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Selected Publications

B. Al-Shayeb, P. Skopintsev, K. M. Soczek, E. C. Stahl, Z. Li, E. Groover, D. Smock, A. R. Eggers, P. Pausch, B. F. Cress, C. J. Huang, B. Staskawicz, D. F. Savage, S. E. Jacobsen, J. F. Banfield, J. A. Doudna, Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell 185, 4574-4586.e16 (2022).

C. He, R. Keren, M. L. Whittaker, I. F. Farag, J. A. Doudna, J. H. D. Cate, J. F. Banfield, Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. Nat Microbiol 6, 354–365 (2021).

B. Al-Shayeb, R. Sachdeva, L.-X. Chen, F. Ward, P. Munk, A. Devoto, C. J. Castelle, M. R. Olm, K. Bouma-Gregson, Y. Amano, C. He, R. Méheust, B. Brooks, A. Thomas, A. Lavy, P. Matheus-Carnevali, C. Sun, D. S. A. Goltsman, M. A. Borton, A. Sharrar, A. L. Jaffe, T. C. Nelson, R. Kantor, R. Keren, K. R. Lane, I. F. Farag, S. Lei, K. Finstad, R. Amundson, K. Anantharaman, J. Zhou, A. J. Probst, M. E. Power, S. G. Tringe, W.-J. Li, K. Wrighton, S. Harrison, M. Morowitz, D. A. Relman, J. A. Doudna, A.-C. Lehours, L. Warren, J. H. D. Cate, J. M. Santini, J. F. Banfield, Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020).

L.-X. Chen, K. Anantharaman, A. Shaiber, A. M. Eren, J. F. Banfield, Accurate and complete genomes from metagenomes. Genome Res 30, 315–333 (2020).

L.-X. Chen, R. Méheust, A. Crits-Christoph, K. D. McMahon, T. C. Nelson, G. F. Slater, L. A. Warren, J. F. Banfield, Large freshwater phages with the potential to augment aerobic methane oxidation. Nat Microbiol 5, 1504–1515 (2020).

A. E. Devoto, J. M. Santini, M. R. Olm, K. Anantharaman, P. Munk, J. Tung, E. A. Archie, P. J. Turnbaugh, K. D. Seed, R. Blekhman, F. M. Aarestrup, B. C. Thomas, J. F. Banfield, Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat Microbiol 4, 693–700 (2019).

S. Diamond, P. F. Andeer, Z. Li, A. Crits-Christoph, D. Burstein, K. Anantharaman, K. R. Lane, B. C. Thomas, C. Pan, T. R. Northen, J. F. Banfield, Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. Nat Microbiol 4, 1356–1367 (2019).

R. Méheust, D. Burstein, C. J. Castelle, J. F. Banfield, The distinction of CPR bacteria from other bacteria based on protein family content. Nat Commun 10, 4173 (2019).

M. R. Olm, N. Bhattacharya, A. Crits-Christoph, B. A. Firek, R. Baker, Y. S. Song, M. J. Morowitz, J. F. Banfield, Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. Sci Adv 5, eaax5727 (2019).

C. J. Castelle, J. F. Banfield, Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life. Cell 172, 1181–1197 (2018).

A. Crits-Christoph, S. Diamond, C. N. Butterfield, B. C. Thomas, J. F. Banfield, Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature 558, 440–444 (2018).

C. M. K. Sieber, A. J. Probst, A. Sharrar, B. C. Thomas, M. Hess, S. G. Tringe, J. F. Banfield, Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol 3, 836–843 (2018).

P. T. West, A. J. Probst, I. V. Grigoriev, B. C. Thomas, J. F. Banfield, Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res 28, 569–580 (2018).

B. Brooks, M. R. Olm, B. A. Firek, R. Baker, B. C. Thomas, M. J. Morowitz, J. F. Banfield, Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun 8, 1814 (2017).

D. Burstein, L. B. Harrington, S. C. Strutt, A. J. Probst, K. Anantharaman, B. C. Thomas, J. A. Doudna, J. F. Banfield, New CRISPR–Cas systems from uncultivated microbes. Nature 542, 237–241 (2017).

M. R. Olm, C. T. Brown, B. Brooks, B. Firek, R. Baker, D. Burstein, K. Soenjoyo, B. C. Thomas, M. Morowitz, J. F. Banfield, Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res 27, 601–612 (2017).


M. R. Olm, C. T. Brown, B. Brooks, J. F. Banfield, dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J 11, 2864–2868 (2017).

