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Items: 45

1.

Polymorphic Immune Mechanisms Regulate Commensal Repertoire.

Khan AA, Yurkovetskiy L, O'Grady K, Pickard JM, de Pooter R, Antonopoulos DA, Golovkina T, Chervonsky A.

Cell Rep. 2019 Oct 15;29(3):541-550.e4. doi: 10.1016/j.celrep.2019.09.010.

PMID:
31618625
2.

Healthy infants harbor intestinal bacteria that protect against food allergy.

Feehley T, Plunkett CH, Bao R, Choi Hong SM, Culleen E, Belda-Ferre P, Campbell E, Aitoro R, Nocerino R, Paparo L, Andrade J, Antonopoulos DA, Berni Canani R, Nagler CR.

Nat Med. 2019 Mar;25(3):448-453. doi: 10.1038/s41591-018-0324-z. Epub 2019 Jan 14.

3.

Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities.

Flynn TM, Koval JC, Greenwald SM, Owens SM, Kemner KM, Antonopoulos DA.

Front Microbiol. 2017 Nov 28;8:2321. doi: 10.3389/fmicb.2017.02321. eCollection 2017.

4.

Natural polyreactive IgA antibodies coat the intestinal microbiota.

Bunker JJ, Erickson SA, Flynn TM, Henry C, Koval JC, Meisel M, Jabri B, Antonopoulos DA, Wilson PC, Bendelac A.

Science. 2017 Oct 20;358(6361). pii: eaan6619. doi: 10.1126/science.aan6619. Epub 2017 Sep 28.

5.

PATRIC as a unique resource for studying antimicrobial resistance.

Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H.

Brief Bioinform. 2019 Jul 19;20(4):1094-1102. doi: 10.1093/bib/bbx083.

PMID:
28968762
6.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.

Lee STM, Kahn SA, Delmont TO, Shaiber A, Esen ÖC, Hubert NA, Morrison HG, Antonopoulos DA, Rubin DT, Eren AM.

Microbiome. 2017 May 4;5(1):50. doi: 10.1186/s40168-017-0270-x.

7.

Mutual reinforcement of pathophysiological host-microbe interactions in intestinal stasis models.

Touw K, Ringus DL, Hubert N, Wang Y, Leone VA, Nadimpalli A, Theriault BR, Huang YE, Tune JD, Herring PB, Farrugia G, Kashyap PC, Antonopoulos DA, Chang EB.

Physiol Rep. 2017 Mar;5(6). pii: e13182. doi: 10.14814/phy2.13182.

8.

Patient-Specific Bacteroides Genome Variants in Pouchitis.

Vineis JH, Ringus DL, Morrison HG, Delmont TO, Dalal S, Raffals LH, Antonopoulos DA, Rubin DT, Eren AM, Chang EB, Sogin ML.

MBio. 2016 Nov 15;7(6). pii: e01713-16. doi: 10.1128/mBio.01713-16.

9.

Genetic deletion of the bacterial sensor NOD2 improves murine Crohn's disease-like ileitis independent of functional dysbiosis.

Corridoni D, Rodriguez-Palacios A, Di Stefano G, Di Martino L, Antonopoulos DA, Chang EB, Arseneau KO, Pizarro TT, Cominelli F.

Mucosal Immunol. 2017 Jul;10(4):971-982. doi: 10.1038/mi.2016.98. Epub 2016 Nov 16.

10.

Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis.

Meisel M, Mayassi T, Fehlner-Peach H, Koval JC, O'Brien SL, Hinterleitner R, Lesko K, Kim S, Bouziat R, Chen L, Weber CR, Mazmanian SK, Jabri B, Antonopoulos DA.

ISME J. 2017 Jan;11(1):15-30. doi: 10.1038/ismej.2016.114. Epub 2016 Sep 20.

11.

Transplanting a Microbial Organ: the Good, the Bad, and the Unknown.

Antonopoulos DA, Chang EB.

MBio. 2016 May 3;7(3). pii: e00572-16. doi: 10.1128/mBio.00572-16.

12.

Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility.

Ward MA, Pierre JF, Leal RF, Huang Y, Shogan B, Dalal SR, Weber CR, Leone VA, Musch MW, An GC, Rao MC, Rubin DT, Raffals LE, Antonopoulos DA, Sogin ML, Hyman NH, Alverdy JC, Chang EB.

Am J Physiol Gastrointest Liver Physiol. 2016 Jun 1;310(11):G973-88. doi: 10.1152/ajpgi.00017.2016. Epub 2016 Apr 14.

