Development of healthy gut microbiota early in life


  • Proceedings of the Nestle sponsored presentation at the FAOPS & PSANZ Conference, Sydney, March 2012.

  • Publication of this supplement has been supported through an independent educational grant from Nestle Australia.

Professor Erika Isolauri, Department of Pediatrics, University of Turku and Turku University Hospital, Kiinamyllynkatu 4-8; 20520, Turku, Finland. Fax: +358-2-3131460; email:


A healthy intestinal microbiota profile in early life is related to health later in life. An aberrant composition is associated with risks of systemic problems, such as obesity, diabetes and allergic diseases, including asthma and enteric inflammatory conditions, sometimes manifesting at 7 years of age. A healthy and balanced gut microbiota profile in infancy, especially with regard to bifidobacteria, is directly related to mode of delivery (natural birth) and quality of breast milk, which in turn is affected by the mother's own systemic health and nutritional status. Pregnant women of normal body weight and healthy microbiota profiles, both gut microbiota and breast milk microbiota, have greater opportunities to pass on compounds, antigens modified by the mother's gut and other agents that promote the development of a healthy immune system in the breastfed infant.


Development of gut microbiota in early life is related to health later in life. As adults, our health is determined by events in utero and in early childhood, especially with regard to the nutritional environment, which influences the maturation, structure and function of our immune system, metabolic health and microbiological programming.

Although the human genotype affects individual susceptibility to disease, this is considered to have only a small direct influence on overall health, that is, the immunological phenotype. It is epigenetic mechanisms (influences in the development of an organism other than DNA sequences) that might permanently affect the activity of human genes in the development of health, especially when such influences take place during the early critical stages of development/maturation. This is the modern version of the programming theory.

Key Points

  • 1A healthy and balanced gut microbiota profile in early life is related to health later in life.
  • 2Development of infant immunity is influenced by mode of delivery and composition of breast milk.
  • 3Quality of breast milk is dependent on the mother's own health, inclusive of weight, microbiota profiles and nutritional status.

The Immature Immune System

What is the first challenge for the immature and inexperienced immune system of the child? The attainment of colonisation of gut microbiota is the key factor that provides experience and maturity to the individual immune system.

We used to think we were colonised by microbes that might create a risk for the immature immune system, but now we know these microbes, which follow logical steps of colonisation, make the gut defence barrier stronger. We are first colonised by facultative anaerobes, followed by higher numbers of bifidobacteria, which typify the gut microbiota of the healthy breastfed baby.

If a step in this process of colonisation goes wrong, the healthy immune system is faced with certain risks.

In general, our gut microbiota is classified as beneficial or harmful, although a large percentage remains as yet unknown. Of the microbes in the intestine, 30–40% still can not be cultured or identified.

We classify lactobacilli and bifidobateria as noninfammatory, as compared with other bacteria, such as clostridia and staphylococci, which are associated with inflammatory response. However, some bacteria, according to individual strains, are more or less beneficial. More needs to be learnt about the roles of these bacteria. Further, there are 20–30 strains of bifidobacteria, which are not all good. It is the strain of bacteria, not the type of bacteria per se, which may be considered as beneficial.

Aberrant Compositional Development of Gut Microbiota

The compositional development of gut microbiota can be linked to the risk of disease. For instance, healthy infants (1 month of age to 12/18 months) harbour a natural predominance of bifidobacteria with specific strains present. In comparison, infants later manifesting atopic sensitisation present with a reduced ratio of bifidobacteria to clostridia and with distinct bifidobacterial microbiota strains.1 This has been detected at the time of breastfeeding, prior to the development of allergic reactions.

The same is the case for development of obesity. Decreased numbers of faecal bifidobacteria have been detected in early infancy in those who later go on to become obese, in comparison with healthy children.2

Colicky infants have also been found more often to harbour larger colonies of Clostridium difficile3 and have different fatty acid profiles and numbers of Lactobacillus, compared with non-colicky infants.4

A recent study has shown a low proportion of Bifidobacterium, and a high proportion of unidentified bacteria, to be directly interconnected with daily amounts of crying in infants.5 An inverse association between infant crying time and bifidobacteria has been shown.

Such studies indicate that the total genetic pool of microbiota constitutes the complex interaction of immune response and nutritional status, and may be related to nutritional, immunological and microbiological programming of a child's health.

Possible Causes of Aberrant Microbiota Development

Mode of delivery

One cause of early aberrant microbiota development is the mode of delivery. In one generation, the rate of Caesarean section delivery has increased 10-fold or more, and a number of studies have revealed this to be related to various morbidities later in life.

