miller, C. S., Sharon, I., Thomas, B. C., Baker, R., Morowitz, M. J., and Banfield, J. F. (2014). Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome 2, 1. doi:10.1186/2049-2618-2-1.
Published data:
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
Brown, C.T., Sharon, I., Thomas, B.C., Castelle, C.J., Morowitz, M.J., and Banfield, J.F. (2013) Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome, 1:30 doi:10.1186/2049-2618-1-30
Published data:
Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla
Kantor, R.S., Wrighton, K.C., Handley, K.M., Sharon, I., Hug, L.A., Castelle, C.J., Thomas, B.C., and Banfield, J.F. (2013). Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla. mBio 4, e00708–13–e00708–13.
Published data:
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
Di Rienzi, S.C., Sharon, I., Wrighton, K.C., Koren, O., Hug, L.A., Thomas, B.C., Goodrich, J.K., Bell, J.T., Spector, T.D., Banfield, J.F.​*, Ley, R.E*​ (2013) The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife, 2013;2:e01102
Published data:
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
Castelle, C.J., Hug, L.A., Wrighton, K.C., Thomas, B.C., Williams, K.H., Wu, D., Tringe, S.G., Singer, S.W., Eisen, J.A., and Banfield, J.F., (2013). Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications, 4:2120 DOI:10.1038/ncomm3120
Published data:
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
Sharon, I. Morowitz, M.J., Thomas, B.C., Costello, E.K., Relman, D.A., and Banfield J.F. (2012) Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Research, 23:111-20 http://www.genome.org/cgi/ doi/10.1101/gr.142315.112
Published data:
Accurate, multi-kb reads resolve complex populations and detect rare microorganisms
Sharon, I., Kertesz, M., Hug, L.A., Pushkarev, D., Blauwkamp, T.A., Castelle, C.J., Amirebrahimi, M., Thomas, B.C., Burstein, D., Tringe S.G., Williams, K.H.and Banfield, J.F. (2015) Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome Research, http://www.genome.org/cgi/doi/10.1101/gr.142315.112
Published data:
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proceedings of the National Academy of Science
Morowitz, M.J., Denef, V.J., Costello, E.K., Thomas, B.C., Poroyko, V., Relman, D.A. and Banfield, J.F. (2010) Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proceedings of the National Academy of Science, doi: 10.1073/pnas.1010992108