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Fun fact: the gestational carrier will have their own genetics changed by the fetus, for a short time anyway.

Gut health is almost entirely dependent on the birth process. Intestinal colonization takes place during the first days of life (really the first minutes), being influenced by the method of delivery, type of lactation, and the environment. Short story: the uterus is sterile, the baby has no microbes. During delivery the baby comes out the vagina and swallows some poop/goop from the mother and those microbes start reproducing quickly. If not vaginal birth, the first colonizers are probably microbes on the breast surface or random hospital microbes on whatever goes in the infant mouth or even simply breathes in. Those first colonizers in the infants gut and set up gut microbiome. Infant microbiome is variable and does change over time due to diet, environment, etc. By about age 2-3 there is no difference between vaginal or surgical birth in healthy infants.

Genetics: the gestational carry does not transfer any other their genetic material to the infant. However, they can influence the expression of some of those genes. The really dumb analogy: you and a friend both buy the same car model, same colour, same day - after 5 years your different experiences have made those cars look and handle differently, despite being the same materials/genetics.

Harvard has a simple infographic discussing epigentics, or how your genetics turn into physical traits/behaviours.

Mothers(carrier) diet has been shown to affect epigenome of fetus in-utero: https://link.springer.com/article/10.1007/s00335-020-09839-z

Thank you for taking the time to respond. So when we talk about epigenetics, does that mean an example of this could be if the mother was really stressed during the pregnancy, the high levels of cortisol could (hypothetically) make the offspring more susceptible to developing a mood disorder later in life? What would be other ways gene expression might be affected by pregnancy (if you don’t mind me asking)?

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I read somewhere that every bit of our body contains bacterials so is it really true that the uterus sterile ??

Like every question and answer in life, it's complicated.

At this point unless we start arguing details, the uterus is close enough to sterile for this type of question.

Cortisol is only one example of a potential stressor. We have no way to link that to any output.

A simpler example is nutrition. There is a famous study of pregnant mothers who were starving in 1944-45 (note: actually starving-to-death-starving, not just a little bit skinny). A pregnant person who is starving is more likely to produce babies that grow into short adults, plus those short adults also have short children (grandchild from the starving mother).