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, J. F. Banfield, Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 7, 13219 (2016).

L. A. Hug, B. J. Baker, K. Anantharaman, C. T. Brown, A. J. Probst, C. J. Castelle, C. N. Butterfield, A. W. Hernsdorf, Y. Amano, K. Ise, Y. Suzuki, N. Dudek, D. A. Relman, K. M. Finstad, R. Amundson, B. C. Thomas, J. F. Banfield, A new view of the tree of life. Nat Microbiol 1, 1–6 (2016).

C. T. Brown, L. A. Hug, B. C. Thomas, I. Sharon, C. J. Castelle, A. Singh, M. J. Wilkins, K. C. Wrighton, K. H. Williams, J. F. Banfield, Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208–211 (2015).

B. Luef, K. R. Frischkorn, K. C. Wrighton, H.-Y. N. Holman, G. Birarda, B. C. Thomas, A. Singh, K. H. Williams, C. E. Siegerist, S. G. Tringe, K. H. Downing, L. R. Comolli, J. F. Banfield, Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 6, 6372 (2015).

C. J. Castelle, K. C. Wrighton, B. C. Thomas, L. A. Hug, C. T. Brown, M. J. Wilkins, K. R. Frischkorn, S. G. Tringe, A. Singh, L. M. Markillie, R. C. Taylor, K. H. Williams, J. F. Banfield, Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling. Current Biology 25, 690–701 (2015).

K. C. Wrighton, C. J. Castelle, M. J. Wilkins, L. A. Hug, I. Sharon, B. C. Thomas, K. M. Handley, S. W. Mullin, C. D. Nicora, A. Singh, M. S. Lipton, P. E. Long, K. H. Williams, J. F. Banfield, Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J 8, 1452–1463 (2014).

C. J. Castelle, L. A. Hug, K. C. Wrighton, B. C. Thomas, K. H. Williams, D. Wu, S. G. Tringe, S. W. Singer, J. A. Eisen, J. F. Banfield, Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun 4, 2120 (2013).

R. S. Kantor, K. C. Wrighton, K. M. Handley, I. Sharon, L. A. Hug, C. J. Castelle, B. C. Thomas, J. F. Banfield, Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 4, e00708-00713 (2013).

V. J. Denef, J. F. Banfield, In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids. Science 336, 462–466 (2012).

K. C. Wrighton, B. C. Thomas, I. Sharon, C. S. Miller, C. J. Castelle, N. C. VerBerkmoes, M. J. Wilkins, R. L. Hettich, M. S. Lipton, K. H. Williams, P. E. Long, J. F. Banfield, Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla. Science 337, 1661–1665 (2012).

P. Narasingarao, S. Podell, J. A. Ugalde, C. Brochier-Armanet, J. B. Emerson, J. J. Brocks, K. B. Heidelberg, J. F. Banfield, E. E. Allen, De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 6, 81–93 (2012).

L. R. Comolli, B. J. Baker, K. H. Downing, C. E. Siegerist, J. F. Banfield, Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J 3, 159–167 (2009).

G. J. Dick, A. F. Andersson, B. J. Baker, S. L. Simmons, B. C. Thomas, A. P. Yelton, J. F. Banfield, Community-wide analysis of microbial genome sequence signatures. Genome Biol 10, R85 (2009).

A. F. Andersson, J. F. Banfield, Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047–1050 (2008).

I. Lo, V. J. Denef, N. C. VerBerkmoes, M. B. Shah, D. Goltsman, G. DiBartolo, G. W. Tyson, E. E. Allen, R. J. Ram, J. C. Detter, P. Richardson, M. P. Thelen, R. L. Hettich, J. F. Banfield, Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446, 537–541 (2007).

R. J. Ram, N. C. VerBerkmoes, M. P. Thelen, G. W. Tyson, B. J. Baker, R. C. Blake, M. Shah, R. L. Hettich, J. F. Banfield, Community Proteomics of a Natural Microbial Biofilm. Science 308, 1915–1920 (2005).

G. W. Tyson, J. Chapman, P. Hugenholtz, E. E. Allen, R. J. Ram, P. M. Richardson, V. V. Solovyev, E. M. Rubin, D. S. Rokhsar, J. F. Banfield, Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004).

R. L. Penn, J. F. Banfield, Imperfect Oriented Attachment: Dislocation Generation in Defect-Free Nanocrystals. Science 281, 969–971 (1998).

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