13.

Spatial scale drives patterns in soil bacterial diversity.

O'Brien SL, Gibbons SM, Owens SM, Hampton-Marcell J, Johnston ER, Jastrow JD, Gilbert JA, Meyer F, Antonopoulos DA.

Environ Microbiol. 2016 Jun;18(6):2039-51. doi: 10.1111/1462-2920.13231. Epub 2016 Mar 21.

14.

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

Kwon MJ, O'Loughlin EJ, Boyanov MI, Brulc JM, Johnston ER, Kemner KM, Antonopoulos DA.

PLoS One. 2016 Jan 22;11(1):e0146689. doi: 10.1371/journal.pone.0146689. eCollection 2016.

15.

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease.

Kamdar K, Khakpour S, Chen J, Leone V, Brulc J, Mangatu T, Antonopoulos DA, Chang EB, Kahn SA, Kirschner BS, Young G, DePaolo RW.

Cell Host Microbe. 2016 Jan 13;19(1):21-31. doi: 10.1016/j.chom.2015.12.006.

16.

Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A.

Bunker JJ, Flynn TM, Koval JC, Shaw DG, Meisel M, McDonald BD, Ishizuka IE, Dent AL, Wilson PC, Jabri B, Antonopoulos DA, Bendelac A.

Immunity. 2015 Sep 15;43(3):541-53. doi: 10.1016/j.immuni.2015.08.007. Epub 2015 Aug 25.

17.

Commensal bacteria protect against food allergen sensitization.

Stefka AT, Feehley T, Tripathi P, Qiu J, McCoy K, Mazmanian SK, Tjota MY, Seo GY, Cao S, Theriault BR, Antonopoulos DA, Zhou L, Chang EB, Fu YX, Nagler CR.

Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13145-50. doi: 10.1073/pnas.1412008111. Epub 2014 Aug 25.

18.

Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity.

Evans CC, LePard KJ, Kwak JW, Stancukas MC, Laskowski S, Dougherty J, Moulton L, Glawe A, Wang Y, Leone V, Antonopoulos DA, Smith D, Chang EB, Ciancio MJ.

PLoS One. 2014 Mar 26;9(3):e92193. doi: 10.1371/journal.pone.0092193. eCollection 2014.

19.

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.

Huse SM, Young VB, Morrison HG, Antonopoulos DA, Kwon J, Dalal S, Arrieta R, Hubert NA, Shen L, Vineis JH, Koval JC, Sogin ML, Chang EB, Raffals LE.

Microbiome. 2014 Feb 14;2(1):5. doi: 10.1186/2049-2618-2-5.

20.

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.

Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML.

Microbiome. 2013 Mar 4;1(1):9. doi: 10.1186/2049-2618-1-9.

21.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.

Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM.

Microbiome. 2013 Mar 4;1(1):8. doi: 10.1186/2049-2618-1-8.

22.

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants.

Claud EC, Keegan KP, Brulc JM, Lu L, Bartels D, Glass E, Chang EB, Meyer F, Antonopoulos DA.

Microbiome. 2013 Jul 10;1(1):20. doi: 10.1186/2049-2618-1-20.

23.

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice.

Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB.

Nature. 2012 Jul 5;487(7405):104-8. doi: 10.1038/nature11225.

24.

Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010.

O'Brien SL, Glass EM, Brulc JM, Gilbert JA, Antonopoulos DA, Meyer F.

Stand Genomic Sci. 2011 Nov 30;5(2):198-202. doi: 10.4056/sigs.1874546. Epub 2011 Nov 15.

25.

Geochemical and microbiological processes contributing to the transformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in contaminated aquifer material.

Kwon MJ, O'Loughlin EJ, Antonopoulos DA, Finneran KT.

Chemosphere. 2011 Aug;84(9):1223-30. doi: 10.1016/j.chemosphere.2011.05.027. Epub 2011 Jun 12.

PMID:
21664641
26.

BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae).

Lemke S, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U.

BMC Genomics. 2011 May 31;12:278. doi: 10.1186/1471-2164-12-278.

27.

Diversity of bacteria at healthy human conjunctiva.

Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, Revanna KV, Gao X, Antonopoulos DA, Slepak VZ, Shestopalov VI.

Invest Ophthalmol Vis Sci. 2011 Jul 20;52(8):5408-13. doi: 10.1167/iovs.10-6939.

28.

Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon.

