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Items: 34

1.

Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women.

Alemán JO, Bokulich NA, Swann JR, Walker JM, De Rosa JC, Battaglia T, Costabile A, Pechlivanis A, Liang Y, Breslow JL, Blaser MJ, Holt PR.

J Transl Med. 2018 Sep 3;16(1):244. doi: 10.1186/s12967-018-1619-z.

2.

Loss of HDAC6 alters gut microbiota and worsens obesity.

Lieber AD, Beier UH, Xiao H, Wilkins BJ, Jiao J, Li XS, Schugar RC, Strauch CM, Wang Z, Brown JM, Hazen SL, Bokulich NA, Ruggles KV, Akimova T, Hancock WW, Blaser MJ.

FASEB J. 2018 Aug 13:fj201701586R. doi: 10.1096/fj.201701586R. [Epub ahead of print]

PMID:
30102568
3.

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J.

Microbiome. 2018 May 17;6(1):90. doi: 10.1186/s40168-018-0470-z.

4.

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
5.

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG.

mSystems. 2016 Oct 18;1(5). pii: e00062-16. eCollection 2016 Sep-Oct.

6.

Antibiotics, birth mode, and diet shape microbiome maturation during early life.

Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, D Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ.

Sci Transl Med. 2016 Jun 15;8(343):343ra82. doi: 10.1126/scitranslmed.aad7121.

7.

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

Bokulich NA, Collins TS, Masarweh C, Allen G, Heymann H, Ebeler SE, Mills DA.

MBio. 2016 Jun 14;7(3). pii: e00631-16. doi: 10.1128/mBio.00631-16.

8.

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet.

Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ.

Genome Med. 2016 Apr 27;8(1):48.

9.

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer.

Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC.

Nat Med. 2016 Mar;22(3):250-3. doi: 10.1038/nm.4039. Epub 2016 Feb 1.

10.

Celecoxib does not alter intestinal microbiome in a longitudinal diet-controlled study.

Bokulich NA, Battaglia T, Aleman JO, Walker JM, Blaser MJ, Holt PR.

Clin Microbiol Infect. 2016 May;22(5):464-5. doi: 10.1016/j.cmi.2016.01.013. Epub 2016 Jan 22. No abstract available.

11.

A new perspective on microbial landscapes within food production.

Bokulich NA, Lewis ZT, Boundy-Mills K, Mills DA.

Curr Opin Biotechnol. 2016 Feb;37:182-189. doi: 10.1016/j.copbio.2015.12.008. Epub 2016 Jan 11. Review.

12.

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.

Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ.

Nat Commun. 2015 Jun 30;6:7486. doi: 10.1038/ncomms8486.

13.

Microbial biogeography of the transnational fermented milk matsoni.

Bokulich NA, Amiranashvili L, Chitchyan K, Ghazanchyan N, Darbinyan K, Gagelidze N, Sadunishvili T, Goginyan V, Kvesitadze G, Torok T, Mills DA.

Food Microbiol. 2015 Sep;50:12-9. doi: 10.1016/j.fm.2015.01.018. Epub 2015 Feb 10.

PMID:
25998810
14.

The soil microbiome influences grapevine-associated microbiota.

Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilbert JA.

MBio. 2015 Mar 24;6(2). pii: e02527-14. doi: 10.1128/mBio.02527-14.

15.

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance.

Bokulich NA, Bergsveinson J, Ziola B, Mills DA.

Elife. 2015 Mar 10;4. doi: 10.7554/eLife.04634.

16.

A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome.

Bokulich NA, Blaser MJ.

Cell Metab. 2014 Nov 4;20(5):701-703. doi: 10.1016/j.cmet.2014.10.012. Epub 2014 Nov 4.

17.

Human milk glycomics and gut microbial genomics in infant feces show a correlation between human milk oligosaccharides and gut microbiota: a proof-of-concept study.

De Leoz ML, Kalanetra KM, Bokulich NA, Strum JS, Underwood MA, German JB, Mills DA, Lebrilla CB.

J Proteome Res. 2015 Jan 2;14(1):491-502. doi: 10.1021/pr500759e. Epub 2014 Oct 28.

18.

Indigenous bacteria and fungi drive traditional kimoto sake fermentations.

Bokulich NA, Ohta M, Lee M, Mills DA.

Appl Environ Microbiol. 2014 Sep;80(17):5522-9. doi: 10.1128/AEM.00663-14. Epub 2014 Jun 27.

