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Items: 1 to 50 of 245

1.

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.

Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, Sieber CMK, Letourneur Q, Ghozlane A, Andersen GL, Li WJ, Hallam SJ, Muyzer G, de Oliveira VM, Inskeep WP, Banfield JF, Gribaldo S.

Nat Microbiol. 2019 Mar 4. doi: 10.1038/s41564-019-0363-3. [Epub ahead of print]

PMID:
30833729
2.

Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network.

Bouma-Gregson K, Olm MR, Probst AJ, Anantharaman K, Power ME, Banfield JF.

ISME J. 2019 Feb 26. doi: 10.1038/s41396-019-0374-3. [Epub ahead of print]

PMID:
30809011
3.

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms.

Olm MR, West PT, Brooks B, Firek BA, Baker R, Morowitz MJ, Banfield JF.

Microbiome. 2019 Feb 15;7(1):26. doi: 10.1186/s40168-019-0638-1.

4.

A Functional Mini-Integrase in a Two-Protein-type V-C CRISPR System.

Wright AV, Wang JY, Burstein D, Harrington LB, Paez-Espino D, Kyrpides NC, Iavarone AT, Banfield JF, Doudna JA.

Mol Cell. 2019 Feb 21;73(4):727-737.e3. doi: 10.1016/j.molcel.2018.12.015. Epub 2019 Jan 29.

PMID:
30709710
5.

Megaphages infect Prevotella and variants are widespread in gut microbiomes.

Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Aarestrup FM, Thomas BC, Banfield JF.

Nat Microbiol. 2019 Jan 28. doi: 10.1038/s41564-018-0338-9. [Epub ahead of print]

PMID:
30692672
6.

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria.

Matheus Carnevali PB, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF.

Nat Commun. 2019 Jan 28;10(1):463. doi: 10.1038/s41467-018-08246-y.

7.

Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea.

Jaffe AL, Castelle CJ, Dupont CL, Banfield JF.

Mol Biol Evol. 2019 Mar 1;36(3):435-446. doi: 10.1093/molbev/msy234.

8.

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.

Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA.

Science. 2018 Nov 16;362(6416):839-842. doi: 10.1126/science.aav4294. Epub 2018 Oct 18.

PMID:
30337455
9.

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome.

Goltsman DSA, Sun CL, Proctor DM, DiGiulio DB, Robaczewska A, Thomas BC, Shaw GM, Stevenson DK, Holmes SP, Banfield JF, Relman DA.

Genome Res. 2018 Oct;28(10):1467-1480. doi: 10.1101/gr.236000.118. Epub 2018 Sep 19.

PMID:
30232199
10.

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations.

Castelle CJ, Brown CT, Anantharaman K, Probst AJ, Huang RH, Banfield JF.

Nat Rev Microbiol. 2018 Oct;16(10):629-645. doi: 10.1038/s41579-018-0076-2.

11.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
12.

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon.

Starr EP, Shi S, Blazewicz SJ, Probst AJ, Herman DJ, Firestone MK, Banfield JF.

Microbiome. 2018 Jul 3;6(1):122. doi: 10.1186/s40168-018-0499-z.

13.

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms.

Brooks B, Olm MR, Firek BA, Baker R, Geller-McGrath D, Reimer SR, Soenjoyo KR, Yip JS, Dahan D, Thomas BC, Morowitz MJ, Banfield JF.

Microbiome. 2018 Jun 20;6(1):112. doi: 10.1186/s40168-018-0493-5.

14.

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis.

Crits-Christoph A, Diamond S, Butterfield CN, Thomas BC, Banfield JF.

Nature. 2018 Jun;558(7710):440-444. doi: 10.1038/s41586-018-0207-y. Epub 2018 Jun 13.

15.

Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages.

Liu X, Li M, Castelle CJ, Probst AJ, Zhou Z, Pan J, Liu Y, Banfield JF, Gu JD.

Microbiome. 2018 Jun 8;6(1):102. doi: 10.1186/s40168-018-0488-2.

16.

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy.

Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, Banfield JF.

Nat Microbiol. 2018 Jul;3(7):836-843. doi: 10.1038/s41564-018-0171-1. Epub 2018 May 28.

PMID:
29807988
17.
18.

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.

Brown CT, Xiong W, Olm MR, Thomas BC, Baker R, Firek B, Morowitz MJ, Hettich RL, Banfield JF.

