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Items: 1 to 50 of 119

1.

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.

Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK.

Front Microbiol. 2018 Aug 15;9:1775. doi: 10.3389/fmicb.2018.01775. eCollection 2018.

2.

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes.

Kroeger ME, Delmont TO, Eren AM, Meyer KM, Guo J, Khan K, Rodrigues JLM, Bohannan BJM, Tringe SG, Borges CD, Tiedje JM, Tsai SM, Nüsslein K.

Front Microbiol. 2018 Jul 23;9:1635. doi: 10.3389/fmicb.2018.01635. eCollection 2018.

3.

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
4.

Large-scale replicated field study of maize rhizosphere identifies heritable microbes.

Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi Q, Knight R, Glavina Del Rio T, Tringe SG, Buckler ES, Dangl JL, Ley RE.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):7368-7373. doi: 10.1073/pnas.1800918115. Epub 2018 Jun 25.

5.

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
6.

Discovery of enzymes for toluene synthesis from anoxic microbial communities.

Beller HR, Rodrigues AV, Zargar K, Wu YW, Saini AK, Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, Keasling JD.

Nat Chem Biol. 2018 May;14(5):451-457. doi: 10.1038/s41589-018-0017-4. Epub 2018 Mar 19.

7.

Peatland Acidobacteria with a dissimilatory sulfur metabolism.

Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A.

ISME J. 2018 Jun;12(7):1729-1742. doi: 10.1038/s41396-018-0077-1. Epub 2018 Feb 23.

8.

Landscape topography structures the soil microbiome in arctic polygonal tundra.

Taş N, Prestat E, Wang S, Wu Y, Ulrich C, Kneafsey T, Tringe SG, Torn MS, Hubbard SS, Jansson JK.

Nat Commun. 2018 Feb 22;9(1):777. doi: 10.1038/s41467-018-03089-z.

9.

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.

10.

Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil.

Yao Q, Li Z, Song Y, Wright SJ, Guo X, Tringe SG, Tfaily MM, Paša-Tolić L, Hazen TC, Turner BL, Mayes MA, Pan C.

Nat Ecol Evol. 2018 Mar;2(3):499-509. doi: 10.1038/s41559-017-0463-5. Epub 2018 Jan 22.

PMID:
29358607
11.

Genomic features of bacterial adaptation to plants.

Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, Devescovi G, Stillman K, Monteiro F, Rangel Alvarez B, Lundberg DS, Lu TY, Lebeis S, Jin Z, McDonald M, Klein AP, Feltcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Tringe SG, Woyke T, Dangl JL.

Nat Genet. 2018 Jan;50(1):138-150. doi: 10.1038/s41588-017-0012-9. Epub 2017 Dec 18.

12.

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations.

Garcia SL, Stevens SLR, Crary B, Martinez-Garcia M, Stepanauskas R, Woyke T, Tringe SG, Andersson SGE, Bertilsson S, Malmstrom RR, McMahon KD.

ISME J. 2018 Mar;12(3):742-755. doi: 10.1038/s41396-017-0001-0. Epub 2017 Dec 8.

13.

Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate.

D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J.

Stand Genomic Sci. 2017 Nov 15;12:67. doi: 10.1186/s40793-017-0279-6. eCollection 2017.

14.

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes.

He S, Stevens SLR, Chan LK, Bertilsson S, Glavina Del Rio T, Tringe SG, Malmstrom RR, McMahon KD.

mSphere. 2017 Sep 27;2(5). pii: e00277-17. doi: 10.1128/mSphere.00277-17. eCollection 2017 Sep-Oct.

15.

Patterns and drivers of fungal community depth stratification in Sphagnum peat.

Lamit LJ, Romanowicz KJ, Potvin LR, Rivers AR, Singh K, Lennon JT, Tringe SG, Kane ES, Lilleskov EA.

FEMS Microbiol Ecol. 2017 Jul 1;93(7). doi: 10.1093/femsec/fix082.

16.

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
17.

A genomic perspective on stoichiometric regulation of soil carbon cycling.

Hartman WH, Ye R, Horwath WR, Tringe SG.

ISME J. 2017 Dec;11(12):2652-2665. doi: 10.1038/ismej.2017.115. Epub 2017 Jul 21.

18.

The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils.

Fernández-González AJ, Martínez-Hidalgo P, Cobo-Díaz JF, Villadas PJ, Martínez-Molina E, Toro N, Tringe SG, Fernández-López M.

