Infant Gut Microbiome and Strain Dynamics

Infants are born near sterile and continually acquire microbial colonists until reaching an adult-like state at around 2-3 years of age. The microbiome 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 leveraging metagenomic analysis and microbiome cultivation with resolution at the strain level to examine features of normal and diseased infant gut colonization during the first years 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 dynamics, such as the role specific microbes and mobile genetic elements play in shaping the community compositions in infants
• How early-life perturbations (i.e., antibiotics and diet) mechanistically affect community assembly
• Transmission of strains and mobile genetic elements between humans and the built environment
• Development of assembly-based metagenomic techniques for strain-level resolution

Relevant publications

Lou et al. Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition (link)

West et al. Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics (link)

Brooks et al. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome (link)

Devoto et al. Megaphages infect Prevotella and variants are widespread in gut microbiomes (link)

Olm et al. Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria (link)

Olm et al. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates (link)

Rahman et al. Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome (link)

Brooks et al. The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms (link)

Brown et al. Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles (link)

Sharon et al. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization (link)