Henry Rutgers Chair of the Human Microbiome
Department of Medicine and Microbiology
RBHS, Robert Wood Johnson Medical School


Center for Advanced Biotechnology and Medicine

M.D., 1973, NYU School of Medicine
Telephone: (848) 445-9834
Fax: (732) 235-5318

Human microbiome, early-life effects and mechanisms on disease development

My lab has been studying pathogenic bacteria and gastrointestinal biology since 1981 and the human microbiome since 2002. We conducted early 16S rRNA surveys of the esophagus, stomach, lung, and skin. Such studies helped establish the baseline present in health that then can be used to assess pathologic relationships. Nearly 20 years ago, we began to hypothesize that some of the diseases of modernization, including obesity, diabetes, malignancies, and immunologic disorders, were due to changes in the ancestral human microbiome. We have had especial emphasis on the role of the gastrointestinal tract microbiome in early life development, with consequences for how normal metabolism and immunity develop. Because of the widespread use of antibiotics, especially in young children, we have explored in animal models their role in perturbing the microbiome, and the downstream effects. More recently, we have been exploring microbiome changes that could be fueling the metabolic and inflammatory disease epidemics of obesity, IBD, asthma, allergies, type 1 diabetes, kidney stones, and particular cancers (including esophageal, gastric), respectively using mouse models to understand underlying mechanisms. We have used multi-“omic” approaches to address these questions. Specimens from mice of defined disease and control phenotypes permit linked analyses of tissue gene expression and gut metagenome with metabolic pathways to identify molecules that can be used for solutions to these problems.

Selected Publications (Since 2012)

Cho I, Yamanishi S, Cox L, Methe BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I, Li H, Alekseyenko AV, Blaser, MJ. Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 2012; 488:621-626. [PMID:22914093]

Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim S, Li H, Gao Z, Mahana D, Zarate Rodriguez JG, Rogers AB, Robine N, Loke P, Blaser MJ. Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. Cell 2014; 158:705-721.

Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber C, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nature Communications 2015; 6:7486. doi: 10.1038/ncomms8486.

Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Science Translational Medicine 2016; 8(343):343ra82. doi: 10.1126/scitranslmed.aad7121.

Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z, Barber C, Kim J, Ng S, Rogers AB, Sumner S, Zhang X-S, Cadwell K, Knights D, Alekseyenko A, Backhed F, Blaser MJ. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nature Microbiology 2016; 1:16140. doi: 10.1038/nmicrobiol.2016.140.

Ruiz VE, Battaglia T, Kurtz ZD, Bijnens L, Ou A, Engstrand I, Zheng X, Iizumi T, Mullins BJ, Müller CL, Cadwell K, Bonneau R, Perez Perez GI, Blaser MJ. A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. Nature Communications 2017; 8, 518 doi:10.1038/s41467-017-00531-6.

Schulfer AF, Battaglia T, Alvarez Y, Bijnens L, Ruiz VE, Ho M, Robinson S, Ward W, Cox LM, Rogers AB, Knights D,Sartor RB, Blaser MJ. Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice. Nature Microbiology 2017; doi: 10.1038/s41564-017-0075-5

Zhang X-S, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalih GA, Ruiz VE, Livanos A, Wout A, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson AR, Rauch M, Blaser MJ. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife 2018; (#30039798)

Blaser MJ. The past and future biology of the human microbiome in an age of extinctions. Cell 2018; 172:1173-77; (#29522739) .