Where do a baby's first microbes come from?

A baby's first microbes come mainly from its mother and its first meals. The gut community is established during birth and matures into an adult-like one within the first few years, so the early days count for a lot. Babies born through the vaginal canal pick up gut microbes similar to the ones their mother carries. The gut microbiota of babies delivered by C-section tends to contain more bacteria such as Escherichia coli and Staphylococcus, and it takes longer to build up the usual beneficial ones. Researchers list birth mode among the most impactful factors on the developing microbiota.

Milk adds more. Breast milk is not sterile: it has its own microbiome of as many as 600 bacterial species, including Bifidobacterium species that help colonise the infant gut. It also contains special sugars called human milk oligosaccharides. The baby cannot digest them, yet they help shape the intestinal flora, and they act as decoys that stop disease-causing microbes from sticking to the gut wall.

Scientists have known about this milk and microbe partnership for a long time. In 1899, the French paediatrician Henri Tissier at the Pasteur Institute looked at the gut microbes of breast-fed infants and found a Y-shaped bacterium he named bifidus, now one of the major groups of gut bacteria in mammals.

One question is still hotly argued: do babies meet microbes before birth? Some reports say the placenta carries its own microbiome, but others suspect contamination of the samples, because such tiny amounts of microbes are easily contaminated. Either way, by the age of one or two the infant's gut flora comes to look much like an adult's.