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Items: 1 to 50 of 115

1.

Earth Microbiome Project and Global Systems Biology.

Gilbert JA, Jansson JK, Knight R.

mSystems. 2018 Apr 10;3(3). pii: e00217-17. doi: 10.1128/mSystems.00217-17. eCollection 2018 May-Jun. No abstract available.

2.

Current understanding of the human microbiome.

Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R.

Nat Med. 2018 Apr 10;24(4):392-400. doi: 10.1038/nm.4517. Review.

PMID:
29634682
3.

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.

4.

The soil microbiome-from metagenomics to metaphenomics.

Jansson JK, Hofmockel KS.

Curr Opin Microbiol. 2018 Feb 15;43:162-168. doi: 10.1016/j.mib.2018.01.013. [Epub ahead of print] Review.

5.

A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

PMID:
29088705
6.

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome.

Maier TV, Lucio M, Lee LH, VerBerkmoes NC, Brislawn CJ, Bernhardt J, Lamendella R, McDermott JE, Bergeron N, Heinzmann SS, Morton JT, González A, Ackermann G, Knight R, Riedel K, Krauss RM, Schmitt-Kopplin P, Jansson JK.

MBio. 2017 Oct 17;8(5). pii: e01343-17. doi: 10.1128/mBio.01343-17.

7.

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill.

Handley KM, Piceno YM, Hu P, Tom LM, Mason OU, Andersen GL, Jansson JK, Gilbert JA.

ISME J. 2017 Nov;11(11):2569-2583. doi: 10.1038/ismej.2017.110. Epub 2017 Aug 4.

8.

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes.

Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M.

Microb Ecol. 2018 Jan;75(1):123-139. doi: 10.1007/s00248-017-1028-5. Epub 2017 Jul 12.

PMID:
28702706
9.

Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach.

Musumeci MA, Lozada M, Rial DV, Mac Cormack WP, Jansson JK, Sjöling S, Carroll J, Dionisi HM.

Mar Drugs. 2017 Apr 9;15(4). pii: E114. doi: 10.3390/md15040114.

10.

Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership.

Bernstein HC, McClure RS, Thiel V, Sadler NC, Kim YM, Chrisler WB, Hill EA, Bryant DA, Romine MF, Jansson JK, Fredrickson JK, Beliaev AS.

mSystems. 2017 Mar 7;2(2). pii: e00181-16. doi: 10.1128/mSystems.00181-16. eCollection 2017 Mar-Apr.

11.

Dynamics of the human gut microbiome in inflammatory bowel disease.

Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK.

Nat Microbiol. 2017 Feb 13;2:17004. doi: 10.1038/nmicrobiol.2017.4.

12.

Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk.

Bergeron N, Williams PT, Lamendella R, Faghihnia N, Grube A, Li X, Wang Z, Knight R, Jansson JK, Hazen SL, Krauss RM.

Br J Nutr. 2016 Dec;116(12):2020-2029. doi: 10.1017/S0007114516004165. Epub 2016 Dec 20.

13.

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome.

Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM, Fansler SJ, Casey CP, Miller DR, Huang Y, Karpen GH, Celniker SE, Brown JB, Borenstein E, Jansson JK, Metz TO, Mao JH.

Nat Microbiol. 2016 Nov 28;2:16221. doi: 10.1038/nmicrobiol.2016.221.

PMID:
27892936
14.

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes.

White RA 3rd, Bottos EM, Roy Chowdhury T, Zucker JD, Brislawn CJ, Nicora CD, Fansler SJ, Glaesemann KR, Glass K, Jansson JK.

mSystems. 2016 Jun 28;1(3). pii: e00045-16. eCollection 2016 May-Jun.

15.

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.

Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R.

mSystems. 2015 Dec 22;1(1). pii: e00009-15. eCollection 2016 Jan-Feb.

16.

Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions.

López JL, Golemba M, Hernández E, Lozada M, Dionisi H, Jansson JK, Carroll J, Lundgren L, Sjöling S, Mac Cormack WP.

FEMS Microbiol Ecol. 2017 Jan 1;93(1). doi: 10.1093/femsec/fiw216.

PMID:
27815287
17.

Trade-offs between microbiome diversity and productivity in a stratified microbial mat.

Bernstein HC, Brislawn C, Renslow RS, Dana K, Morton B, Lindemann SR, Song HS, Atci E, Beyenal H, Fredrickson JK, Jansson JK, Moran JJ.

ISME J. 2017 Feb;11(2):405-414. doi: 10.1038/ismej.2016.133. Epub 2016 Nov 1.

18.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

Armstrong A, Valverde A, Ramond JB, Makhalanyane TP, Jansson JK, Hopkins DW, Aspray TJ, Seely M, Trindade MI, Cowan DA.

Sci Rep. 2016 Sep 29;6:34434. doi: 10.1038/srep34434.

19.

A multi-omic future for microbiome studies.

