This is a nice story, and one that’s being told more and more—but when you look closer, you can see plot holes.
Through studies in mice and people, it’s clear that C-sections and antibiotics can change the microbiome. But there’s a tendency to assume that these changes are bad, that they last, and that they matter. And I’m not sure we have enough evidence to warrant any of those conclusions.
Consider two new studies, published today, one led by Moran Yassour and Ramnik Xavier from the Broad Institute and the other by Nicholas Bokulich and Martin Blaser from New York University. The two teams collected stool samples from babies, 39 and 43 of them respectively, over their first three years of life.
Both showed that a common group of bacteria called Bacteroides is conspicuously rare from the guts of first-year infants born through C-sections. Is that a disruption? Is it a bad thing inflicted on the microbiome by an unnatural birth? Not quite. Xavier’s team also saw that a fifth of their vaginally delivered babies had the same low-Bacteroides signature, for reasons they still don’t understand.
And just last month, Xavier’s team published a paper linking high Bacteroides levels in infants to poorer health. These microbes dominate the guts of Finnish and Estonian infants, and they silence the developing immune system at a time when it must acclimate to the microbes it commonly encounters. This might explain why Finland and Estonia have relatively high rates of early-onset autoimmune diseases, caused by panicky, hyperactive immune systems that haven’t been properly calibrated. It might also explain why such diseases are rare in Russian infants, who carry far lower levels of Bacteroides.
What about other microbes? Last year, in a study of 319 babies, a Canadian team found a connection between low levels of four bacteria with anti-inflammatory properties and later risk of asthma. C-sections have been linked to higher asthma risk, so you’d expect that babies delivered this way would have low levels of the same bacterial quartet. Not so: in Blaser’s study, two of the four—Lachnospira and Veillonella—were overrepresented in the guts of C-section infants.
To summarise: ¯\_(ツ)_/¯
We still don’t really understand what these microbes are doing, so we can’t infer what their absence or presence implies. A change might be good or bad, depending on a multitude of circumstances, such as a baby’s genes or the other bacteria that it carries.
The two new studies also found that antibiotics reduce the diversity of species in the microbiome, both within individual infants and between them as a group. Xavier’s team showed that the drugs destabilize the bacterial communities, making them more prone to fluctuations, while Blaser’s group found that they delay the rate at which the microbes mature into their adult state.