The Infant Gut Microflora

The trillions of microorganisms in the gut (including many types of bacteria) play an essential role in supporting strong immune and digestive systems. At birth, an infant’s gut flora is obtained from the mother and environment around them. Originally thought to be born sterile, new research is indicating some microbes may travel via the placenta to the foetus1. During birth, infants born vaginally are exposed mainly to microbes that originate from the mother, whereas those delivered by caesarean section appear to acquire intestinal flora mainly from the environment2. Breast milk is a natural source of continuous bacteria, with bifidobacteria understood to be the predominant species in a breastfed infants gut2. The two most predominant species appear to be Bifidobacterium breve and Bifidobacterium infantis3. Breast milk also naturally contains a prebiotic1, which is essentially a food source for probiotics such as bifidobacteria, imperative to selectively increase numbers in the immature and developing gut.


The Gut Flora and Immunity

Particularly in early life, the composition of the gut flora profoundly influences the development of the immune system and the gut mucosal lining1,2. This is not surprising, as up to 70% of immune cells are located within the gut4. A strong protective gut flora and immune system are imperative to protect the infant against the common cold, respiratory infections, infectious diarrhea, and other stomach bugs. The incidence of allergic diseases such as eczema, asthma and hay fever are ever increasing in early life and are associated with an altered or less diverse gut microflora, an impaired gut lining and a malfunction of the immune system5.

The Gut Flora and Digestion

A balanced gut flora is necessary to assist in the digestion of milk and the later introduction of solids, regular healthy bowel movements and a strong protective gut lining (where food absorption takes place). Any imbalance could lead to digestive symptoms such as constipation, diarrhea, bloating, flatulence and cramping. It is important that the digestive system works effectively so that the infant is able to gain adequate nutrients to function and grow optimally and to reduce the risk of pain associated with poor digestion. The gut flora appears to be imbalanced in infants suffering from colic6. They often have fewer levels of beneficial Lactobacilli that produce much less gas than potential pathogens.

The Gut Flora and the Brain Connection

It is already widely accepted that the brain sends signals to the gut, which is why stress and other emotions can contribute to gut symptoms. However, research is now indicating that the signals also travel the opposite way. Gastrointestinal symptoms have been found to be strongly correlated with the severity of autism7. An abnormal gut flora is repeatedly observed in these children7. It has been suggested that pathogenic micro-organisms produce toxins8 that could potentially cross the blood-brain barrier and interfere with brain development.

The Use of probiotic supplements in Infants

Probiotics have been shown to positively influence the infant’s gut flora balance6 and developing immune system9, showing promising results in the prevention and management of infectious diarrhea and allergies in particular10. Probiotics given to infants from birth seem to increase resistance to common coughs and colds and reduce the need for antibiotic use11.

As with many studies, results vary and probiotic supplementation often appears to be more effective as prevention opposed to treatment12. Probiotics are generally not found in commercial formulas due to the required high water temperature destroying the live bacteria. Probiotic powders should be added to the formula once at the temperature ready for consumption by the infant.


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  2. Fanaro S, Chierici R, Guerrini P, Vigi V. 2003. Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl. Sep;91(441):48-55.
  3. Roger LC, Costabile A, Holland DT, Hoyles L, McCartney AL. 2010. Examination of faecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life. Microbiology. Nov;156(Pt 11):3329-41.
  4. Vighi G, Marcucci F, Sensi L, Di Cara G, Frati F. 2008. Allergy and the gastrointestinal system. Clin Exp Immunol. Sep;153 Suppl 1:3-6. 
  5. Ly NP1, Litonjua A, Gold DR, Celedón JC. 2011. Gut microbiota, probiotics, and vitamin D: interrelated exposures influencing allergy, asthma, and obesity? J Allergy Clin Immunol. May;127(5):1087-94.
  6. Savino F, Cordisco L, Tarasco V, Palumeri E, Calabrese R, Oggero R, Roos S, Matteuzzi D. 2010. Lactobacillus reuteri DSM 17938 in infantile colic: a randomized, double-blind, placebo-controlled trial. Pediatrics. Sep;126(3):e526-33.
  7. West R, Roberts E, Sichel L, Sichel J. 2013. Improvements in gastrointestinal symptoms among children with autism spectrum disorder receiving Delpro® probiotic and immunomodulator formulation. J Prob Health. 1:1.
  8. Parracho HM, Bingham MO, Gibson GR, McCartney AL. 2005. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J Med Microbiol. Oct;54(Pt 10):987-91.
  9. Cross ML. 2002. Microbes versus microbes: immune signals generated by probiotic lactobacilli and their role in protection against microbial pathogens. FEMS Immunol Med Microbiol. Dec 13;34(4):245-53.
  10. Johnston BC, Goldenberg JZ, Vandvik PO, Sun X, Guyatt GH. 2011. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev. Nov 9;(11):CD004827.
  11. Kukkonen K, Savilahti E, Haahtela T, Juntunen-Backman K, Korpela R, Poussa T, Tuure T, Kuitunen M. 2008. Long-term safety and impact on infection rates of postnatal probiotic and prebiotic (synbiotic) treatment: randomized, double-blind, placebo-controlled trial. Pediatrics. Jul;122(1):8-12
  12. Lee J, Seto D, Bielory L. 2008. Meta-analysis of clinical trials of probiotics for prevention and treatment of pediatric atopic dermatitis. J Allergy Clin Immunol. Jan;121(1):116-121.e11.