Jansson JK, Baker ES.

Nat Microbiol. 2016 Apr 26;1:16049. doi: 10.1038/nmicrobiol.2016.49. No abstract available.

PMID:
27572648
20.

Gut Microbial Alterations Associated With Protection From Autoimmune Uveitis.

Nakamura YK, Metea C, Karstens L, Asquith M, Gruner H, Moscibrocki C, Lee I, Brislawn CJ, Jansson JK, Rosenbaum JT, Lin P.

Invest Ophthalmol Vis Sci. 2016 Jul 1;57(8):3747-58. doi: 10.1167/iovs.16-19733.

21.

Microbiome-wide association studies link dynamic microbial consortia to disease.

Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R.

Nature. 2016 Jul 7;535(7610):94-103. doi: 10.1038/nature18850. Review.

PMID:
27383984
22.

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments.

Matos MN, Lozada M, Anselmino LE, Musumeci MA, Henrissat B, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lundgren L, Dionisi HM.

Environ Microbiol. 2016 Dec;18(12):4471-4484. doi: 10.1111/1462-2920.13433. Epub 2016 Jul 18.

PMID:
27348213
23.

Spotlight on… Janet K. Jansson.

Jansson JK.

FEMS Microbiol Lett. 2016 Aug;363(15). pii: fnw135. doi: 10.1093/femsle/fnw135. Epub 2016 Jun 23. No abstract available.

24.

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation.

Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E.

mSystems. 2016 Jan-Feb;1(1). pii: e00013-15. Epub 2016 Jan 19.

25.

Back to the Future of Soil Metagenomics.

Nesme J, Achouak W, Agathos SN, Bailey M, Baldrian P, Brunel D, Frostegård Å, Heulin T, Jansson JK, Jurkevitch E, Kruus KL, Kowalchuk GA, Lagares A, Lappin-Scott HM, Lemanceau P, Le Paslier D, Mandic-Mulec I, Murrell JC, Myrold DD, Nalin R, Nannipieri P, Neufeld JD, O'Gara F, Parnell JJ, Pühler A, Pylro V, Ramos JL, Roesch LF, Schloter M, Schleper C, Sczyrba A, Sessitsch A, Sjöling S, Sørensen J, Sørensen SJ, Tebbe CC, Topp E, Tsiamis G, van Elsas JD, van Keulen G, Widmer F, Wagner M, Zhang T, Zhang X, Zhao L, Zhu YG, Vogel TM, Simonet P.

Front Microbiol. 2016 Feb 10;7:73. doi: 10.3389/fmicb.2016.00073. eCollection 2016. No abstract available.

26.

Tools for the Microbiome: Nano and Beyond.

Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GC, Wright AT, Young TD.

ACS Nano. 2016 Jan 26;10(1):6-37. doi: 10.1021/acsnano.5b07826. Epub 2015 Dec 22. Review.

PMID:
26695070
27.

Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage.

Dicksved J, Jansson JK, Lindberg JE.

J Anim Sci Biotechnol. 2015 Dec 18;6:53. doi: 10.1186/s40104-015-0054-8. eCollection 2015.

28.

Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice.

Mao JH, Langley SA, Huang Y, Hang M, Bouchard KE, Celniker SE, Brown JB, Jansson JK, Karpen GH, Snijders AM.

Sci Rep. 2015 Nov 9;5:16247. doi: 10.1038/srep16247.

29.

Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments.

Guibert LM, Loviso CL, Borglin S, Jansson JK, Dionisi HM, Lozada M.

Microb Ecol. 2016 Jan;71(1):100-12. doi: 10.1007/s00248-015-0698-0. Epub 2015 Nov 7.

PMID:
26547568
30.

MICROBIOME. A unified initiative to harness Earth's microbiomes.

Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA; Unified Microbiome Initiative Consortium.

Science. 2015 Oct 30;350(6260):507-8. doi: 10.1126/science.aac8480. Epub 2015 Oct 28. No abstract available.

PMID:
26511287
31.

Complete Genome Sequence of Bacillus amyloliquefaciens Strain Co1-6, a Plant Growth-Promoting Rhizobacterium of Calendula officinalis.

Köberl M, White RA 3rd, Erschen S, Spanberger N, El-Arabi TF, Jansson JK, Berg G.

Genome Announc. 2015 Aug 13;3(4). pii: e00862-15. doi: 10.1128/genomeA.00862-15.

32.

Insights into the respiratory tract microbiota of patients with cystic fibrosis during early Pseudomonas aeruginosa colonization.

Keravec M, Mounier J, Prestat E, Vallet S, Jansson JK, Burgaud G, Rosec S, Gouriou S, Rault G, Coton E, Barbier G, Héry-Arnaud G.

Springerplus. 2015 Aug 9;4:405. doi: 10.1186/s40064-015-1207-0. eCollection 2015.

33.

