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Items: 1 to 50 of 107

1.

Dietary Patterns Correspond with Microbiome Composition (FS07-02-19).

Johnson A, Vangay P, Knights D.

Curr Dev Nutr. 2019 Jun 13;3(Suppl 1). pii: nzz040.FS07-02-19. doi: 10.1093/cdn/nzz040.FS07-02-19. eCollection 2019 Jun.

2.

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.

Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, Kim AD, Shmagel AK, Syed AN; Personalized Microbiome Class Students, Walter J, Menon R, Koecher K, Knights D.

Cell Host Microbe. 2019 Jun 12;25(6):789-802.e5. doi: 10.1016/j.chom.2019.05.005.

PMID:
31194939
3.

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders.

Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC.

Nat Commun. 2019 May 1;10(1):2012. doi: 10.1038/s41467-019-09964-7.

4.

Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks.

Vangay P, Hillmann BM, Knights D.

Gigascience. 2019 May 1;8(5). pii: giz042. doi: 10.1093/gigascience/giz042.

5.

Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus).

Clayton JB, Shields-Cutler RR, Hoops SL, Al-Ghalith GA, Sha JCM, Johnson TJ, Knights D.

Am J Primatol. 2019 Apr 18:e22977. doi: 10.1002/ajp.22977. [Epub ahead of print]

PMID:
30997937
6.

Nutrient-based diet modifications impact on the gut microbiome of the Javan slow loris (Nycticebus javanicus).

Cabana F, Clayton JB, Nekaris KAI, Wirdateti W, Knights D, Seedorf H.

Sci Rep. 2019 Mar 11;9(1):4078. doi: 10.1038/s41598-019-40911-0.

7.

Genetic effects on the commensal microbiota in inflammatory bowel disease patients.

Aschard H, Laville V, Tchetgen ET, Knights D, Imhann F, Seksik P, Zaitlen N, Silverberg MS, Cosnes J, Weersma RK, Xavier R, Beaugerie L, Skurnik D, Sokol H.

PLoS Genet. 2019 Mar 8;15(3):e1008018. doi: 10.1371/journal.pgen.1008018. eCollection 2019 Mar.

8.

The Effects of Glucosamine and Chondroitin Sulfate on Gut Microbial Composition: A Systematic Review of Evidence from Animal and Human Studies.

Shmagel A, Demmer R, Knights D, Butler M, Langsetmo L, Lane NE, Ensrud K.

Nutrients. 2019 Jan 30;11(2). pii: E294. doi: 10.3390/nu11020294.

9.

Characterization of Campylobacter jejuni, Campylobacter upsaliensis, and a novel Campylobacter sp. in a captive non-human primate zoological collection.

Clayton JB, Danzeisen JL, Johnson TJ, Trent AM, Hayer SS, Murphy T, Wuenschmann A, Elder M, Shen Z, Mannion A, Bryant E, Knights D, Fox JG.

J Med Primatol. 2019 Apr;48(2):114-122. doi: 10.1111/jmp.12393. Epub 2018 Dec 9.

PMID:
30536921
10.

Evaluating the Information Content of Shallow Shotgun Metagenomics.

Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D.

mSystems. 2018 Nov 13;3(6). pii: e00069-18. doi: 10.1128/mSystems.00069-18. eCollection 2018 Nov-Dec.

11.

US Immigration Westernizes the Human Gut Microbiome.

Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R, Paw B, Pergament SL, Saenyakul P, Xiong M, Kim AD, Kim G, Masopust D, Martens EC, Angkurawaranon C, McGready R, Kashyap PC, Culhane-Pera KA, Knights D.

Cell. 2018 Nov 1;175(4):962-972.e10. doi: 10.1016/j.cell.2018.10.029.

12.

Urinary microbiome associated with chronic allograft dysfunction in kidney transplant recipients.

Wu JF, Muthusamy A, Al-Ghalith GA, Knights D, Guo B, Wu B, Remmel RP, Schladt DP, Alegre ML, Oetting WS, Jacobson PA, Israni AK.

