Where does the human microbiota come from?
There are two levels at which we can address this question. On the time scale of a human life, the microbiota begins to develop at birth, with an infant picking up microbes mostly from the birth canal during a natural birth or mostly from the skin of caregivers if the birth was by cesarean section. (Update as of June 2014: a recently published study suggests that some live bacteria are transferred across the placenta, so the colonization of an infant may even begin before birth.) The ecological process of ‘colonization’ continues for months, though, with lots more opportunities for transfer of microbes to the infant from other humans, and from food, animals, and the environment generally. Breast-feeding seems to have a particularly strong effect on the infant gut microbiota, both because live microbes are transferred from the mother, and because breastmilk contains compounds that promote the growth of certain bacterial types within the Bifidobacterium genus, which have numerous health benefits.
The composition of the still-developing infant gut microbiota (containing relatively few types of microbes) seems to be rather chaotic during this time, with the community temporarily dominated by an unpredictable sequence of microbial types that may not be typical gut microbes at all, or at least that aren’t usually found at such high abundance in older children or adults. As more and more microbial types successively colonize the infant gut, and as the infant’s diet becomes more diverse and similar to an adult diet, the composition of the gut microbiota tends to become both more diverse and more stable over time. Weaning is usually described as the time when the child’s gut community becomes ‘adult-like’, but weaning is more of an important milestone in the middle a gradual transition, and not so much a moment with a sharp break between ‘before’ and ‘after’.
At a longer, evolutionary time scale, the process of people getting their microbiota mostly from their mother, kin and social group extends unbroken into the past, so the human microbiota has co-evolved with us for as long as we’ve been human. The microbial communities at analogous body sites of all mammals (especially the gut microbiota, which is the component most often studied) are unmistakably similar to each other, and quite different in composition from the microbial communities of any other environment. The co-evolution of vertebrate animals with their microbiota undoubtedly extends at least as far back as the transition of amphibians to terrestrial habitats, and quite probably further back into the evolutionary history of fishes (although the topic has barely been addressed). And here’s one really cool consequence of long term co-evolution: microbes that are specialized to live on us and get passed on to our kids experience natural selection to promote our evolutionary fitness (because it helps their fitness too). And in the same way, we experience natural selection to maintain our association with beneficial microbes. Having a shared evolutionary fate over many generations is a prescription for cross-species mutualism…in general, both us and our microbiota benefit each other.
There are two levels at which we can address this question. On the time scale of a human life, the microbiota begins to develop at birth, with an infant picking up microbes mostly from the birth canal during a natural birth or mostly from the skin of caregivers if the birth was by cesarean section. (Update as of June 2014: a recently published study suggests that some live bacteria are transferred across the placenta, so the colonization of an infant may even begin before birth.) The ecological process of ‘colonization’ continues for months, though, with lots more opportunities for transfer of microbes to the infant from other humans, and from food, animals, and the environment generally. Breast-feeding seems to have a particularly strong effect on the infant gut microbiota, both because live microbes are transferred from the mother, and because breastmilk contains compounds that promote the growth of certain bacterial types within the Bifidobacterium genus, which have numerous health benefits.
The composition of the still-developing infant gut microbiota (containing relatively few types of microbes) seems to be rather chaotic during this time, with the community temporarily dominated by an unpredictable sequence of microbial types that may not be typical gut microbes at all, or at least that aren’t usually found at such high abundance in older children or adults. As more and more microbial types successively colonize the infant gut, and as the infant’s diet becomes more diverse and similar to an adult diet, the composition of the gut microbiota tends to become both more diverse and more stable over time. Weaning is usually described as the time when the child’s gut community becomes ‘adult-like’, but weaning is more of an important milestone in the middle a gradual transition, and not so much a moment with a sharp break between ‘before’ and ‘after’.
At a longer, evolutionary time scale, the process of people getting their microbiota mostly from their mother, kin and social group extends unbroken into the past, so the human microbiota has co-evolved with us for as long as we’ve been human. The microbial communities at analogous body sites of all mammals (especially the gut microbiota, which is the component most often studied) are unmistakably similar to each other, and quite different in composition from the microbial communities of any other environment. The co-evolution of vertebrate animals with their microbiota undoubtedly extends at least as far back as the transition of amphibians to terrestrial habitats, and quite probably further back into the evolutionary history of fishes (although the topic has barely been addressed). And here’s one really cool consequence of long term co-evolution: microbes that are specialized to live on us and get passed on to our kids experience natural selection to promote our evolutionary fitness (because it helps their fitness too). And in the same way, we experience natural selection to maintain our association with beneficial microbes. Having a shared evolutionary fate over many generations is a prescription for cross-species mutualism…in general, both us and our microbiota benefit each other.