The Microbiome in Early Childhood

Thought to be essentially sterile in utero, the human body is rapidly colonized by a range of microbes immediately following birth. These relatively simple microbial communities grow in complexity and differentiate until they reach an adult-like configuration around three years of age. These microbes participate in many complex physiological and immunological processes, such as aiding in digestion, directing immune system development, and excluding pathogens. This process of microbiome maturation is not well understood, but can be crucial for the establishment of a “healthy” microbiome.

Using both microbe-centric and host-centric multi-‘omic approaches, we are investigating this process of microbial community assembly across body sites, as well as how it is altered during periods of disease, treatment, and through interactions with care-takers and their environment. 

Current Projects:

  • VEO-IBD and the Microbiome (currently enrolling)
  • The Tsimane Microbiome Project
  • The Impact of Antibiotics on Microbiome Assembly
  • WASH Benefits and the Microbiome - The impact of water, sanitation, hand washing, and nutrition interventions on the assembly and maturation of infant gut microbiome in rural Bangladesh


Relevant Publications

Treatment-Specific Composition of the Gut Microbiota Is Associated With Disease Remission in a Pediatric Crohn’s Disease Cohort

Daniel Sprockett, Natalie Fischer, Rotem Sigall Boneh, Dan Turner, Jarek Kierkus, Malgorzata Sladek, Johanna C. Escher, Eytan Wine, Baruch Yerushalmi, Jorge Amil Dias, Ron Shaoul, Michal Kori, Scott B Snapper, Susan Holmes, Athos Bousvaros, Arie Levine, David A. Relman (2019) Inflammatory Bowel Diseases.

Role of priority effects in the early-life assembly of the gut microbiota

Daniel Sprockett, Tadashi Fukami, and David A. Relman (2018) Nature Reviews Gastroenterology & Hepatology.

C. difficile, aging and the gut: can microbiome rejuvenation keep us young and healthy?

Natalie Fischer and David A. Relman (2017) The Journal of Infectious Diseases.

Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant

Elizabeth K. Costello, Christine L. Sun, Erica M. Carlisle, Michael J. Morowitz, Jillian F. Banfield, and David A. Relman (2017) Scientific Reports.

Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants

Elizabeth K. Costello, Erica M. Carlisle, Elisabeth M. Bik, Michael J. Morowitz, and David A. Relman (2013) mBio.