Wang Y, Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, Chervonsky A, Chang EB.

PLoS One. 2010 Oct 22;5(10):e13607. doi: 10.1371/journal.pone.0013607.

29.

Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.

Wang Y, Antonopoulos DA, Zhu X, Harrell L, Hanan I, Alverdy JC, Meyer F, Musch MW, Young VB, Chang EB.

Appl Microbiol Biotechnol. 2010 Dec;88(6):1333-42. doi: 10.1007/s00253-010-2921-8. Epub 2010 Oct 8.

30.

Abundance and diversity of dockerin-containing proteins in the fiber-degrading rumen bacterium, Ruminococcus flavefaciens FD-1.

Rincon MT, Dassa B, Flint HJ, Travis AJ, Jindou S, Borovok I, Lamed R, Bayer EA, Henrissat B, Coutinho PM, Antonopoulos DA, Berg Miller ME, White BA.

PLoS One. 2010 Aug 30;5(8):e12476. doi: 10.1371/journal.pone.0012476.

31.

Metagenomic profiling of a microbial assemblage associated with the California mussel: a node in networks of carbon and nitrogen cycling.

Pfister CA, Meyer F, Antonopoulos DA.

PLoS One. 2010 May 6;5(5):e10518. doi: 10.1371/journal.pone.0010518.

32.

Maternal activation of gap genes in the hover fly Episyrphus.

Lemke S, Busch SE, Antonopoulos DA, Meyer F, Domanus MH, Schmidt-Ott U.

Development. 2010 May;137(10):1709-19. doi: 10.1242/dev.046649. Erratum in: Development. 2010 Aug 1;137(15):2604.

33.

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.

Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F.

PLoS Comput Biol. 2009 Dec;5(12):e1000593. doi: 10.1371/journal.pcbi.1000593. Epub 2009 Dec 11.

34.

Diversity and strain specificity of plant cell wall degrading enzymes revealed by the draft genome of Ruminococcus flavefaciens FD-1.

Berg Miller ME, Antonopoulos DA, Rincon MT, Band M, Bari A, Akraiko T, Hernandez A, Thimmapuram J, Henrissat B, Coutinho PM, Borovok I, Jindou S, Lamed R, Flint HJ, Bayer EA, White BA.

PLoS One. 2009 Aug 14;4(8):e6650. doi: 10.1371/journal.pone.0006650.

35.

Perturbation of the small intestine microbial ecology by streptomycin alters pathology in a Salmonella enterica serovar typhimurium murine model of infection.

Garner CD, Antonopoulos DA, Wagner B, Duhamel GE, Keresztes I, Ross DA, Young VB, Altier C.

Infect Immun. 2009 Jul;77(7):2691-702. doi: 10.1128/IAI.01570-08. Epub 2009 May 11.

36.

16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis.

Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, Antonopoulos DA, Chang EB, Claud EC.

ISME J. 2009 Aug;3(8):944-54. doi: 10.1038/ismej.2009.37. Epub 2009 Apr 16.

37.

Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation.

Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB.

Infect Immun. 2009 Jun;77(6):2367-75. doi: 10.1128/IAI.01520-08. Epub 2009 Mar 23.

38.

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases.

Brulc JM, Antonopoulos DA, Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, Coutinho PM, Henrissat B, Nelson KE, White BA.

Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1948-53. doi: 10.1073/pnas.0806191105. Epub 2009 Jan 30.

39.

Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples.

Galbraith EA, Antonopoulos DA, White BA.

Methods Mol Biol. 2008;410:295-333.

PMID:
18642606
40.

Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea.

Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, Schmidt TM, Young VB.

J Infect Dis. 2008 Feb 1;197(3):435-8. doi: 10.1086/525047.

PMID:
18199029
41.

Conservation and divergence in cellulosome architecture between two strains of Ruminococcus flavefaciens.

Jindou S, Borovok I, Rincon MT, Flint HJ, Antonopoulos DA, Berg ME, White BA, Bayer EA, Lamed R.

J Bacteriol. 2006 Nov;188(22):7971-6. Epub 2006 Sep 22.

42.
43.
45.

Characterization of the gene encoding glutamate dehydrogenase ( gdhA) from the ruminal bacterium Ruminococcus flavefaciens FD-1.

Antonopoulos DA, Aminov RI, Duncan PA, White BA, Mackie RI.

Arch Microbiol. 2003 Mar;179(3):184-90. Epub 2003 Feb 12.

PMID:
12610723

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