- Integrative Clinical and Biospecimen Core (Joel Pekow, MD, Sonia Kupfer, MD, Christopher Weber, MD, PhD): Offering the patient registry, tissue biobanking facilities, and support in designing clinical studies in areas such as human gut microbiomes in health and disease, IBD, gastroenterology, and hepatology, and celiac diseases.
- Host-Microbe Core (Eugene Chang, MD, Alexander Chervonsky, MD, PhD, Betty Theriault, DVM, DACLAM, Ran Blekhman, PhD): Provides unique approaches to the study of host-microbe interactions, including cell/tissue models and gnotobiotic mouse technologies. The Core also offers bioinformatics analysis and interpretation of microbiome data and other genomic data in the context of digestive disorders. This includes, but not limited to, processing and analysis of data generated by 16S rRNA sequencing, metagenomic shotgun sequencing, metabolomics, transcriptomics, and epigenomics, as well as integration of various datasets using various statistical and computational approaches.
- Tissue Engineering and Cell Models Core (Cambrian Liu, PhD, Candace Cham, PhD): Offering unique cell and tissue models, enteroids/organoids, and mouse models along with molecular and genetic engineering approaches to develop new model systems.
- Multiparametric Host Cell Analysis Core (Luis Barreiro, PhD,Valeria Abadie, PhD): The MHC core aims to provide expert consultation, training, experimental and bioinformatic support in the use of the growing array of highly specialized cutting-edge technologies that are available for flow cytometry and genomic analysis, specifically related to the study of gastrointestinal disease.
Publications
1. Kennedy MS, Freiburger A, Cooper M, Beilsmith K, St George ML, Kalski M, Cham C, Guzzetta A, Ng SC, Chan FK, DeLeon O, RubinD, Henry CS, Bergelson J, Chang EB. Diet outperforms microbial transplant to drive microbiome recovery in mice. Nature. 2025 Jun;642(8068):747-755. PubMed PMID: 40307551.
2. DeLeon O, Mocanu M, Tan A, Sidebottom AM, Koval J, Ceccato HD, Kralicek S, Colgan JJ, St George MM, Lake JM, Cooper M, Xu J, Moore J, Su Q, Xu Z, Ng SC, Chan FKL, Tun HM, Cham CM, Liu CY, Rubin DT, Martinez-Guryn K, Chang EB. Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects. Cell. 2025 Jul 24;188(15):3927-3941.e13. PubMed Central PMCID: PMC12330209.
3. Pierre JF, Peters BM, La Torre D, Sidebottom AM, Tao Y, Zhu X, Cham CM, Wang L, Kambal A, Harris KG, Silva JF, Zaborina O, Alverdy JC, Herzog H, Witchley J, Noble SM, Leone VA, Chang EB. Peptide YY: A Paneth cell antimicrobial peptide that maintains Candida gut commensalism. Science. 2023 Aug 4;381(6657):502-508. PubMed Central PMCID: PMC10876062.
4. Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature. 2012 Jul 5;487(7405):104-8. PubMed Central PMCID: PMC3393783.
5. Leone VA, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host Microbe. 2015 May 13;17(5):681-689. PMCID: PMC4433408.