Sci Rep. 2017 Jul 20;7(1):6008. doi: 10.1038/s41598-017-06112-3.

19.

Single-cell genomics for the masses.

Tringe SG.

Nat Biotechnol. 2017 Jul 12;35(7):635-636. doi: 10.1038/nbt.3914. No abstract available.

20.

Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.

Staley C, Ferrieri AP, Tfaily MM, Cui Y, Chu RK, Wang P, Shaw JB, Ansong CK, Brewer H, Norbeck AD, Markillie M, do Amaral F, Tuleski T, Pellizzaro T, Agtuca B, Ferrieri R, Tringe SG, Paša-Tolić L, Stacey G, Sadowsky MJ.

Microbiome. 2017 Jun 24;5(1):65. doi: 10.1186/s40168-017-0287-1.

21.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

Gontang EA, Aylward FO, Carlos C, Glavina Del Rio T, Chovatia M, Fern A, Lo CC, Malfatti SA, Tringe SG, Currie CR, Kolter R.

PLoS One. 2017 May 18;12(5):e0177189. doi: 10.1371/journal.pone.0177189. eCollection 2017.

22.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems.

Jungbluth SP, Glavina Del Rio T, Tringe SG, Stepanauskas R, Rappé MS.

PeerJ. 2017 Apr 6;5:e3134. doi: 10.7717/peerj.3134. eCollection 2017.

23.

The Tale of a Neglected Energy Source: Elevated Hydrogen Exposure Affects both Microbial Diversity and Function in Soil.

Khdhiri M, Piché-Choquette S, Tremblay J, Tringe SG, Constant P.

Appl Environ Microbiol. 2017 May 17;83(11). pii: e00275-17. doi: 10.1128/AEM.00275-17. Print 2017 Jun 1.

24.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions.

Men Y, Yu K, Bælum J, Gao Y, Tremblay J, Prestat E, Stenuit B, Tringe SG, Jansson J, Zhang T, Alvarez-Cohen L.

Appl Environ Microbiol. 2017 Mar 31;83(8). pii: e03508-16. doi: 10.1128/AEM.03508-16. Print 2017 Apr 15.

25.

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms.

Meyer KM, Klein AM, Rodrigues JL, Nüsslein K, Tringe SG, Mirza BS, Tiedje JM, Bohannan BJ.

Mol Ecol. 2017 Mar;26(6):1547-1556. doi: 10.1111/mec.14011. Epub 2017 Feb 10.

26.

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.

27.

In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community.

Zargar K, Saville R, Phelan RM, Tringe SG, Petzold CJ, Keasling JD, Beller HR.

Sci Rep. 2016 Aug 10;6:31362. doi: 10.1038/srep31362.

28.

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant.

Wagner MR, Lundberg DS, Del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T.

Nat Commun. 2016 Jul 12;7:12151. doi: 10.1038/ncomms12151.

29.

Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms.

Hausmann B, Knorr KH, Schreck K, Tringe SG, Glavina Del Rio T, Loy A, Pester M.

ISME J. 2016 Oct;10(10):2365-75. doi: 10.1038/ismej.2016.42. Epub 2016 Mar 25.

30.

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups.

Piché-Choquette S, Tremblay J, Tringe SG, Constant P.

PeerJ. 2016 Mar 10;4:e1782. doi: 10.7717/peerj.1782. eCollection 2016.

31.

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.

Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G.

Front Microbiol. 2016 Feb 25;7:211. doi: 10.3389/fmicb.2016.00211. eCollection 2016.

32.

'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.

Ikeda-Ohtsubo W, Strassert JF, Köhler T, Mikaelyan A, Gregor I, McHardy AC, Tringe SG, Hugenholtz P, Radek R, Brune A.

Environ Microbiol. 2016 Sep;18(8):2548-64. doi: 10.1111/1462-2920.13234. Epub 2016 Apr 21.

33.

Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs.

Beam JP, Bernstein HC, Jay ZJ, Kozubal MA, Jennings Rd, Tringe SG, Inskeep WP.

Front Microbiol. 2016 Feb 15;7:25. doi: 10.3389/fmicb.2016.00025. eCollection 2016.

34.

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity.

Fonseca-García C, Coleman-Derr D, Garrido E, Visel A, Tringe SG, Partida-Martínez LP.

