This Scientific American article states that "[human] infestation [by bacteria] begins at birth". This would suggest that unborn babies are free from any bacteria. However, if the mother catches a bacterial infection, her unborn baby risks catching it, too. This would seem to contradict the Scientific American article.

Presumably, when a human egg is fertilized by a sperm, the resulting cell may be free of any bacteria. At some point, bacteria begin to colonize the growing human body. Which bacteria are the earliest to colonize, and at what point in the development cycle does this occur?

In particular: does the health of the foetus depend on the presence of certain bacteria?

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    $\begingroup$ "However, if the mother catches a bacterial infection, her unborn baby risks catching it, too." Sorry, I just caught this; I thought you meant perinatal infections. In general, this applies to viruses and a few bacteria/protozoa: Listeria, spirochetes, toxoplasma, etc. However, these are the exception. Your statement makes it sound commonplace. It's not. $\endgroup$ Jul 27, 2015 at 4:46
  • $\begingroup$ related:biology.stackexchange.com/questions/44457/… $\endgroup$
    – Muze
    Mar 21, 2016 at 22:54

1 Answer 1


Babies are bacteria-free at birth. The meconium (the first stool) contains no bacteria if secured early enough.

Meconium is a sterile mucilaginous material that accumulates in the fetal intestine and is expelled soon after birth. It contains secretions of intestinal glands, gut constituents (proteins, bile acids, fatty acids, and steroids), and components of amniotic fluid and vernix caseosa.

Bacterial colonization of infants begins at birth - literally. They pick up bacteria from the mother's vaginal canal in passing, which they swallow. This is not seen in infants delivered by C-section. The importance of colonization picked up through normal birth is such, that some hospitals are swabbing the vagina of mothers delivering by CS and colonizing the oropharynx that way. Breast-milk also contains lactobacilli and bifidobacteria that probably contribute to the initial establishment of the gut flora of newborns.

And, yes, an infection the mother has while delivering must be taken into account. Herpes and Group B strep are both dangerous for a neonate.

The first microbes to colonize the intestines of newborn babies are the aerobic bacteria Escherichia coli and Streptococci. Later, the gut is colonized with anaerobic bacteria, e.g. Bacteroides, Bifidobacteria, and Clostridia. In 1–2 y, the gastrointestinal tract of infants has developed a natural microflora, which resembles the microflora of adults.

The infant continues to pick up bacteria from all people they come into regular contact with, including nurses.

The effect of the maternal flora on the initial gut colonization may be less than expected as the fecal flora of infants started to resemble both the fecal flora of the mother as well as that of the first nurse. Breast milk may contain bacteria which colonizes the gut as well

Infants aren't overwhelmed by infection due to the presence of antimicrobial peptides found on their skin, GI tract, and immunity is conferred via breast milk.

Several AMP have been characterized in vernix and skin of the newborn, indicating a well-developed innate immune system, which may play a pivotal role at the time of postnatal colonization.

Antimicrobial Components of the Neonatal Gut Affected Upon Colonization
Dynamics of gut colonization and source of intestinal flora in healthy newborn infants
Protection of the Neonate by the Innate Immune System of Developing Gut and of Human Milk
Establishment and development of lactic acid bacteria and bifidobacteria microbiota in breast-milk and the infant gut

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    $\begingroup$ I have found these articles which contradict what you write: sciencenews.org/blog/growth-curve/… symbionticism.blogspot.ca/2013/08/… directorsblog.nih.gov/2014/05/28/… $\endgroup$ Jul 26, 2015 at 19:41
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    $\begingroup$ @JamesNewton - I've seen contradictory studies (few) as well. Frankly, I don't think they're enough yet. I read the umbilical cord blood study (not a report of it). I also could cite animal studies. If mammals were born with some bacteria, germ-free mammal lines would be impossible. While I agree that the uterus is not necessarily germ free (and therefor the placenta is also at risk), right now this is a bit new, like Helicobacter pylori as causative of ulcers was. Time (and more research) will tell. $\endgroup$ Jul 26, 2015 at 21:00
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    $\begingroup$ @JamesNewton - Also, I have a lot of contradictory seeming-evidence: The two people born aseptically who survived SCID in an aseptic environment (they had sterile feces), germ-free animal models (as mentioned earlier), and the results of many studies linking bacterial colonization of the uterus with infertility, miscarriages, etc., as well as the results of studies of anmiotic fluid and PROM (premature rupture of membranes) in neonates. Maybe coincidental, but not ready to throw the baby out with the bathwater yet. $\endgroup$ Jul 26, 2015 at 21:15
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    $\begingroup$ In medicine, there's a saying: Be neither first nor last. I've taken that to heart for 30+ years. I don't jump on bandwagons, but am not the last one to try something new. The health of my patients - not my ego - are my primary concern. My favorite role models in medicine (I have a bunch) are Barry Marshall and Robin Warren. That should say something. (P.S. If you have a better answer, please post it.) $\endgroup$ Jul 26, 2015 at 21:30
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    $\begingroup$ @WYSIWYG - I cannot speak to earthworm placental function at all. Lots of crazy stuff happens in other kinds of mammals, let alone invertebrates. $\endgroup$ Jul 27, 2015 at 5:18

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