Bacterial colonization reprograms the neonatal gut metabolome

Microbial colonization and succession in the gut of human infants are linked to health and disease later in life. Although the taxonomic and functional characteristics of the infant microbiome just after birth have been extensively investigated, we are just beginning to decipher its impact on the biochemical environment. To examine this, we characterized the microbiome, proteome, and metabolome of meconium samples from 88 newborn infants. Using shotgun metagenomic DNA sequencing, we found that human DNA accounted for >75% of sequence reads in 52 samples. High levels of human DNA were found preferentially in samples collected within 16 hours of birth. Quantification by 16S qPCR confirmed that absolute bacterial abundance was low in samples with high human DNA. Escherichia coli, Enterococcus faecalis, and Bacteroides vulgatus were the most commonly detected species, and they did not exhibit a strong phylogenetic or pan-genome signature unique to meconium. The number of strains increased with time after birth at a rate of 1.2 strains per day