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Items: 1 to 50 of 111

1.

The importance of designating type material for uncultured taxa.

Chuvochina M, Rinke C, Parks DH, Rappé MS, Tyson GW, Yilmaz P, Whitman WB, Hugenholtz P.

Syst Appl Microbiol. 2018 Jul 18. pii: S0723-2020(18)30200-5. doi: 10.1016/j.syapm.2018.07.003. [Epub ahead of print]

2.

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.

Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, Muir JG, Gibson PR, Cuív PÓ, Hugenholtz P, Tyson GW, Morrison M.

ISME J. 2018 Aug 1. doi: 10.1038/s41396-018-0225-7. [Epub ahead of print]

PMID:
30068938
3.

Host-linked soil viral ecology along a permafrost thaw gradient.

Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, Singleton CM, Solden LM, Naas AE, Boyd JA, Hodgkins SB, Wilson RM, Trubl G, Li C, Frolking S, Pope PB, Wrighton KC, Crill PM, Chanton JP, Saleska SR, Tyson GW, Rich VI, Sullivan MB.

Nat Microbiol. 2018 Aug;3(8):870-880. doi: 10.1038/s41564-018-0190-y. Epub 2018 Jul 16.

PMID:
30013236
4.

Genome-centric view of carbon processing in thawing permafrost.

Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, Hoelzle RD, Lamberton TO, McCalley CK, Hodgkins SB, Wilson RM, Purvine SO, Nicora CD, Li C, Frolking S, Chanton JP, Crill PM, Saleska SR, Rich VI, Tyson GW.

Nature. 2018 Aug;560(7716):49-54. doi: 10.1038/s41586-018-0338-1. Epub 2018 Jul 16.

PMID:
30013118
5.

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
6.

Methanotrophy across a natural permafrost thaw environment.

Singleton CM, McCalley CK, Woodcroft BJ, Boyd JA, Evans PN, Hodgkins SB, Chanton JP, Frolking S, Crill PM, Saleska SR, Rich VI, Tyson GW.

ISME J. 2018 Oct;12(10):2544-2558. doi: 10.1038/s41396-018-0065-5. Epub 2018 Jun 28.

7.

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction.

Cai C, Leu AO, Xie GJ, Guo J, Feng Y, Zhao JX, Tyson GW, Yuan Z, Hu S.

ISME J. 2018 Aug;12(8):1929-1939. doi: 10.1038/s41396-018-0109-x. Epub 2018 Apr 16.

PMID:
29662147
8.

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes.

Boyd JA, Woodcroft BJ, Tyson GW.

Nucleic Acids Res. 2018 Jun 1;46(10):e59. doi: 10.1093/nar/gky174.

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.

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2018 Feb;3(2):253. doi: 10.1038/s41564-017-0083-5.

PMID:
29234139
11.

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion.

Shiffman ME, Soo RM, Dennis PG, Morrison M, Tyson GW, Hugenholtz P.

PeerJ. 2017 Nov 16;5:e4075. doi: 10.7717/peerj.4075. eCollection 2017.

12.

Erratum for Skennerton et al., "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea".

Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ.

MBio. 2017 Oct 3;8(5). pii: e01561-17. doi: 10.1128/mBio.01561-17. No abstract available.

13.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2017 Nov;2(11):1533-1542. doi: 10.1038/s41564-017-0012-7. Epub 2017 Sep 11. Erratum in: Nat Microbiol. 2017 Dec 12;:.

PMID:
28894102
14.

Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds.

Tout J, Astudillo-García C, Taylor MW, Tyson GW, Stocker R, Ralph PJ, Seymour JR, Webster NS.

Environ Microbiol Rep. 2017 Dec;9(6):750-755. doi: 10.1111/1758-2229.12591. Epub 2017 Oct 13.

PMID:
28892304
15.

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities.

Lambert BS, Raina JB, Fernandez VI, Rinke C, Siboni N, Rubino F, Hugenholtz P, Tyson GW, Seymour JR, Stocker R.

Nat Microbiol. 2017 Oct;2(10):1344-1349. doi: 10.1038/s41564-017-0010-9. Epub 2017 Aug 28.

PMID:
28848238
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.

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea.

Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ.

MBio. 2017 Aug 1;8(4). pii: e00530-17. doi: 10.1128/mBio.00530-17. Erratum in: MBio. 2017 Oct 3;8(5):.

