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The microbiome for the baby comes from the mother as it passes through the birth canal or in the case c-section to a lesser degree via breast feeding - bootstrapping us for healthy digestive tract.

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Of note - it is common for mothers to receive antibiotics during delivery for a great many reasons. This can delay the development of the gut microbiome in babies, and is potentially linked to colic.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8170024/

In some c-section cases they’ll perform “vaginal seeding”, wherein the microbiome from the mother’s vaginal canal is swabbed onto the face, mouth, etc. of the newborn.

https://my.clevelandclinic.org/health/treatments/22096-vagin...

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