Front Microbiol. 2016 Feb 12;7:150. doi: 10.3389/fmicb.2016.00150. eCollection 2016.

35.

High-resolution phylogenetic microbial community profiling.

Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T.

ISME J. 2016 Aug;10(8):2020-32. doi: 10.1038/ismej.2015.249. Epub 2016 Feb 9.

36.

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.

Bendall ML, Stevens SL, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR.

ISME J. 2016 Jul;10(7):1589-601. doi: 10.1038/ismej.2015.241. Epub 2016 Jan 8.

37.

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.

Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J.

Front Microbiol. 2015 Oct 31;6:1205. doi: 10.3389/fmicb.2015.01205. eCollection 2015.

38.

Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis.

Oyserman BO, Noguera DR, del Rio TG, Tringe SG, McMahon KD.

ISME J. 2016 Apr;10(4):810-22. doi: 10.1038/ismej.2015.155. Epub 2015 Nov 10.

39.

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community.

Bowers RM, Clum A, Tice H, Lim J, Singh K, Ciobanu D, Ngan CY, Cheng JF, Tringe SG, Woyke T.

BMC Genomics. 2015 Oct 24;16:856. doi: 10.1186/s12864-015-2063-6.

40.

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.

Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida-Martinez LP, Tringe SG.

New Phytol. 2016 Jan;209(2):798-811. doi: 10.1111/nph.13697. Epub 2015 Oct 15.

41.

Primer and platform effects on 16S rRNA tag sequencing.

Tremblay J, Singh K, Fern A, Kirton ES, He S, Woyke T, Lee J, Chen F, Dangl JL, Tringe SG.

Front Microbiol. 2015 Aug 4;6:771. doi: 10.3389/fmicb.2015.00771. eCollection 2015.

42.

PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa.

Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina del Rio T, Jones CD, Tringe SG, Dangl JL.

Science. 2015 Aug 21;349(6250):860-4. doi: 10.1126/science.aaa8764. Epub 2015 Jul 16.

43.

Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.

Beam JP, Jay ZJ, Schmid MC, Rusch DB, Romine MF, Jennings Rde M, Kozubal MA, Tringe SG, Wagner M, Inskeep WP.

ISME J. 2016 Jan;10(1):210-24. doi: 10.1038/ismej.2015.83. Epub 2015 Jul 3.

44.

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

He S, Malfatti SA, McFarland JW, Anderson FE, Pati A, Huntemann M, Tremblay J, Glavina del Rio T, Waldrop MP, Windham-Myers L, Tringe SG.

MBio. 2015 May 19;6(3):e00066-15. doi: 10.1128/mBio.00066-15.

45.

Diverse uncultivated ultra-small bacterial cells in groundwater.

Luef B, Frischkorn KR, Wrighton KC, Holman HY, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing KH, Comolli LR, Banfield JF.

Nat Commun. 2015 Feb 27;6:6372. doi: 10.1038/ncomms7372.

PMID:
25721682
46.

Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling.

Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, Frischkorn KR, Tringe SG, Singh A, Markillie LM, Taylor RC, Williams KH, Banfield JF.

Curr Biol. 2015 Mar 16;25(6):690-701. doi: 10.1016/j.cub.2015.01.014. Epub 2015 Feb 19.

47.

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.

Sharon I, Kertesz M, Hug LA, Pushkarev D, Blauwkamp TA, Castelle CJ, Amirebrahimi M, Thomas BC, Burstein D, Tringe SG, Williams KH, Banfield JF.

Genome Res. 2015 Apr;25(4):534-43. doi: 10.1101/gr.183012.114. Epub 2015 Feb 9.

48.

Aquifer environment selects for microbial species cohorts in sediment and groundwater.

Hug LA, Thomas BC, Brown CT, Frischkorn KR, Williams KH, Tringe SG, Banfield JF.

ISME J. 2015 Aug;9(8):1846-56. doi: 10.1038/ismej.2015.2. Epub 2015 Feb 3.

49.

High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.

Zhou J, He Z, Yang Y, Deng Y, Tringe SG, Alvarez-Cohen L.

MBio. 2015 Jan 27;6(1). pii: e02288-14. doi: 10.1128/mBio.02288-14. Review.

50.

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor.

Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, Liu WT.

ISME J. 2015 Aug;9(8):1710-22. doi: 10.1038/ismej.2014.256. Epub 2015 Jan 23.

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