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Babies are born with bacteria in their stomachs. I heard on The radio that when a child is given antibiotics for the first time unique bacteria in the stomach are destroyed and cannot be replaced. Is this true, and, if so, does this have negative effects on the health of the newborn?

Closely Related, but different: What bacteria do unborn babies contain?

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It's a fascinating topic! While most of the bacteria known to colonize babies comes from the vaginal tract during birth and then later, through breastfeeding, although there is evidence to suggest that microbial colonization may begin before birth.

Regarding what these bacteria are, our microbiomes are composed of probably hundreds of species of bacteria from at least four major phyla: actinobacteria, proteobacteria, firmicutes and bacteroidetes (see the review for more on them).

As for taking antibiotics, I find it highly unlikely that taking antibiotics would completely destroy any native gut flora species. I certainly can't find any evidence to suggest that that might be the case. In general, when we have to take antibiotics, the offending bacteria are a relatively small population, compared to our native species and are less well-adapted to our body environment. Antibiotics work with our own immune defenses to clear our system of pathogenic species. Antibiotics also hurt our native flora, but less so than the ones that make us sick.

As for your last question regarding health, I wouldn't exactly say that having a microbiome promotes better health, so much as that your microbiome is critical for survival and health. There are actually nutrients that we need for survival that we cannot digest without our microbiota and a wide number of diseases, from immune disorders to potentially depression, can arise from an unhealthy microbiome.

As a fun bit of trivia to ponder in parting, our bodies are composed of 90% bacterial cells by count. Sweet dreams... :-)

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    $\begingroup$ The 90% bacterial cell number is most likely too high by an order of magnitude. See this paper. $\endgroup$
    – Chris ♦
    Commented Mar 21, 2016 at 8:02
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    $\begingroup$ I think you missed one important part of the question - the claim that antibiotics destroy bacteria in the body. They don't - not by far. They can affect the balance of bacteria (some are more affected by that particular antibiotic than others), and they reduce their populations and do a bit of selection, but they simply can't kill all of even one kind of bacteria. If they could, antibiotics would cure any bacterial infection instantly, which simply isn't the case - they just tip the fight in your favour. Not to mention that many parts of the body aren't easily accessible by antibiotics. $\endgroup$
    – Luaan
    Commented Mar 21, 2016 at 9:24
  • $\begingroup$ Interesting fact : Knowing that a baby born by caesarean is not likely to come in conatact with useful microbes of the vagina of the mother, Rob Knight, a microbiologist applied them on his baby with a swab from his wife's vagina ! $\endgroup$
    – biogirl
    Commented Mar 21, 2016 at 14:06
  • $\begingroup$ Good point, @Luaan! I definitely missed that. Thanks for adding to it. In future, I'll try to keep my answers to daylight hours, when I'm most awake. ;-) $\endgroup$
    – Forest
    Commented Mar 21, 2016 at 15:20
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    $\begingroup$ Suggests is the key word. The preceding statement is thought to be correct: "Colonization of mucosa in the digestive, respiratory, urogenital tracts, as well as the skin begins at, or perhaps even before, the time of birth when a newborn is exposed to a mother’s microbiota." There aren't really good studies yet about in utero gut microbiomes, but a lot to suggest otherwise at this time. If you have a some good studies to support your statement (there wasn't any reference cited in that article), I'm very interested in reading them. Thanks. $\endgroup$
    – anongoodnurse
    Commented Mar 22, 2016 at 16:57

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