An interesting review article from last year (free access) which discusses information from many different species, several non-mammalian, that show that, not too surprisingly, our mothers are the source of our microbiome. They speculate that the bacterial contamination of breast milk with probiotic organisms, one of the sources of that microbiome, may actually be due to the presence of an entero-mammary pathway, so the good bugs may be actual transported in lymph to the breast. There doesn’t seem much evidence for that, but it is an interesting idea: colostrum which has been collected as aseptically as possible is colonized.
I found that article following a link from a blog post by the excellent Ed Yong, he writes about other ways in which breast milk affects the microbiome, including new data which suggest that the secretory IgA in breast milk (the actual initial research article was about mice). The results of the series of projects where mice were engineered to produce breast milk without IgA showed :
Early exposure to maternal SIgA prevented the translocation of aerobic bacteria from the neonatal gut into draining lymph nodes, including the opportunistic pathogen Ochrobactrum anthropi. By the age of weaning, mice that received maternal SIgA in breast milk had a significantly different gut microbiota from mice that did not receive SIgA, and these differences were magnified when the mice reached adulthood. Early exposure to SIgA in breast milk resulted in a pattern of intestinal epithelial cell gene expression in adult mice that differed from that of mice that were not exposed to passive SIgA, (Rogier EW, et al: Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression. PNAS 2014.)
So the effects of breast milk derived IgA on the intestinal microbiome persisted into adulthood.
Another article by Ed Yong recounts the investigation of microbiomes from isolated, indigenous peoples, and shows that they seem to have much more microbial diversity and some very different patterns to what he refers to as WEIRD people, (Western Educated Industrialized Rich and Democratic) from which almost all the published data have been derived so far. So that means that almost everyone I know is weird, I thought so! Plus they got their microbiomes from their mothers, so we have something else to blame our Mums for.