There's strong evidence that babies inherit their gut microbiomes from their mothers, but it's been unclear if the microbiome transmission takes place in the womb, at birth, or after birth; there are likely multiple paths of transmission unfolding over time. Microbial diversity is crucial to building up many functions, including the immune system, digestion, and even combating complex diseases. Recent research has found a connection between our gut microbiomes and our mental health as well.

However, studying the direct transmission of these microbes and identifying the strains of bacteria has been difficult until recently. Now researchers at the Centre for Integrative Biology at the University of Trento (UoT), Italy, have developed methods to track this microbial “vertical transmission,” as it’s called, and made some new discoveries in their methodological study, published in mSystems, an open access journal from the American Society for Microbiology.

“We know the infant increases [its] microbial diversity after birth and will continue doing so until being an adult,” senior study author Nicola Segata, an assistant professor at UoT, tells mental_floss. “We needed to understand from where microbes are coming in the first place.”

Many microbes are likely transmitted from mother to infant at birth and just after birth through direct contact with the birth canal, the skin, and through breast milk, but they had not yet done thorough investigations of the strains of bacteria to corroborate this. This is also important in the case of identifying the transmission of microbes that are dangerous to the infant’s health, such as Group B Streptococcus, which can cause an infection, and even death, in infants.

Segata explains, “Our contribution is really tracking which bacteria are moving from mother to infant. It was already known that certain microbes were present in the mother and infant but each had a different strain of, say, E. coli or Bifidobacterium. We looked to see if mothers and infants had the same strain of E. coli, or if it was a different strain from other infants and mothers.”

Taking fecal and breast milk samples from five mother-infant pairs when the infants were 3 months, 10 months, and, for one pair, at 16 months of age, Segata and his team used a technique called shotgun metagenomic sequencing of 24 microbiome samples of either fecal or breastmilk samples to determine which microbes were present. (This technique makes it possible to sample genes from all organisms in a sample.) Then they used another method known as metatranscriptomics to study RNA in fecal samples to identify active microbes.

“Each mother and infant pair had different strains of bacteria, but when you match each mother and her infant, they have the same strain, so this is strong evidence of the strain coming from the mother,” Segata says.

Another important discovery, Segata says, is that “these strains acquired from the mother are also active in the infant gut, they are alive. It’s important that the strains moving from mother to infant are active, colonizing.”

While this study allowed them to say confidently, “We can track microbe transmission from mother to infant,” Segata says their next study will allow them to identify which microbes, and whether they will survive in the infant gut.