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Key Message #3 – Opportunities to Affect Microbial Colonisation of the Gut

Microbial Colonisation of the Gut

The foetal and neonatal periods are the developmental periods of extraordinary plasticity (adaptation) and much of the structural and physiological development at this time is now known to remain with us into adulthood.

By 12 months of age, the composition of the infant’s microbiome starts to resemble that of an adult gut and we are no longer able to permanently influence the structure and diversity of this bacterial community.

Key factors that have been shown to impact gut microbiome development during this period are the mode of delivery, feeding type, hospitalisation, gestational age (pre-term) and antibiotic administration[1].

Colonisation at birth

The first colonisation of the gastrointestinal tract (GIT) by the microbiota occurs at birth. Although there is some evidence to show that there are low numbers of foetal and placental microbiota, this is currently considered to be part of the preparation of the baby’s immune system for the outside world and the intestine of the healthy newborn infant can be considered to be sterile.

The microbial flora is acquired immediately following birth via contamination/inoculation from the environment the baby is born into. The newborn gut is a perfect microbial habitat as it contains food, moisture and warmth, which enable the microbes to colonise and start to grow.

For vaginal birth, the first colonisation is from the vaginal, skin and rectal microflora of the mother – 90% of the microbiota present in the baby in the first few days of life have been shown to reflect the vaginal flora of the mum, being mainly lactobacillus species (primarily acidophilus strains).

For caesarean-section (C-section) birth, this first colonisation comes from skin and hospital environment flora.

As a result, the microbial population of the gastrointestinal tract of babies born by vaginal birth differs significantly from that of babies born by C-section, as follows:

Vaginal Birth

Dominant types:

Lactobacilli (mainly acidophilus types)

Propionibacteria (Staphylococci)

Enterobacteria (various including E. coli)

Minor colonisers:





Dominant types:

Staphylococci (S. aureus (MRSA)

Enterococci (E. faecium, E. faecalis)


Minor colonisers:


Colonisation via feeding

The second way in which the infant microbiome is colonised is via breastmilk, which has the ability to affect the development of the microflora through two mechanisms [1] and [2]:

Deposition of the small intestinal flora of the mother to the baby via breast milk, and

Stimulation of the large intestinal flora by prebiotic oligosaccharides present in breast milk.

Human milk was traditionally considered to be sterile, but recent research has shown that it provides a continuous supply of bacteria to the infant’s gut. Both colostrum and breast milk contain commensal bacteria and the bacteria present in the gut microbiota of breastfed infants has been shown to reflect that found in their mother’s breast milk.

Intestinal bacteria are transferred to the breast tissue via the dendritic cells during pregnancy in preparation for breast milk production. This ‘mammary microbiota’ development has been shown to start during the last trimester of pregnancy, reaching the highest levels at the end of this period. It then remains at relatively constant levels throughout breastfeeding, declines quickly once weaning starts and disappears completely when there is no milk in the mammary gland.

Breast milk also contains oligosaccharides that play a key role in driving the diversity of the infant gut microbiota by selectively stimulating the growth and activity of beneficial bacteria.

Beautiful pregnant woman isolated on white background – ProVen Probiotics

Why supplement?

The composition of breast milk reflects the health and diet of the mother and supplementation of the mother’s diet with probiotics and prebiotics during both pregnancy and lactation may help to optimise this bacterial colonisation of the baby’s GI tract. Providing supplementation directly to the baby may also help to support this and is particularly useful if the infant is formula-fed.

Want to know more?

Pro-Ven Probiotics aim to provide the best support for both you and your health. If you wish to know more about gut health, and staying healthy please do not hesitate to call us on 01639 825107 or alternatively, learn more via our blogs or in-depth proven research.

ProVen Probiotics, Unit 2 Christchurch Road, Baglan Industrial Park, Port Talbot, SA12 7DJ. Tel: 01639 825107

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