The Finnish Birth Cohort study compared asthma rates in children at 7 years of age and found vaginally delivered children had lower rates of asthma compared with those delivered by Caesarean section (366/8826 (4.25%) vs. 1684/51 039 (3.3%], odds ratio 1.27 (1.13–1.42), P < 0.001).6

In the Turku Birth Cohort again from Finland, a greater number of positive allergy tests were detected among the Caesarean delivery group than the vaginal delivery group.6

A large cohort study from Holland, the KOALA study, found that the mode of delivery directly affected asthma risk.7

The overall increase in asthma rates among Caesarean-delivered children revealed in a number of meta-analyses has been recorded by Thavagnanam et al.8 (Fig. 1).

Figure 1.

Meta-analysis of studies of asthma and Caesarean section using the random-effects model, studies ordered by publication date. aTest for heterogeneity χ2 = 40.36, df = 22, P = 0.01; I2[95% confidence interval (CI)] = 46% (11%, 67%); test for overall effect Z = 6.36, P < 0.001. bExcludes studies [16, 28, 29]; test for heterogeneity χ2 = 28.01, df = 19, P = 0.08; I2 (95% CI) = 32% (0%, 61%); test for overall effect Z = 6.76, P = 0.001. This figure was published in Thavagnanam, S., Fleming, J., Bromley, A., Shields, M. D. and Cardwell, C. R. A meta-analysis of the association between Caesarean section and childhood asthma. Clin Exp Allergy, 38: 629–633 (2008). Reproduced with kind permission from Wiley-Blackwell.

With regard to obesity, recent studies from Brazil, a country with one of the highest rates of Caesarean section deliveries, have found higher rates of obesity among young adults9 and children who were delivered by Caesarean section compared with those delivered vaginally.10

In terms of enteric inflammatory diseases, a retrospective multi-centre case-control study of 1950 children in Germany across 26 university hospitals and 16 nonacademic children's hospitals, found an enhanced likelihood of being born by Caesarean section among those with celiac disease, but there was no association with those who had Crohn's disease or ulcerative colitis.11

Association between mode of delivery and type I diabetes was examined in a meta-analysis of observational studies, and an increased risk of 20% was detected among those delivered by Caesarean section.12

In Caesarean section delivery children, colonisation by Bifidobacterium-like bacteria can be delayed by up to 1 month,13 which is an immunologically significant delay. Further, in vaginally delivered children, greater total numbers and diversity of microbiota were detected.14

Biasucci et al. found the predominant microbiota in vaginally delivered, healthy children were B. longum and B. catenulatum.15 Mode of delivery has also been found to affect oral microbiota in children, inclusive of diversity and overall numbers.16 In essence, vaginally delivered children have been found to have acquired bacterial communities more resembling that of their own mothers compared with those delivered by Caesarean section, and these differences in microbiota colonisation could still be evidenced at 7 years of age.17

Thus, it is the mode of delivery and associated environments that contribute to the overall microbiota community in the newborn infant, acquired through the mouth and through skin contact, all determined at birth and within the first days of life.

But what is happening in these first days? As an example, let us examine the problem of obesity. Pregnancy frequently creates the first step in a metabolically healthy woman towards becoming overweight. Intrauterine overnutrition, that is, greater weight gain during pregnancy, and postpartum weight retention also lead to larger birth size of the newborn, obesity in infancy, overweight in childhood and a fourfold risk of adult obesity10 and development of asthma.

In a study of 25 overweight children and 24 normal-weight controls aged 7 years, matched for all possible confounding factors (such as gestational age, birth body mass index (BMI), mode of delivery, breastfeeding, use of antibiotics and probiotics), an examination was made of their overall colonisation patterns from birth onwards. The study found that those later becoming overweight had lower counts of bifidobacteria at the ages of both 6 and 12 months than normal-weight controls, as well as lower levels of total Bifidobacterium genus pool, and specifically of B. longum and B. breve.2

Microbiota is therefore seen to influence the complex interaction between immune response and nutritional status. At the same time, microbiota profiles are themselves influenced by mode of delivery. Together, these play significant roles in the nutritional, immunological and microbiological programming of infant health.

Thus it is shown that the mother provides the first inoculum for the child and this influences the risk of becoming overweight or allergic later in life and that Bifidobacterium species intervene and are determinants in these risks.


The next step in colonisation in the first months of life is breastfeeding. There is considerable debate about the importance of the duration of breastfeeding. However, it is important to consider the ‘quality’ of breastfeeding.

What is breast milk? It is a very interesting mixture, containing a number of anti-inflammatory compounds that modify the feeding child's immunity development (fatty acids, antioxidants, nucleotides, glutamine, lactoferrin and immunoglobulin A (IgA)). This is done passively, by passing on these compounds to the infant who is born deficient in such compounds as IgA, but also actively by providing cytokines, such as transforming growth factor β (TGF-β), which stimulate the maturation of the infant's own immune system and consequent IgA levels.

