PennCHOP Microbiome Program Publications

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Below is a list of selected publications from the PennCHOP Microbiome Program. View and download a complete list of publications.

Firrman J, Liu L, Mahalak KK, Hu W, Bittinger K, Moustafa AM, Narrowe A, Tomasula P. An in vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner. Front in Nutr. 2023 Feb; 9:1040744
Mahalak KK, Firrman J, Narrowe AB, Hu W, Jones SM, Bittinger K, Moustafa AM, Liu L. Fructooligosaccharide (FOS) from chicory root differentially modifies the in vitro gut microbiota in an age-dependent manner. Front in Nutr. 2023 Jan; 9: 1058910
Xiang Z, Wakade RS, Ribeiro AA, Hu W, Bittinger K, Simon-Soro A, Kim D, Krysan DJ, Liu Y, Koo H. Human tooth as a fungal niche: Candida albicans traits in dental plaque isolates. mBio. 2023 Jan; e0276922. PMID: 36602308
Zhang Y, Li Y, Barber AF, Noya SB, Williams JA, Li F, Daniel SG, Bittinger K, Fang J, Sehgal A. The microbiome stabilizes circadian rhythms in the gut. Proc Natl Acad Sci U S A.. 2023 Jan; 120(5):e2217532120. PMID: 36689661
Kennedy KM, de Goffau MC, Perez-Muñoz ME, et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature. 2023 Jan; 613(7945):639-649. PMID: 36697862
Bianco C, Moustafa AM, O’Brien, Martin M, Read TD, Kreiswirth B, Planet PJ. Pre-epidemic evolution of USA300 clade and molecular key for classification. Front in Cell and Infect Micro. 2023 Jan; 13
Mancin L, Wu GD, Paoli A. Gut microbiota-bile acid-skeletal muscle axis. Trends Microbiol. 2022 Oct; S0966-842X(22)00286-4. PMID: 36319506
Merenstein C, Bushman FD, Collman RG. Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance. Microbiome. 2022 Oct; 10(1):165. PMID: 36195943
Mahalk et al. Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome. Int. J. Mol. Sci. 2022 Oct; 23(21):12973
Lee IK, Jacome DA, Cho JK, Tu V, Young AJ, Dominguez T, Northrup JD, Etersque JM, Lee HS, Ruff A, Aklilu O, Bittinger K, Glaser LJ, Dorgan D, Hadjiliadis D, Kohli RM, Mach RH, Mankoff DA, Doot RK, Sellmyer MA. Imaging sensitive and drug-resistant bacterial infection with [11C]-trimethoprim. J Clin Invest. 2022 Sep; 132(18):e156679. PMID: 36106638. PMCID: PMC9479701
Verburgt CM, Dunn KA, Mohammed G, Lewis JD, Wine E, Sigall Boneh R, Gerasimidis K, et al. Successful dietary therapy in paediatric Crohn's Disease is associated with shifts in bacterial dysbiosis and inflammatory metabotype towards healthy controls. J Crohns Colitis. 2022 Sep; jjac105. Online ahead of print. PMID: 36106847
Viana AS, Botelho AN, Feder A, Moustafa AM, Santos Silva DN, et al. High frequency of increased triclosan MIC among CC5 MRSA and risk of misclassification of the SCCmec into types. J Antimicrob Chemother. 2022 Sep; dkac322. Online ahead of print. PMID: 36173394
McGinniss JE, Whiteside SA, Deek RA, Simon-Soro A, Graham-Wooten J, Oyster M, Brown MD, Cantu E, et al. The Lung Allograft Microbiome Associates with Pepsin, Inflammation, and Primary Graft Dysfunction. Am J Respir Crit Care Med. 2022 Sep; Online ahead of print. PMID: 36103583
Anton L, Ferguson B, Freidman ES, Gerson KD, Brown AG, Elovitz MA. Gardnerella vaginalis alters cervicovaginal epithelial cell function through microbe-specific immune responses. Microbiome. 2022 Aug; 10(1):119. PMID: 35922830
Stein R, Daniel SG, Baldassano RN, Feigenbaum K, Kachelries K, Sigall-Boneh R, Weston S, Levine A, Bittinger K. Outcomes and predictors of sustained remission after drug withdrawal in pediatric Crohn's disease. J Pediatr Gastroenterol Nutr. 2022 Aug; Epub ahead of print. PMID: 35976282
Sinha SR, Haileselassie Y, Nguyen LP, Tropini C, Wang M, Becker LS, Sim D, Jarr K, Spear ET, Singh G, Namkoong H, Bittinger K, Fischbach MA, Sonnenburg JL, Habtezion A. Dysbiosis-induced secondary bile acid deficiency promotes intestinal inflammation. Cell Host Microbe. 2022 Aug; 27(4):659-670.e5. PMID: 32101703. PMCID: PMC8172352
Ricardo-Gonzalez RR, Kotas ME, O'Leary CE, Singh K, Damsky W, Liao C, Arouge E, Tenvooren I, Marquez DM, Schroeder AW, Cohen JN, Fassett MS, Lee J, Daniel SG, Bittinger K, Díaz RE, Fraser JS, Ali N, Ansel KM, Spitzer MH, Liang HE, Locksley RM. Innate type 2 immunity controls hair follicle commensalism by Demodex mites. Immunity. 2022 Aug; S1074-7613(22)00378-8. Epub ahead of print. PMID: 36044899
Breton J, Tanes C, Tu V, Albenberg L, Rowley S, Devas N, Hwang R, Kachelries K, Wu GD, Baldassano RN, Bittinger K, Mattei P. A microbial signature for paediatric perianal Crohn's Disease. J Crohns Colitis. 2022 Aug; 16(8):1281-1292. Epub 2022 Feb 25. PMID: 35211723
Bartolo L, Afroz S, Pan YG, Xu R, Williams L, Lin CF, Tanes C, Bittinger K, Friedman ES, Gimotty PA, Wu GD, Su LF. SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens. Sci Immunol. 2022 Jul; eabn3127. PMID: 35857619. PMCID: PMC9348748
Vajravelu RK, Shapiro JM, Ni J, Thanawala SU, Lewis JD, El-Serag HB. Risk for post-colonoscopy irritable bowel syndrome in patients with and without antibiotic exposure: A retrospective cohort study. Clin Gastroenterol Hepatol. 2022 Jun; 20(6):e1305-e1322. Epub 2021 Sep 3. PMID: 34481956