Draft Genome Sequence of Paenibacillus polymyxa Strain Mc5Re-14, an Antagonistic Root Endophyte of Matricaria chamomilla.

Köberl M, White RA 3rd, Erschen S, El-Arabi TF, Jansson JK, Berg G.

Genome Announc. 2015 Aug 6;3(4). pii: e00861-15. doi: 10.1128/genomeA.00861-15.

34.

Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens.

Köberl M, White RA 3rd, Erschen S, El-Arabi TF, Jansson JK, Berg G.

Genome Announc. 2015 Aug 6;3(4). pii: e00860-15. doi: 10.1128/genomeA.00860-15.

35.

Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies.

Carrillo-Araujo M, Taş N, Alcántara-Hernández RJ, Gaona O, Schondube JE, Medellín RA, Jansson JK, Falcón LI.

Front Microbiol. 2015 May 19;6:447. doi: 10.3389/fmicb.2015.00447. eCollection 2015.

36.

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses.

Schostag M, Stibal M, Jacobsen CS, Bælum J, Taş N, Elberling B, Jansson JK, Semenchuk P, Priemé A.

Front Microbiol. 2015 Apr 30;6:399. doi: 10.3389/fmicb.2015.00399. eCollection 2015.

37.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.

Hultman J, Waldrop MP, Mackelprang R, David MM, McFarland J, Blazewicz SJ, Harden J, Turetsky MR, McGuire AD, Shah MB, VerBerkmoes NC, Lee LH, Mavrommatis K, Jansson JK.

Nature. 2015 May 14;521(7551):208-12. doi: 10.1038/nature14238. Epub 2015 Mar 4.

PMID:
25739499
38.

FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.

Prestat E, David MM, Hultman J, Taş N, Lamendella R, Dvornik J, Mackelprang R, Myrold DD, Jumpponen A, Tringe SG, Holman E, Mavromatis K, Jansson JK.

Nucleic Acids Res. 2014 Oct 29;42(19):e145. doi: 10.1093/nar/gku702. Epub 2014 Sep 26.

39.

The Earth Microbiome project: successes and aspirations.

Gilbert JA, Jansson JK, Knight R.

BMC Biol. 2014 Aug 22;12:69. doi: 10.1186/s12915-014-0069-1. No abstract available.

40.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP.

PLoS Biol. 2014 Aug 5;12(8):e1001920. doi: 10.1371/journal.pbio.1001920. eCollection 2014 Aug.

41.

Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill.

Mason OU, Han J, Woyke T, Jansson JK.

Front Microbiol. 2014 Jul 8;5:332. doi: 10.3389/fmicb.2014.00332. eCollection 2014.

42.

The microbial ecology of permafrost.

Jansson JK, Taş N.

Nat Rev Microbiol. 2014 Jun;12(6):414-25. doi: 10.1038/nrmicro3262. Epub 2014 May 12. Review.

PMID:
24814065
43.

Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities.

Lamendella R, Strutt S, Borglin S, Chakraborty R, Tas N, Mason OU, Hultman J, Prestat E, Hazen TC, Jansson JK.

Front Microbiol. 2014 Apr 3;5:130. doi: 10.3389/fmicb.2014.00130. eCollection 2014.

44.

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments.

Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA.

Front Microbiol. 2014 Mar 25;5:108. doi: 10.3389/fmicb.2014.00108. eCollection 2014.

45.

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest.

Taş N, Prestat E, McFarland JW, Wickland KP, Knight R, Berhe AA, Jorgenson T, Waldrop MP, Jansson JK.

ISME J. 2014 Sep;8(9):1904-19. doi: 10.1038/ismej.2014.36. Epub 2014 Apr 10.

46.

Tackling soil diversity with the assembly of large, complex metagenomes.

Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4904-9. doi: 10.1073/pnas.1402564111. Epub 2014 Mar 14. Erratum in: Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):6115.

47.

Microbial ecology of chlorinated solvent biodegradation.

David MM, Cecillon S, Warne BM, Prestat E, Jansson JK, Vogel TM.

Environ Microbiol. 2015 Dec;17(12):4835-50. doi: 10.1111/1462-2920.12413. Epub 2014 Mar 17.

PMID:
24517489
48.

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.

Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK.

ISME J. 2014 Jul;8(7):1464-75. doi: 10.1038/ismej.2013.254. Epub 2014 Jan 23.

49.

Meta-analyses of studies of the human microbiota.

Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R.

Genome Res. 2013 Oct;23(10):1704-14. doi: 10.1101/gr.151803.112. Epub 2013 Jul 16.

50.

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies.

Nicora CD, Anderson BJ, Callister SJ, Norbeck AD, Purvine SO, Jansson JK, Mason OU, David MM, Jurelevicius D, Smith RD, Lipton MS.

Proteomics. 2013 Oct;13(18-19):2776-85. doi: 10.1002/pmic.201300003. Epub 2013 Aug 16.

PMID:
23776032

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