MBio. 2018 Apr 10;9(2). pii: e00441-18. doi: 10.1128/mBio.00441-18.

19.

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life.

Castelle CJ, Banfield JF.

Cell. 2018 Mar 8;172(6):1181-1197. doi: 10.1016/j.cell.2018.02.016. Review.

20.

Genome-reconstruction for eukaryotes from complex natural microbial communities.

West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF.

Genome Res. 2018 Apr;28(4):569-580. doi: 10.1101/gr.228429.117. Epub 2018 Mar 1.

21.

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle.

Anantharaman K, Hausmann B, Jungbluth SP, Kantor RS, Lavy A, Warren LA, Rappé MS, Pester M, Loy A, Thomas BC, Banfield JF.

ISME J. 2018 Jun;12(7):1715-1728. doi: 10.1038/s41396-018-0078-0. Epub 2018 Feb 21.

22.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

23.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.

Probst AJ, Ladd B, Jarett JK, Geller-McGrath DE, Sieber CMK, Emerson JB, Anantharaman K, Thomas BC, Malmstrom RR, Stieglmeier M, Klingl A, Woyke T, Ryan MC, Banfield JF.

Nat Microbiol. 2018 Mar;3(3):328-336. doi: 10.1038/s41564-017-0098-y. Epub 2018 Jan 29.

24.

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome.

Rahman SF, Olm MR, Morowitz MJ, Banfield JF.

mSystems. 2018 Jan 9;3(1). pii: e00123-17. doi: 10.1128/mSystems.00123-17. eCollection 2018 Jan-Feb.

25.

A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.

Lavy A, Keren R, Yu K, Thomas BC, Alvarez-Cohen L, Banfield JF, Ilan M.

Environ Microbiol. 2018 Feb;20(2):800-814. doi: 10.1111/1462-2920.14013. Epub 2017 Dec 15.

26.

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome.

Brooks B, Olm MR, Firek BA, Baker R, Thomas BC, Morowitz MJ, Banfield JF.

Nat Commun. 2017 Nov 27;8(1):1814. doi: 10.1038/s41467-017-02018-w.

27.

Complete 4.55-Megabase-Pair Genome of "Candidatus Fluviicola riflensis," Curated from Short-Read Metagenomic Sequences.

Banfield JF, Anantharaman K, Williams KH, Thomas BC.

Genome Announc. 2017 Nov 22;5(47). pii: e01299-17. doi: 10.1128/genomeA.01299-17.

28.

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome.

Dudek NK, Sun CL, Burstein D, Kantor RS, Aliaga Goltsman DS, Bik EM, Thomas BC, Banfield JF, Relman DA.

Curr Biol. 2017 Dec 18;27(24):3752-3762.e6. doi: 10.1016/j.cub.2017.10.040. Epub 2017 Nov 16.

29.

Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill.

Probst AJ, Hu P, Sun CL, Dubinsky EA, Sieber CMK, Banfield JF, Andersen GL.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E8950-E8952. doi: 10.1073/pnas.1712466114. Epub 2017 Oct 10. No abstract available.

30.

Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment.

Ino K, Hernsdorf AW, Konno U, Kouduka M, Yanagawa K, Kato S, Sunamura M, Hirota A, Togo YS, Ito K, Fukuda A, Iwatsuki T, Mizuno T, Komatsu DD, Tsunogai U, Ishimura T, Amano Y, Thomas BC, Banfield JF, Suzuki Y.

ISME J. 2018 Jan;12(1):31-47. doi: 10.1038/ismej.2017.140. Epub 2017 Sep 8.

31.

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, Banfield JF.

Front Microbiol. 2017 Jul 28;8:1435. doi: 10.3389/fmicb.2017.01435. eCollection 2017.

32.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893.

PMID:
28787424
33.

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.

Olm MR, Brown CT, Brooks B, Banfield JF.

ISME J. 2017 Dec;11(12):2864-2868. doi: 10.1038/ismej.2017.126. Epub 2017 Jul 25.

34.

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

Xiong W, Brown CT, Morowitz MJ, Banfield JF, Hettich RL.

Microbiome. 2017 Jul 10;5(1):72. doi: 10.1186/s40168-017-0290-6.

35.

Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders.

Hu P, Dubinsky EA, Probst AJ, Wang J, Sieber CMK, Tom LM, Gardinali PR, Banfield JF, Atlas RM, Andersen GL.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7432-7437. doi: 10.1073/pnas.1703424114. Epub 2017 Jun 26.

