CHOP Microbiome Center Publications



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View a compilation of publications from 2017-2022 by researchers who used resources in the CHOP Microbiome Center. 

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
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
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
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. 2022 Dec
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
Liang G, Gao H, Bushman FD. The pediatric virome in health and disease. Cell Host Microbe. 2022 May; 30(5):639-649. PMID: 35550667
Dawwas GK, Brensinger CM, Vajravelu RK, Wu Q, Kelly CR, Laine L, Wu GD, Lewis JD. Long-term outcomes following multiply recurrent Clostridioides difficile infection and fecal microbiota transplantation. Clin Gastroenterol Hepatol. 2022 Apr; 0(4):806-816.e6. E pub 2020 Dec 8. PMID: 33307184
Redding LE, Tu V, Abbas A, Alvarez M, Zackular JP, Gu C, Bushman FD, Kelly DJ, Barnhart D, Lee JJ, Bittinger K. Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations. Anaerobe. 2022 Apr; 74:102539. Epub 2022 Feb 23. PMID: 35217150
Firrman J, Liu L, Mahalak K, Tanes C, Bittinger K, Tu V, Bobokalonov J, Mattei L, Zhang H, Van den Abbeele P. The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production. FEMS Microbiol Ecol. 2022 Apr; fiac038. Epub ahead of print. PMID: 35383853
Mennella JA, Li Y, Bittinger K, Friedman ES, Zhao C, Li H, Wu GD, Trabulsi JC. The macronutrient composition of infant formula produces differences in gut microbiota maturation that associate with weight gain velocity and weight status. Nutrients. 2022 Mar; 14(6):1241. PMID: 35334900. PMCID: PMC8951061
Chassaing B, Compher C, Bonhomme B, Liu Q, Tian Y, Walters W, Nessel L, Delaroque C, Hao F, Gershuni V, Chau L, Ni J, Bewtra M, Albenberg L, Bretin A, McKeever L, Ley RE, Patterson AD, Wu GD, Gewirtz AT, Lewis JD. Randomized controlled-feeding study of dietary emulsifier carboxymethylcellulose reveals detrimental impacts on the gut microbiota and metabolome. Gastroenterology. 2022 Mar; 162(3):743-756. PMID: 34774538
Nashed L, Mani J, Hazrati S, Stern DB, Subramanian P, Mattei LM, Bittinger K, Hu W, Levy S, Maxwell GL, Hourigan SK. Gut microbiota changes are detected in asymptomatic very young children with SARS-CoV-2 infection. Gut. 2022 Feb; PMID: 35135843
Simon-Soro A, Ren Z, Krom B, Hoogenkamp M, Cabello-Yeves P, Daniel S, Bittinger K, Tomas I, Koo H, Mira A. Polymicrobial aggregates in human saliva build the oral biofilm. mBio. 2022 Feb; 13(1):e0013122. PMID: 35189700. PMCID: PMC8903893
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 pediatric perianal Crohn's Disease. J Crohns Colitis. 2022 Feb; jjac032. Epub ahead of print. PMID: 35211723
Kastl A, Zong W*, Gershuni VM, Friedman ES, Tanes C, Boateng A, Mitchell WJ, O'Connor K, Bittinger K, Terry NA, Christina Bales C, Lindsey Albenberg L, Gary D Wu GD. Dietary fiber-based regulation of bile salt hydrolase activity in the gut microbiota and its relevance to human disease. Gut Microbes. 2022 Jan; 14(1): 2083417. PubMed PMID: 3565883 (*co-first author)
Elgarten C, Tanes C, Lee JJ, Danziger Isakov LA, Grimley MS, Green M, Michaels MG, Barnum JL, Ardura MI, Auletta JJ, Blumenstock J, Sief AE, Bittinger K, Fisher BT. Early stool microbiome and metabolome signatures in pediatric patients undergoing allogeneic hematopoietic cell transplantation. Pediatric Blood and Cancer. 2022 Jan; 69(1):e29384. Epub 2021 28 Oct. PMID: 34709713
Servetas SL, Daschner PJ, Guyard C, Thomas V, Affagard H, Sergaki C, Sokol H, Wargo JA, Wu GD, Sabot P. Evolution of FMT - From early clinical to standardized treatments. Biologicals. 2022 Jan; S1045-1056(22)00004-5. PMID: 35086768
Ferro LE, Crowley LN, Bittinger K, Freidman ES, Decker, JE, Russel K, Katz S, Kim JK, Trabulsi JC. Effects of prebiotics, probiotics, and synbiotics on the infant gut microbiota and other health outcomes: A systematic review. Crit Rev in Food Sci and Nutr. 2022 Jan
Palchaudhuri S, Mehta SJ, Snider CK, Parsikia A, Hudson L, Compher C, Lewis JD, Wu GD, Pickett-Blakely O. Causes of readmissions for patients discharged on enteral nutrition. PEN J Parenter Enteral Nutr. 2022 Jan; PMID: 35040141