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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.


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.


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. 2016 Jul 25. pii: S1931-5244(16)30128-1. doi: 10.1016/j.trsl.2016.07.013. 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 PC.

Aliment Pharmacol Ther. 2016 Oct;44(7):715-27. doi: 10.1111/apt.13750.


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.


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.


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.


Bygiene: The New Paradigm of Bidirectional Hygiene.

Al-Ghalith GA, Knights D.

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


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.


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.


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.


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.


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.

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