19.

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.

Bokulich NA, Thorngate JH, Richardson PM, Mills DA.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):E139-48. doi: 10.1073/pnas.1317377110. Epub 2013 Nov 25.

20.

Prebiotic oligosaccharides in premature infants.

Underwood MA, Kalanetra KM, Bokulich NA, Mirmiran M, Barile D, Tancredi DJ, German JB, Lebrilla CB, Mills DA.

J Pediatr Gastroenterol Nutr. 2014 Mar;58(3):352-60. doi: 10.1097/MPG.0000000000000211.

PMID:
24135979
21.

A comparison of two probiotic strains of bifidobacteria in premature infants.

Underwood MA, Kalanetra KM, Bokulich NA, Lewis ZT, Mirmiran M, Tancredi DJ, Mills DA.

J Pediatr. 2013 Dec;163(6):1585-1591.e9. doi: 10.1016/j.jpeds.2013.07.017. Epub 2013 Aug 29.

22.

Monitoring Seasonal Changes in Winery-Resident Microbiota.

Bokulich NA, Ohta M, Richardson PM, Mills DA.

PLoS One. 2013 Jun 19;8(6):e66437. doi: 10.1371/journal.pone.0066437. Print 2013.

23.

Facility-specific "house" microbiome drives microbial landscapes of artisan cheesemaking plants.

Bokulich NA, Mills DA.

Appl Environ Microbiol. 2013 Sep;79(17):5214-23. doi: 10.1128/AEM.00934-13. Epub 2013 Jun 21.

24.

Surface microbes in the neonatal intensive care unit: changes with routine cleaning and over time.

Bokulich NA, Mills DA, Underwood MA.

J Clin Microbiol. 2013 Aug;51(8):2617-24. doi: 10.1128/JCM.00898-13. Epub 2013 Jun 5.

25.

The microbiology of malting and brewing.

Bokulich NA, Bamforth CW.

Microbiol Mol Biol Rev. 2013 Jun;77(2):157-72. doi: 10.1128/MMBR.00060-12. Review.

26.

Probiotic administration in congenital heart disease: a pilot study.

Ellis CL, Bokulich NA, Kalanetra KM, Mirmiran M, Elumalai J, Haapanen L, Schegg T, Rutledge JC, Raff G, Mills DA, Underwood MA.

J Perinatol. 2013 Sep;33(9):691-7. doi: 10.1038/jp.2013.41. Epub 2013 Apr 18.

27.

Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities.

Bokulich NA, Mills DA.

Appl Environ Microbiol. 2013 Apr;79(8):2519-26. doi: 10.1128/AEM.03870-12. Epub 2013 Feb 1.

28.

Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities.

Lewis ZT, Bokulich NA, Kalanetra KM, Ruiz-Moyano S, Underwood MA, Mills DA.

Anaerobe. 2013 Feb;19:62-9. doi: 10.1016/j.anaerobe.2012.12.005. Epub 2012 Dec 20.

29.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG.

Nat Methods. 2013 Jan;10(1):57-9. doi: 10.1038/nmeth.2276. Epub 2012 Dec 2.

30.

Routine habitat change: a source of unrecognized transient alteration of intestinal microbiota in laboratory mice.

Ma BW, Bokulich NA, Castillo PA, Kananurak A, Underwood MA, Mills DA, Bevins CL.

PLoS One. 2012;7(10):e47416. doi: 10.1371/journal.pone.0047416. Epub 2012 Oct 17.

31.

Next-generation approaches to the microbial ecology of food fermentations.

Bokulich NA, Mills DA.

BMB Rep. 2012 Jul;45(7):377-89.

32.

Next-generation sequencing reveals significant bacterial diversity of botrytized wine.

Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA.

PLoS One. 2012;7(5):e36357. doi: 10.1371/journal.pone.0036357. Epub 2012 May 1.

33.

Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale.

Bokulich NA, Bamforth CW, Mills DA.

PLoS One. 2012;7(4):e35507. doi: 10.1371/journal.pone.0035507. Epub 2012 Apr 18.

34.

Differentiation of mixed lactic acid bacteria communities in beverage fermentations using targeted terminal restriction fragment length polymorphism.

Bokulich NA, Mills DA.

Food Microbiol. 2012 Aug;31(1):126-32. doi: 10.1016/j.fm.2012.02.007. Epub 2012 Feb 21.

PMID:
22475950

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