Clin Transplant. 2018 Dec;32(12):e13436. doi: 10.1111/ctr.13436. Epub 2018 Nov 18.

PMID:
30372560
13.

An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study.

Muñiz Pedrogo DA, Chen J, Hillmann B, Jeraldo P, Al-Ghalith G, Taneja V, Davis JM, Knights D, Nelson H, Faubion WA, Raffals L, Kashyap PC.

Inflamm Bowel Dis. 2019 Apr 11;25(5):902-913. doi: 10.1093/ibd/izy318.

PMID:
30321331
14.

High-Throughput flaA Short Variable Region Sequencing to Assess Campylobacter Diversity in Fecal Samples From Birds.

Zhang Q, Al-Ghalith GA, Kobayashi M, Segawa T, Maeda M, Okabe S, Knights D, Ishii S.

Front Microbiol. 2018 Sep 25;9:2201. doi: 10.3389/fmicb.2018.02201. eCollection 2018.

15.

'Please make comfortable': prescribing opioids in the wake of Gosport.

Knights D, Knights F, Barclay S.

Br J Gen Pract. 2018 Oct;68(675):462-463. doi: 10.3399/bjgp18X698705. No abstract available.

16.

Essentials of Global Health: a book for students, by students.

Bhopal A, Knights D, Knights F, Bertani L, Gopfert A, Guinto R, Langham F, Lefebvre A, Turner-Moss E, Wanjau W, Wiley E, Kumar P, Sethia B; Essentials of Global Health.

Lancet Glob Health. 2018 Oct;6(10):e1069. doi: 10.1016/S2214-109X(18)30379-6. No abstract available.

17.

CLOUD: a non-parametric detection test for microbiome outliers.

Montassier E, Al-Ghalith GA, Hillmann B, Viskocil K, Kabage AJ, McKinlay CE, Sadowsky MJ, Khoruts A, Knights D.

Microbiome. 2018 Aug 6;6(1):137. doi: 10.1186/s40168-018-0514-4.

18.

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model.

Clayton JB, Al-Ghalith GA, Long HT, Tuan BV, Cabana F, Huang H, Vangay P, Ward T, Minh VV, Tam NA, Dat NT, Travis DA, Murtaugh MP, Covert H, Glander KE, Nadler T, Toddes B, Sha JCM, Singer R, Knights D, Johnson TJ.

Sci Rep. 2018 Jul 24;8(1):11159. doi: 10.1038/s41598-018-29277-x.

19.

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity.

Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ.

Elife. 2018 Jul 25;7. pii: e37816. doi: 10.7554/eLife.37816.

20.

Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment.

Burns MB, Montassier E, Abrahante J, Priya S, Niccum DE, Khoruts A, Starr TK, Knights D, Blekhman R.

PLoS Genet. 2018 Jun 20;14(6):e1007376. doi: 10.1371/journal.pgen.1007376. eCollection 2018 Jun.

21.

The gut microbiome of nonhuman primates: Lessons in ecology and evolution.

Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ.

Am J Primatol. 2018 Jun;80(6):e22867. doi: 10.1002/ajp.22867. Epub 2018 Jun 4. Review.

PMID:
29862519
22.

American Gut: an Open Platform for Citizen Science Microbiome Research.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

23.

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies.

Shields-Cutler RR, Al-Ghalith GA, Yassour M, Knights D.

Front Microbiol. 2018 Apr 23;9:785. doi: 10.3389/fmicb.2018.00785. eCollection 2018.

24.

SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control.

Al-Ghalith GA, Hillmann B, Ang K, Shields-Cutler R, Knights D.

mSystems. 2018 Apr 24;3(3). pii: e00202-17. doi: 10.1128/mSystems.00202-17. eCollection 2018 May-Jun.

25.

Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice.

Le Bastard Q, Ward T, Sidiropoulos D, Hillmann BM, Chun CL, Sadowsky MJ, Knights D, Montassier E.

Sci Rep. 2018 Apr 18;8(1):6219. doi: 10.1038/s41598-018-24342-x.

