Newborn and Mother


Today I want to talk about how we acquire our gut flora. This should be of interest to expectant parents everywhere.

A newborn infant was initially thought to be born with a sterile gut, but new research suggests that the acquisition of its unique microbiota begins in the womb. It appears that colonization of the fetus’s GI tract begins before delivery with ingestion of amniotic fluid containing microbes from the mother.

However, the majority of an infant’s gut flora is acquired when the baby passes through the birth canal swallowing the mother’s native bacteria.

In the case of Caesarean section, the child will also acquire their gut flora from the mother via amniotic fluid as well as contact with the mother shortly after birth. Nevertheless, the initial exposure after birth is more likely to be the result of contact with the surrounding environment such as the nursing staff, the hospital environment and other infants.

Children born by Caesarean section have lower counts of Bacteroides fragilis and bifidobacteria but higher counts of Clostridium difficile, a gram-positive pathogen responsible for severe diarrhea and inflammation of the colon. They also have reduced diversity of bacteria compared to their vaginally delivered counterparts.

Clostridium difficile is almost exclusively acquired in hospital settings as hospitalization and being born prematurely have been consistently associated with it. Antibiotic treatment in infants is also highly associated with elevated C. difficile counts as well as reduced counts of Bifidobacterium and Bacteroides.

The main gut flora populations of Caesarean-born children may be disturbed for up to six months after birth in contrast to one month for infants born vaginally. Disordered gut flora predisposes to increased vulnerability to infections of all types.

The baby’s gastrointestinal tract is first colonized by facultative aerobic bacteria. Facultative aerobic bacteria are bacteria that can exist in either an oxygen-rich or oxygen-free (anaerobic) environment.

When these bacteria expand, they consume all the air in the GI tract creating an anaerobic environment that is then colonized by increasing numbers of anaerobic microbes. Bifidobacterium, Bacteroides, Clostridium and Ruminococcus are the predominant anaerobes that soon displace these aerobic bacteria.

Other factors influencing what the baby’s microbiota consists of include the hygiene conditions of the infant as well as infant feeding.

After birth, environmental, oral and skin bacteria are easily transferred from the mother and anyone in contact with the baby through suckling, kissing and caressing.

Infants that are breast fed have a colonic gut flora that is dominated by bifidobacteria and lower numbers of E. coli, C. difficile, B. fragilis and Lactobacillus than bottle-fed babies. However, after the introduction of solid food, the gut flora of breast-fed children becomes similar to formula-fed infants.

Once the child’s gut flora is transformed into the adult-type, it remains amazingly consistent over long periods of time. Because these early bacterial colonizers regulate the gene expression of cells lining the digestive tract, they create a favorable environment for themselves that inhibits the growth of other bacteria introduced later. So the initial colonization of the digestive tract is extremely important.

This initial colonization also trains the immune system to differentiate between friendly gut microbes and pathogens. Otherwise there is a risk that the intestinal immune system will mount an inflammatory immune response against what would otherwise be considered commensal gut flora.

Friendly gut flora also trains the immune system to distinguish the difference between innocuous ingested or inhaled substances to prevent an activation of an inappropriate immune response. It is now widely accepted that the composition of the gut flora directly affects the development of allergic diseases in the gut, respiratory system and skin. Dysregulation of this system is the cause of allergies and asthma.

It should be clear that the state of the pregnant mother’s gut flora will have important impacts on her child’s microbiota. If the mother has a diverse and healthy gut flora, she will pass this on to her offspring. However, if the mother has disordered gut flora, this too will be passed to her offspring handicapping her child’s ability to develop a healthy gut and immune system.

Add in a Caesarean birth, formula feeding and early antibiotic treatment and the difficulty of establishing a healthy infant microbiota and gastrointestinal tract is compounded.

Any woman out there reading this who is contemplating motherhood owes it to herself and her unborn child to correct any suspected gut dysbiosis prior to giving birth. This also includes expectant fathers as bacteria is shared within a household, especially through sexual contact.

Otherwise you may risk having a child who will spend a good chunk of their childhood, and possibly adulthood, dealing with the consequences of intestinal inflammation, allergies, compromised immunity and inflammatory responses due to increased intestinal permeability.

There is a hypothesis that postulates that infant and childhood gut dysbiosis is the cause of autism-spectrum disorders. In light of what we’ve learned so far about the effects of endotoxemia, this isn’t in the least bit surprising to me because as you’ll learn in future posts, endotoxemia also affects the brain and central nervous system.



Manco M., Putignani L., Botazzo G. F. (2010) Gut Microbiota, Lipopolysaccharides, and Innate Immunity in the Pathogenesis of Obesity and Cardiovascular Risk. Endocrine Reviews, 31(6): 817-844.

McLoughlin R. M. and Mills K. H. G. (2011) Influence of gastrointestinal commensal bacteria on the immune responses that mediate allergy and asthma. Journal of Allergy and Clinical Immunology, 127: 1097-1107.

Mshvildadze M., Neu J., (2010). The infant intestinal microbiome: Friend or foe? Early Human Development 86 Supplement 1: 67-71.

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