Banfield Laboratory

University of California, Berkeley

The Human Microbiome

Infants are born near sterile and continually acquire microbial colonists until reaching an adult-like state at around 2-3 years of age. The microbiota during the first 100 days of life is especially important, as dysbiosis during this “critical window” has been linked to a number of problems later in life, especially relating to the developing immune system. In premature infants, who typically spend the first 2-4 months in the hospital, aberrations during colonization can also lead to illness, death, or long-term disability.


The Banfield lab, through funding from the NIH and Sloan Foundation, is using a high-throughput phylogenetic and metagenomic approach with resolution at the strain level, to examine features of normal and diseased infant gut colonization during the first critical weeks of life. We aim to leverage this strain-level resolution to learn more about the lifestyle of these founding colonists and track their dispersal patterns. Some specific areas of interest are:


• Community assembly and the role of specific microbes in infants

• Transmission of strains between humans and the built environment

• Development of assembly-based metagenomic techniques for strain-level resolution