18.

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community.

Pedroso MM, Selleck C, Enculescu C, Harmer JR, Mitić N, Craig WR, Helweh W, Hugenholtz P, Tyson GW, Tierney DL, Larrabee JA, Schenk G.

Metallomics. 2017 Aug 16;9(8):1157-1168. doi: 10.1039/c7mt00195a.

PMID:
28749495
19.

Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes.

Dennis PG, Virdis B, Vanwonterghem I, Hassan A, Hugenholtz P, Tyson GW, Rabaey K.

Sci Rep. 2016 Dec 19;6:39114. doi: 10.1038/srep39114.

20.

Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps.

Skennerton CT, Haroon MF, Briegel A, Shi J, Jensen GJ, Tyson GW, Orphan VJ.

ISME J. 2016 Nov;10(11):2679-2692. doi: 10.1038/ismej.2016.55. Epub 2016 Apr 8.

21.

pH and Organic Carbon Dose Rates Control Microbially Driven Bioremediation Efficacy in Alkaline Bauxite Residue.

Santini TC, Malcolm LI, Tyson GW, Warren LA.

Environ Sci Technol. 2016 Oct 18;50(20):11164-11173. Epub 2016 Sep 28.

PMID:
27681196
22.

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota.

Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW.

Nat Microbiol. 2016 Oct 3;1:16170. doi: 10.1038/nmicrobiol.2016.170.

PMID:
27694807
23.

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics.

Rinke C, Low S, Woodcroft BJ, Raina JB, Skarshewski A, Le XH, Butler MK, Stocker R, Seymour J, Tyson GW, Hugenholtz P.

PeerJ. 2016 Sep 22;4:e2486. doi: 10.7717/peerj.2486. eCollection 2016.

24.

Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

Robbins SJ, Evans PN, Parks DH, Golding SD, Tyson GW.

Front Microbiol. 2016 Jun 8;7:731. doi: 10.3389/fmicb.2016.00731. eCollection 2016.

25.

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

Vanwonterghem I, Jensen PD, Rabaey K, Tyson GW.

Environ Microbiol. 2016 Sep;18(9):3144-58. doi: 10.1111/1462-2920.13382. Epub 2016 Jul 22.

PMID:
27317862
26.

OrfM: a fast open reading frame predictor for metagenomic data.

Woodcroft BJ, Boyd JA, Tyson GW.

Bioinformatics. 2016 Sep 1;32(17):2702-3. doi: 10.1093/bioinformatics/btw241. Epub 2016 May 3.

27.

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon.

Angly FE, Pantos O, Morgan TC, Rich V, Tonin H, Bourne DG, Mercurio P, Negri AP, Tyson GW.

PeerJ. 2016 Mar 8;4:e1758. doi: 10.7717/peerj.1758. eCollection 2016.

28.

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events.

Angly FE, Heath C, Morgan TC, Tonin H, Rich V, Schaffelke B, Bourne DG, Tyson GW.

PeerJ. 2016 Jan 5;4:e1511. doi: 10.7717/peerj.1511. eCollection 2016.

29.

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres.

Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P.

Front Microbiol. 2016 Jan 7;6:1469. doi: 10.3389/fmicb.2015.01469. eCollection 2015.

30.

Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska.

Kao-Kniffin J, Woodcroft BJ, Carver SM, Bockheim JG, Handelsman J, Tyson GW, Hinkel KM, Mueller CW.

Sci Rep. 2015 Dec 18;5:18165. doi: 10.1038/srep18165.

31.

The influence of hydrogeological disturbance and mining on coal seam microbial communities.

Raudsepp MJ, Gagen EJ, Evans P, Tyson GW, Golding SD, Southam G.

Geobiology. 2016 Mar;14(2):163-75. doi: 10.1111/gbi.12166. Epub 2015 Nov 6.

PMID:
26541089
32.

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.

Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW.

Science. 2015 Oct 23;350(6259):434-8. doi: 10.1126/science.aac7745.

33.

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm.

Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL.

Environ Microbiol. 2016 Jan;18(1):273-87. doi: 10.1111/1462-2920.13019. Epub 2015 Oct 21.

PMID:
26279094
34.

Selective Enrichment Establishes a Stable Performing Community for Microbial Electrosynthesis of Acetate from CO₂.

