2018

Lack of Detection of a Human Placenta Microbiome in Samples from Preterm and Term Deliveries.
Leiby JS, McCormick K, Sherrill-Mix S, Clarke El, Kessler LR, Hofstaedter CE, Roche AM, Mattei LM, Bittinger K, Elovitz MA, Leite R, Parry S, Bushman FD. Microbiome, 6(1):196, Oct 30, 2018. doi: 10.1186/s40168-018-0575-4. PMID: 30376898.

Cervicovaginal Fungi and Bacteria Associated with Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population.
Godoy-Vitorino F, Romaguera J, Zhao C, Vargas-Robles D, Ortiz-Morales G, Vázquez-Sánchez F, Sanchez-Vázquez M, de la Garza-Casillas M, Martinez-Ferrer M, White JR, Bittinger K, Dominguez-Bello MG, Blaser MJ. Front. Microbiol, Oct 23, 2018. https://doi.org/10.3389/fmicb.2018.02533.

Antiseptic Agents Elicit Short-Term, Personalized, and Body Site-Specific Shifts in Resident Skin Bacterial Communities.
SanMiguel AJ, Meisel JS, Horwinski J, Zheng Q, Bradley CW, Grice EA. J Invest Dermatol. 2018 Oct;138(10):2234-2243. doi: 10.1016/j.jid.2018.04.022. Epub 2018 May 9. PMID: 29753031.

Characterisation of the Nasal Microbiota in Granulomatosis with Polyangiitis.
Rhee RL, Sreih AG, Najem CE, Grayson PC, Zhao C, Bittinger K, Collman RG, Merkel PA. Ann Rheum Dis, 77(10):1448-1453, Oct 2018. doi: 10.1136/annrheumdis-2018-213645. Epub 2018 Jul 11. PMID: 29997110.

Longitudinal Study of the Psoriasis-Associated Skin Microbiome during Therapy with Ustekinumab in a Randomized Phase 3b Clinical Trial.
Loesche MA, Farahi K, Capone K, Fakharzadeh S, Blauvelt A, Duffin KC, DePrimo SE, Muñoz-Elías EJ, Brodmerkel C, Dasgupta B, Chevrier M, Smith K, Horwinski J, Tyldsley A, Grice EA. J Invest Dermatol. 2018 Sep;138(9):1973-1981. doi: 10.1016/j.jid.2018.03.1501. Epub 2018 Mar 17. PMID: 29559344.

T Cell Dynamics and Response of the Microbiota after Gene Therapy to Treat X-linked Severe Combined Immunodeficiency.
Clarke EL, Connell AJ, Six E, Kadry NA, Abbas AA, Hwang Y, Everett JK, Hofstaedter CE, Marsh R, Armant M, Kelsen J, Notarangelo LD, Collman RG, Hacein-Bey-Abina S, Kohn DB, Cavazzana M, Fischer A, Williams DA, Pai SY, Bushman FD. Genome Med. 2018 Sep 28;10(1):70. doi: 10.1186/s13073-018-0580-z. PMID: 30261899.

Bidirectional Transfer of Anelloviridae Lineages between Graft and Host during Lung Transplantation.
Abbas AA, Young JC, Clarke EL, Diamond JM, Imai I, Haas AR, Cantu E, Lederer DJ, Meyer K, Milewski RK, Olthoff KM, Shaked A, Christie JD, Bushman FD, Collman RG. Am J Transplant. 2018 Sep 11. doi: 10.1111/ajt.15116. [Epub ahead of print] PMID: 30203917.

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid.
Friedman ES, Li Y, Shen TD, Jiang J, Chau L, Adorini L, Babakhani F, Edwards J, Shapiro
D, Zhao C, Carr RM, Bittinger K, Li H, Wu GD. Gastroenterology, Aug 22, 2018. doi:
10.1053/j.gastro.2018.08.022. PMID: 30144429. [Epub ahead of print].

Considerations for Best Practices in Studies of Fiber or Other Dietary Components and the Intestinal Microbiome.
Klurfeld DM, Davis CD, Karp RW, Allen-Vercoe E, Chang EB, Chassaing B, Fahey GC, Hamaker BR, Holscher HD, Lampe JW, Marette A, Martens E, O'Keefe SJ, Rose DJ, Saarela M, Schneeman BO, Slavin JL, Sonnenburg JL, Swanson KS, Wu GD, Lynch CJ. Am J Physiol Endocrinol Metab. 2018 Aug 21. doi: 10.1152/ajpendo.00058.2018. [Epub ahead of print].

Establishing a Mucosal Gut Microbial Community in Vitro Using an Artificial Simulator.
Liu L, Firrman J, Tanes C, Bittinger K, Thomas-Gahring A, Wu GD, Van den Abbeele P, Tomasula P. PLos One, 13(7):1-20, e0197692, Jul 17, 2018. doi: 10.1371/journal.pone.0197692. eCollection 2018.

Fungi in the Wound Microbiome.
Kalan L, Grice EA. Adv Wound Care (New Rochelle). 2018 Jul 1;7(7):247-255. doi: 10.1089/wound.2017.0756. Review. PMID: 29984114.