36.

Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant.

Costello EK, Sun CL, Carlisle EM, Morowitz MJ, Banfield JF, Relman DA.

Sci Rep. 2017 Jun 19;7(1):3764. doi: 10.1038/s41598-017-03821-7.

37.

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea.

Paul BG, Burstein D, Castelle CJ, Handa S, Arambula D, Czornyj E, Thomas BC, Ghosh P, Miller JF, Banfield JF, Valentine DL.

Nat Microbiol. 2017 Apr 3;2:17045. doi: 10.1038/nmicrobiol.2017.45.

38.

Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments.

Hernsdorf AW, Amano Y, Miyakawa K, Ise K, Suzuki Y, Anantharaman K, Probst A, Burstein D, Thomas BC, Banfield JF.

ISME J. 2017 Aug;11(8):1915-1929. doi: 10.1038/ismej.2017.39. Epub 2017 Mar 28.

39.

The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis.

Olm MR, Butterfield CN, Copeland A, Boles TC, Thomas BC, Banfield JF.

MBio. 2017 Feb 21;8(1). pii: e01969-16. doi: 10.1128/mBio.01969-16.

40.

Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings.

Rahman SF, Kantor RS, Huddy R, Thomas BC, van Zyl AW, Harrison STL, Banfield JF.

Microbiologyopen. 2017 Jun;6(3). doi: 10.1002/mbo3.446. Epub 2017 Feb 19.

41.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

Kantor RS, Huddy RJ, Iyer R, Thomas BC, Brown CT, Anantharaman K, Tringe S, Hettich RL, Harrison ST, Banfield JF.

Environ Sci Technol. 2017 Mar 7;51(5):2944-2953. doi: 10.1021/acs.est.6b04477. Epub 2017 Feb 13.

42.

Asgard archaea illuminate the origin of eukaryotic cellular complexity.

Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ.

Nature. 2017 Jan 19;541(7637):353-358. doi: 10.1038/nature21031. Epub 2017 Jan 11.

43.

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates.

Olm MR, Brown CT, Brooks B, Firek B, Baker R, Burstein D, Soenjoyo K, Thomas BC, Morowitz M, Banfield JF.

Genome Res. 2017 Apr;27(4):601-612. doi: 10.1101/gr.213256.116. Epub 2017 Jan 10.

44.

Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation.

Castelle CJ, Brown CT, Thomas BC, Williams KH, Banfield JF.

Sci Rep. 2017 Jan 9;7:40101. doi: 10.1038/srep40101.

45.

New CRISPR-Cas systems from uncultivated microbes.

Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF.

Nature. 2017 Feb 9;542(7640):237-241. doi: 10.1038/nature21059. Epub 2016 Dec 22.

46.

Short- and Long-Range Attractive Forces That Influence the Structure of Montmorillonite Osmotic Hydrates.

Tester CC, Aloni S, Gilbert B, Banfield JF.

Langmuir. 2016 Nov 22;32(46):12039-12046. Epub 2016 Nov 10.

47.

Disturbances of the Perioperative Microbiome Across Multiple Body Sites in Patients Undergoing Pancreaticoduodenectomy.

Rogers MB, Aveson V, Firek B, Yeh A, Brooks B, Brower-Sinning R, Steve J, Banfield JF, Zureikat A, Hogg M, Boone BA, Zeh HJ, Morowitz MJ.

Pancreas. 2017 Feb;46(2):260-267. doi: 10.1097/MPA.0000000000000726.

48.

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.

Butterfield CN, Li Z, Andeer PF, Spaulding S, Thomas BC, Singh A, Hettich RL, Suttle KB, Probst AJ, Tringe SG, Northen T, Pan C, Banfield JF.

PeerJ. 2016 Nov 8;4:e2687. eCollection 2016.

49.

Measurement of bacterial replication rates in microbial communities.

Brown CT, Olm MR, Thomas BC, Banfield JF.

Nat Biotechnol. 2016 Dec;34(12):1256-1263. doi: 10.1038/nbt.3704. Epub 2016 Nov 7.

50.

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.

Wrighton KC, Castelle CJ, Varaljay VA, Satagopan S, Brown CT, Wilkins MJ, Thomas BC, Sharon I, Williams KH, Tabita FR, Banfield JF.

ISME J. 2016 Nov;10(11):2702-2714. doi: 10.1038/ismej.2016.53. Epub 2016 May 3.

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