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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.


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.


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.


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 Jan 31. pii: S1083-8791(18)30041-7. doi: 10.1016/j.bbmt.2018.01.025. [Epub ahead of print]


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;:.


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. Review.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


In defence of the 'tick-box approach': why end-of-life care is no exception.

Knights D.

Br J Gen Pract. 2016 Jun;66(647):290-1. doi: 10.3399/bjgp16X685357. No abstract available.


Erratum to: Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection.

Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, De La Cochetiere MF, Batard E, Knights D.

Genome Med. 2016 May 26;8(1):61. No abstract available.


Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection.

Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, de la Cochetiere MF, Batard E, Knights D.

Genome Med. 2016 Apr 28;8(1):49. doi: 10.1186/s13073-016-0301-4. Erratum in: Genome Med. 2016;8(1):61.


NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.

Al-Ghalith GA, Montassier E, Ward HN, Knights D.

PLoS Comput Biol. 2016 Jan 28;12(1):e1004658. doi: 10.1371/journal.pcbi.1004658. eCollection 2016 Jan.


Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment.

Danzeisen JL, Clayton JB, Huang H, Knights D, McComb B, Hayer SS, Johnson TJ.

Front Vet Sci. 2015 Nov 20;2:56. doi: 10.3389/fvets.2015.00056. eCollection 2015.


Bygiene: The New Paradigm of Bidirectional Hygiene.

Al-Ghalith GA, Knights D.

Yale J Biol Med. 2015 Nov 24;88(4):359-65. eCollection 2015 Dec. Review.


Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.

Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng AC, Doench JG, Root DE, Clish CB, Xavier RJ.

Nat Commun. 2015 Jul 21;6:7838. doi: 10.1038/ncomms8838.


Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment.

Burns MB, Lynch J, Starr TK, Knights D, Blekhman R.

Genome Med. 2015 Jun 24;7(1):55. doi: 10.1186/s13073-015-0177-8. eCollection 2015.


Chemotherapy-driven dysbiosis in the intestinal microbiome.

Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E, Knights D.

Aliment Pharmacol Ther. 2015 Sep;42(5):515-28. doi: 10.1111/apt.13302. Epub 2015 Jul 6.


Antibiotics, pediatric dysbiosis, and disease.

Vangay P, Ward T, Gerber JS, Knights D.

Cell Host Microbe. 2015 May 13;17(5):553-64. doi: 10.1016/j.chom.2015.04.006. Review.


Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ.

Microbiome. 2015 Mar 30;3:10. doi: 10.1186/s40168-015-0070-0. eCollection 2015.


The guts of obesity: progress and challenges in linking gut microbes to obesity.

Al-Ghalith GA, Vangay P, Knights D.

Discov Med. 2015 Feb;19(103):81-8. Review.


Complementary amplicon-based genomic approaches for the study of fungal communities in humans.

Heisel T, Podgorski H, Staley CM, Knights D, Sadowsky MJ, Gale CA.

PLoS One. 2015 Feb 23;10(2):e0116705. doi: 10.1371/journal.pone.0116705. eCollection 2015.


Complex host genetics influence the microbiome in inflammatory bowel disease.

Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ.

Genome Med. 2014 Dec 2;6(12):107. doi: 10.1186/s13073-014-0107-1. eCollection 2014.


Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.


Rethinking "enterotypes".

Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, McDonald D, Knight R.

Cell Host Microbe. 2014 Oct 8;16(4):433-7. doi: 10.1016/j.chom.2014.09.013.


Multi-omics analysis of inflammatory bowel disease.

Huang H, Vangay P, McKinlay CE, Knights D.

Immunol Lett. 2014 Dec;162(2 Pt A):62-8. doi: 10.1016/j.imlet.2014.07.014. Epub 2014 Aug 15. Review.


The treatment-naive microbiome in new-onset Crohn's disease.

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ.

Cell Host Microbe. 2014 Mar 12;15(3):382-392. doi: 10.1016/j.chom.2014.02.005.


The Liverpool Care Pathway for the dying: what went wrong?

Knights D, Wood D, Barclay S.

Br J Gen Pract. 2013 Oct;63(615):509-10. doi: 10.3399/bjgp13X673559. No abstract available.


A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system.

Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R.

Elife. 2013 Oct 15;2:e01104. doi: 10.7554/eLife.01104.


Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.

Knights D, Lassen KG, Xavier RJ.

Gut. 2013 Oct;62(10):1505-10. doi: 10.1136/gutjnl-2012-303954. Review.


Do health partnerships with organisations in lower income countries benefit the UK partner? A review of the literature.

Jones FA, Knights DP, Sinclair VF, Baraitser P.

Global Health. 2013 Aug 30;9:38. doi: 10.1186/1744-8603-9-38. Review.


Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.


Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.

Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada JR, Guarner F, Azpiroz F.

Gut. 2014 Mar;63(3):401-8. doi: 10.1136/gutjnl-2012-303013. Epub 2013 Jun 13.

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