HmmUFOtu: An HMM and Phylogenetic Placement Based Ultra-Fast Taxonomic Assignment and OTU Picking Tool for Microbiome Amplicon Sequencing Studies.
Zheng Q, Bartow-McKenney C, Meisel JS, Grice EA. Genome Biol. 2018 Jun 27;19(1):82. doi: 10.1186/s13059-018-1450-0. PMID: 29950165.

Toxin-Positive Clostridium difficile Latently Infect Mouse Colonies and Protect Against Highly Pathogenic C. difficile.
Etienne-Mesmin L, Chassaing B, Adekunle O, Mattei LM, Bushman FD, Gewirtz AT.
Gut, 67(5):860-871, May 2018. doi: 10.1136/gutjnl-2016-313510. Epub 2017 Feb 20.
PMID: 28219893; PMCID: PMC5941301 [Available 2019-05-01].

Evaluation of a Therapy for Idiopathic Chronic Enterocolitis in Rhesus Macaques (Macaca mulatta) and Linked Microbial Community Correlates.
Taylor JM, Clarke EL, Baker K, Lauder A, Kim D, Bailey A, Wu GD, Collman RG, Doyle-Meyers L, Russell-Lodrigue K, Blanchard J, Bushman FD, Bohm R. PeerJ. 2018 Apr 11;6:e4612. doi: 10.7717/peerj.4612. eCollection 2018. PMID: 29666764.

Microbes vs. Chemistry in the Origin of the Anaerobic Gut Lumen.
Friedman ES, Bittinger K, Esipova TV, Hou L, Chau L, Jiang J, Mesaros C, Lund PJ, Liang X, FitzGerald GA, Goulian M, Lee D, Garcia BA, Blair IA, Vinogradov SA, Wu GD. PNAS, Apr 2, 2018. pii:201718635. doi.org/10.1073/pnas.1718635115. PMID 29610310.

Allometry and Ecology of the Bilaterian Gut Microbiome.
Sherrill-Mix S, McCormick K, Lauder A, Bailey A, Zimmerman L, Yingying L, Ndjango JB, Bertolani P, Colin C, Hart JA, Hart TB, Georgiev AV, Sanz CM, Morgan DB, Atencia R, Cox D, Muller MN, Sommer V, Piel A, Stewart FA, Speede S, Roman J, Wu G, Taylor J, Bohm R, Rose HM, Carlson J, Mjungu D, Schmidt P, Gaughan C, Bushman JI, Schmidt E, Bittinger K, Collman R, Hahn B, Bushman FD. mBio, 9(2), Mar 27, 2018. pii:e00319-18. doi:10.1128/mBio.00319-18. PMID: 29588401. PMCID: PMC5874926.

The Microbiota of Traumatic, Open Fracture Wounds is Associated with Mechanism of Injury.
Bartow-McKenney C, Hannigan GD, Horwinski J, Hesketh P, Horan AD, Mehta S, Grice EA. Wound Repair Regen. 2018 Mar;26(2):127-135. doi: 10.1111/wrr.12642. Epub 2018 Sep 20. PMID: 29802752.

Gut Microbiota Modulates Adoptive Cell Therapy via CD8α Dendritic Cells and IL-12.
Uribe-Herranz M, Bittinger K, Rafail, S, Guedan S, Pierini S, Tanes C, Ganetsky A, Morgan MA, Gill S, Tanyi JL, Bushman FD, June CH, Facciabene A. JCI Insight, 3(4):e94952, Feb 22, 2018. doi.org/10.1172/jci.insight.94952. [Epub ahead of print]. PMID: 29467322.

Functional Imaging of the Interaction between Gut Microbiota and the Human Host: A Proof-of-Concept Clinical Study Evaluating Novel Use for 18F-FDG PET-CT.
Boursi B, Werner TJ, Gholami S, Houshmand S, Mamtani R, Lewis JD, Wu GD, Alavi A, Yang YX. PLoS One. 2018 Feb 15;13(2):e0192747. doi: 10.1371/journal.pone.0192747. eCollection 2018. PMID: 29447210.

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction.
Zhou Y, Xu ZZ, He Y, Yang Y, Liu L, Lin Q, Nie Y, Li M, Zhi F, Liu S, Amir A, González A, Tripathi A, Chen M, Wu GD, Knight R, Zhou H, Chen Y. mSystems. 2018 Jan 30;3(1). pii: e00188-17. doi: 10.1128/mSystems.00188-17. eCollection 2018 Jan-Feb. PMID: 29404425.

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low-Microbial Content Samples.
Clarke EL, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Rękawiecki B, Majewska H, Dubaniewicz A, Litzky LA, Feldman MD, Bittinger K, Rossman MD, Patterson KC, Bushman FD, Collman RG. Am J Respir Crit Care Med, 197(2):225-234, Jan 15, 2018. doi.org/10.1164/rccm.201705-0891OC. PMID: 28846439; PMCID: PMC5768903 [available 2019-01-15].

Commensal Microbiota Modulate Gene Expression in the Skin
Meisel JS, Sfyroera G, Bartow-McKenney C, Gimblet C, Bugayev J, Horwinski J, Kim B, Brestoff JR, Tyldsley AS, Zheng Q, Hodkinson BP, Artis D, Grice EA. Microbiome. 2018 Jan 30;6(1):20. doi: 10.1186/s40168-018-0404-9. PubMed PMID: 29378633; PubMed Central PMCID: PMC5789709.

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. PubMed PMID: 29255284.

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