26.

Development of the Human Mycobiome over the First Month of Life and across Body Sites.

Ward TL, Dominguez-Bello MG, Heisel T, Al-Ghalith G, Knights D, Gale CA.

mSystems. 2018 Mar 6;3(3). pii: e00140-17. doi: 10.1128/mSystems.00140-17. eCollection 2018 May-Jun.

27.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.

PMID:
29440750
28.

Pretransplant Gut Colonization with Intrinsically Vancomycin-Resistant Enterococci (E. gallinarum and E. casseliflavus) and Outcomes of Allogeneic Hematopoietic Cell Transplantation.

Rashidi A, Ebadi M, Shields-Cutler RR, DeFor TE, Al-Ghalith GA, Ferrieri P, Young JH, Dunny GM, Knights D, Weisdorf DJ.

Biol Blood Marrow Transplant. 2018 Jun;24(6):1260-1263. doi: 10.1016/j.bbmt.2018.01.025. Epub 2018 Jan 31.

29.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.

30.

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications.

Le Bastard Q, Al-Ghalith GA, Grégoire M, Chapelet G, Javaudin F, Dailly E, Batard E, Knights D, Montassier E.

Aliment Pharmacol Ther. 2018 Feb;47(3):332-345. doi: 10.1111/apt.14451. Epub 2017 Dec 5.

PMID:
29205415
31.

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice.

Schulfer AF, Battaglia T, Alvarez Y, Bijnens L, Ruiz VE, Ho M, Robinson S, Ward T, Cox LM, Rogers AB, Knights D, Sartor RB, Blaser MJ.

Nat Microbiol. 2018 Feb;3(2):234-242. doi: 10.1038/s41564-017-0075-5. Epub 2017 Nov 27.

32.

HOMINID: a framework for identifying associations between host genetic variation and microbiome composition.

Lynch J, Tang K, Priya S, Sands J, Sands M, Tang E, Mukherjee S, Knights D, Blekhman R.

Gigascience. 2017 Dec 1;6(12):1-7. doi: 10.1093/gigascience/gix107.

33.

Functional Genomics of Host-Microbiome Interactions in Humans.

Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R.

Trends Genet. 2018 Jan;34(1):30-40. doi: 10.1016/j.tig.2017.10.001. Epub 2017 Oct 26. Review.

34.

High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut.

Heisel T, Montassier E, Johnson A, Al-Ghalith G, Lin YW, Wei LN, Knights D, Gale CA.

mSphere. 2017 Oct 11;2(5). pii: e00351-17. doi: 10.1128/mSphere.00351-17. eCollection 2017 Sep-Oct.

35.

Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults.

Karl JP, Meydani M, Barnett JB, Vanegas SM, Barger K, Fu X, Goldin B, Kane A, Rasmussen H, Vangay P, Knights D, Jonnalagadda SS, Saltzman E, Roberts SB, Meydani SN, Booth SL.

Am J Clin Nutr. 2017 Oct;106(4):1052-1061. doi: 10.3945/ajcn.117.155424. Epub 2017 Aug 16.

36.

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi).

Springer A, Fichtel C, Al-Ghalith GA, Koch F, Amato KR, Clayton JB, Knights D, Kappeler PM.

Ecol Evol. 2017 Jun 15;7(15):5732-5745. doi: 10.1002/ece3.3148. eCollection 2017 Aug.

37.

Moving beyond de novo clustering in fungal community ecology.

Cline LC, Song Z, Al-Ghalith GA, Knights D, Kennedy PG.

New Phytol. 2017 Nov;216(3):629-634. doi: 10.1111/nph.14752. Epub 2017 Aug 7. No abstract available.

38.

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time.

Torres S, Clayton JB, Danzeisen JL, Ward T, Huang H, Knights D, Johnson TJ.

PeerJ. 2017 Mar 9;5:e3075. doi: 10.7717/peerj.3075. eCollection 2017.

39.

A Microbiome Foundation for the Study of Crohn's Disease.