Patil SA, Arends JB, Vanwonterghem I, van Meerbergen J, Guo K, Tyson GW, Rabaey K.

Environ Sci Technol. 2015 Jul 21;49(14):8833-43. doi: 10.1021/es506149d. Epub 2015 Jun 30.

PMID:
26079858
35.

Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.

Soo RM, Woodcroft BJ, Parks DH, Tyson GW, Hugenholtz P.

PeerJ. 2015 May 21;3:e968. doi: 10.7717/peerj.968. eCollection 2015.

36.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW.

Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. Epub 2015 May 14.

37.

Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome.

Wang JT, Daly JN, Willner DL, Patil J, Hall RA, Schembri MA, Tyson GW, Hugenholtz P.

J Microbiol Biol Educ. 2015 May 1;16(1):50-60. doi: 10.1128/jmbe.v16i1.816. eCollection 2015 May.

38.

A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments.

Hu S, Zeng RJ, Haroon MF, Keller J, Lant PA, Tyson GW, Yuan Z.

Sci Rep. 2015 Mar 3;5:8706. doi: 10.1038/srep08706.

39.
40.

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix.

Pantos O, Bongaerts P, Dennis PG, Tyson GW, Hoegh-Guldberg O.

ISME J. 2015 Sep;9(9):1916-27. doi: 10.1038/ismej.2015.3. Epub 2015 Feb 10.

41.

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking.

Sekiguchi Y, Ohashi A, Parks DH, Yamauchi T, Tyson GW, Hugenholtz P.

PeerJ. 2015 Jan 27;3:e740. doi: 10.7717/peerj.740. eCollection 2015.

42.

Chemotaxis by natural populations of coral reef bacteria.

Tout J, Jeffries TC, Petrou K, Tyson GW, Webster NS, Garren M, Stocker R, Ralph PJ, Seymour JR.

ISME J. 2015 Aug;9(8):1764-77. doi: 10.1038/ismej.2014.261. Epub 2015 Jan 23.

43.

Methane dynamics regulated by microbial community response to permafrost thaw.

McCalley CK, Woodcroft BJ, Hodgkins SB, Wehr RA, Kim EH, Mondav R, Crill PM, Chanton JP, Rich VI, Tyson GW, Saleska SR.

Nature. 2014 Oct 23;514(7523):478-81. doi: 10.1038/nature13798.

PMID:
25341787
44.

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW.

PeerJ. 2014 Sep 30;2:e603. doi: 10.7717/peerj.603. eCollection 2014.

45.

Expanding our view of genomic diversity in Candidatus Accumulibacter clades.

Skennerton CT, Barr JJ, Slater FR, Bond PL, Tyson GW.

Environ Microbiol. 2015 May;17(5):1574-85. doi: 10.1111/1462-2920.12582. Epub 2014 Aug 27.

PMID:
25088527
46.

STAMP: statistical analysis of taxonomic and functional profiles.

Parks DH, Tyson GW, Hugenholtz P, Beiko RG.

Bioinformatics. 2014 Nov 1;30(21):3123-4. doi: 10.1093/bioinformatics/btu494. Epub 2014 Jul 23.

47.

Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques.

Vanwonterghem I, Jensen PD, Ho DP, Batstone DJ, Tyson GW.

Curr Opin Biotechnol. 2014 Jun;27:55-64. doi: 10.1016/j.copbio.2013.11.004. Epub 2013 Nov 28. Review.

PMID:
24863897
48.

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters.

Vanwonterghem I, Jensen PD, Dennis PG, Hugenholtz P, Rabaey K, Tyson GW.

ISME J. 2014 Oct;8(10):2015-28. doi: 10.1038/ismej.2014.50. Epub 2014 Apr 17.

49.

An expanded genomic representation of the phylum cyanobacteria.

Soo RM, Skennerton CT, Sekiguchi Y, Imelfort M, Paech SJ, Dennis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P.

Genome Biol Evol. 2014 May;6(5):1031-45. doi: 10.1093/gbe/evu073.

50.

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

Angly FE, Dennis PG, Skarshewski A, Vanwonterghem I, Hugenholtz P, Tyson GW.

Microbiome. 2014 Apr 7;2:11. doi: 10.1186/2049-2618-2-11. eCollection 2014.

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