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I understand that it's feasible the bacteria within the gastrointestinal tract originate from the food we eat and air we breath, but where does this population of microbes originate from?

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Actually, the bacteria in the human gut originate from the birth canal. There are vast differences in the gut microbiome between kids born vaginally and those born by C-section, and these differences can have health consequences later in life. – Larry_Parnell Mar 24 '12 at 0:02
That's an interesting difference you point out, but ultimately, from where did the bacteria from the birth canal? Is it even known, or just a symbiosis that has existed before homo sapiens evolved? – leonardo Mar 24 '12 at 0:13
@Larry_Parnell do you have any reference? It seems really interesting! – Zenon Mar 27 '12 at 16:51
One of the Potential and major cause of vaginal infections and micro-flora is due to the hygienic habits are not followed during cleaning ass after defecation. There are certain important rules to clean the region appropriately. – VAR121 Sep 26 '12 at 4:36

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Most of the initial colonisation is said to be coincidental ('happenstance' as the textbook puts it!) exposure.

It's then fairly predictable depending on:

  • type of delivery (as Larry commented);
  • feeding; and
  • receipt of antibiotics.

In terms of feeding, there are differences in flora between babies fed human milk and those that are given cow's milk.

There's a section called 'Establishment and Composition of Normal Flora' in chapter 187 of Principles and Practice of Pediatric Infectious Diseases (3rd ed) by Long which discusses the above.

It's also said that hormones may influence indigenous flora. For example, premenarcheal and postmenopausal vaginal flora are very different to those present during the childbearing period.[1].

  1. Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases. 7th ed. 2009. Churchill Livingstone.
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There is some interesting information here from the Human Microbiome Project, but no details regarding the source of vaginal microflora. I would say that the sources would be gut and skin.

Ethical issues of manipulating a baby's microbiome are brought to light here.

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