The early human gut microbiota affects health and disease states during life, and research efforts have focused on understanding initial colonization, development and function. Bittinger, Zemel, Wu and colleagues studied the gut microbiome, proteome and metabolome in the faecal samples of newborns taken during their first days after birth. By 16 h, bacteria became detectable using molecular methods, and the detected bacterial strains did not exhibit a genomic signature. The proteomic and the faecal metabolomic profiles were altered upon the appearance of bacteria and were consistent with anaerobic rather than aerobic bacterial growth; several amino acids decreased whereas several products of bacterial fermentation increased with the detection of bacteria. In sum, the findings of the study suggest a biochemical shift in the infant samples associated with the appearance of bacteria.