Gevers D, Kugathasan S, Knights D, Kostic AD, Knight R, Xavier RJ.

Cell Host Microbe. 2017 Mar 8;21(3):301-304. doi: 10.1016/j.chom.2017.02.012.

40.

Infant fungal communities: current knowledge and research opportunities.

Ward TL, Knights D, Gale CA.

BMC Med. 2017 Feb 13;15(1):30. doi: 10.1186/s12916-017-0802-z. Review.

41.

Substituting whole grains for refined grains in a 6-wk randomized trial has a modest effect on gut microbiota and immune and inflammatory markers of healthy adults.

Vanegas SM, Meydani M, Barnett JB, Goldin B, Kane A, Rasmussen H, Brown C, Vangay P, Knights D, Jonnalagadda S, Koecher K, Karl JP, Thomas M, Dolnikowski G, Li L, Saltzman E, Wu D, Meydani SN.

Am J Clin Nutr. 2017 Mar;105(3):635-650. doi: 10.3945/ajcn.116.146928. Epub 2017 Feb 8.

42.

Substituting whole grains for refined grains in a 6-wk randomized trial favorably affects energy-balance metrics in healthy men and postmenopausal women.

Karl JP, Meydani M, Barnett JB, Vanegas SM, Goldin B, Kane A, Rasmussen H, Saltzman E, Vangay P, Knights D, Chen CO, Das SK, Jonnalagadda SS, Meydani SN, Roberts SB.

Am J Clin Nutr. 2017 Mar;105(3):589-599. doi: 10.3945/ajcn.116.139683. Epub 2017 Feb 8. Erratum in: Am J Clin Nutr. 2017 Aug;106(2):708.

43.

Addressing disillusionment among young vets.

Clarke C, Knights D, Finch G.

Vet Rec. 2016 Dec 10;179(23):603-604. doi: 10.1136/vr.i6561. No abstract available.

PMID:
27932726
44.
45.

Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice.

Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z, Barber C, Kim J, Ng S, Rogers AB, Sumner S, Zhang XS, Cadwell K, Knights D, Alekseyenko A, Bäckhed F, Blaser MJ.

Nat Microbiol. 2016 Aug 22;1(11):16140. doi: 10.1038/nmicrobiol.2016.140.

46.

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.

Maldonado-Gómez MX, Martínez I, Bottacini F, O'Callaghan A, Ventura M, van Sinderen D, Hillmann B, Vangay P, Knights D, Hutkins RW, Walter J.

Cell Host Microbe. 2016 Oct 12;20(4):515-526. doi: 10.1016/j.chom.2016.09.001. Epub 2016 Sep 29.

47.

Captivity humanizes the primate microbiome.

Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, Travis DA, Long HT, Tuan BV, Minh VV, Cabana F, Nadler T, Toddes B, Murphy T, Glander KE, Johnson TJ, Knights D.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10376-81. doi: 10.1073/pnas.1521835113. Epub 2016 Aug 29.

48.

Toward revision of antimicrobial therapies in hematopoietic stem cell transplantation: target the pathogens, but protect the indigenous microbiota.

Khoruts A, Hippen KL, Lemire AM, Holtan SG, Knights D, Young JH.

Transl Res. 2017 Jan;179:116-125. doi: 10.1016/j.trsl.2016.07.013. Epub 2016 Jul 25. Review.

49.

Gut microbiome predictors of treatment response and recurrence in primary Clostridium difficile infection.

Khanna S, Montassier E, Schmidt B, Patel R, Knights D, Pardi DS, Kashyap P.

Aliment Pharmacol Ther. 2016 Oct;44(7):715-727. doi: 10.1111/apt.13750. Epub 2016 Aug 2.

50.

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies.

Gohl DM, Vangay P, Garbe J, MacLean A, Hauge A, Becker A, Gould TJ, Clayton JB, Johnson TJ, Hunter R, Knights D, Beckman KB.

Nat Biotechnol. 2016 Sep;34(9):942-9. doi: 10.1038/nbt.3601. Epub 2016 Jul 25.

PMID:
27454739

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