There are also antimicrobial agents and oligosaccharides that help to enhance the future bacteria in the child's intestine. There are antigens present in breast milk, such as β-lactoglobulin, ovalbumin and gliadin, all of which have been structurally modified or degraded by the mother's gastrointestinal tract, so that they are presented to the infant in breast milk without causing inflammation.

This admixture of compounds, antigens and agents in breast milk educate the child to become tolerant of certain foods and the anticipated environment later in life. This is in contrast to previous teachings, where avoidance of foods, such as cow's milk, citrus, fish and so on, was encouraged so as not to create allergic reactions. Now it is suggested that exposure is necessary to build up tolerance to these things, thus avoiding allergic reactions.

So, breast milk is clearly not sterile. It contains a range of bifidobacteria and lactobacilli strains, and in particular B. longum and B. lactis, which, importantly, are not typical strains found in an adult,18 but are typically infantile bifidobacteria. This indicates that breast milk is a unique environment, specifically created by various biological processes occurring in the lactating mother. It is also influenced via exchanges from the baby's mouth and from oligosaccharides in the milk, which enhance bacterial numbers.

Bifidobacteria numbers in breast milk are directly affected by the mother's immunological status. Babies at 1 month, solely breastfed by their allergic and skin prick test-positive mothers, had lower levels of bifidobacteria.19 Similarly, weight gain had influence on composition of gut microbiota in pregnant women. Bacteroides and staphylococcus were found to be significantly higher in overweight pregnant women, and Bifidobacterium counts were lower in women with excessive weight gain during pregnancy compared to those with lower weight gain,20 with similar findings in the breast milk of such mothers, along with higher levels of TGF-β2 and soluble CD14 (which enhances immune recognition) in normal-weight mothers.21 Further, TGF-β levels in breast milk have been promoted by providing probiotics to the pregnant and lactating mother.22

Thus it can be seen that Bifidobacterium colonisation frequencies and counts among mother–infant pairs correlate.19,23 Infant probability of being appropriately colonised by bifidobacteria is lower when the mother has higher BMI, excessive weight gain during pregnancy and the child is delivered via Caesarean section, and higher when the mother is of normal weight, has appropriate bifidobacteria colonisation in her own gut and in breast milk and is breastfeeding. Therefore, it is the latter scenario that should be the target for intervention by diet and probiotics.

The Role of Microbiota

The promotion of specific strains of the healthy gut microbiota provides:

  • • Balance in the gut microbiota
  • • Enhanced energy efficiency
  • • Enhanced macrophage activity and phagocytosis
  • • Tightening of the intestinal epithelium and strengthened gut barrier function
  • • Competitive exclusion of pathogens by impeding their adhesion potential
  • • Induction of mucin production
  • • Stimulation of gut humoral immunity (IgA)
  • • Augmentation of antigen-specific immune responses, lowering the risk of reinfection

How do microbes influence our weight? This is currently a very interesting topic. Bäckhed et al. showed in their animal experimental models that certain microbes ferment unabsorbable carbohydrates into short-chain fatty acids, providing higher energy harvest and de novo synthesis of triglycerides in the liver.24

Then there is suppression of fasting-induced adipose factor, inducing an increase in lipoprotein lipase and leading to an increase in fatty storage in the liver. Thus, microbes influence the quantity of energy harvested and stored in the body.

But obesity is not just energy intake. It is also high blood pressure, hyperglycaemia, hyperinsulinaemia and low-grade inflammation.

It was shown by Cani et al.25 in animal experimentation models that germ-free animals receiving high-energy diets did not gain weight, but when they colonised these animals with microbiota, the animals gained weight on the same diets. When colonies of microbiota were transferred to normal-weight animals, the receiving animals then gained weight. Examination revealed higher levels of blood lipopolysaccharides in these animals, which the authors labelled metabolic endotoxemia. There was also a drop in the levels of gut bifidobacteria.

In pregnant women who have excessive weight gain, higher levels of blood glucose, high serum insulin levels, higher levels of insulin resistance and higher Homeostasis Model Assessment (an indication of insulin resistance) index have been detected.26

In an intervention study during the first trimester of pregnancy, and continued throughout pregnancy, delivery and lactation, mothers who were metabolically healthy but having an allergic condition and manifesting positive skin prick tests were given nutritional counselling (individual guidance on normal, healthy diets, by a nutritionist).27 Comparisons were made against controls (women who received standard counselling at well women clinics) and women who received counselling and a mixture of probiotics through the same stages of pregnancy, delivery and lactation. On monitoring the health of these women, the risk of high blood glucose concentrations among those who received counselling was lower; however, in those who received counselling plus probiotics, blood glucose was significantly lower (Fig. 2). Thus, the risk of gestational diabetes can be reduced by dietary counselling and the introduction of probiotics, as well as the risk of having a larger baby (which is also linked to gestational diabetes).

Figure 2.

Proportion of mothers with high glucose values during (>4.8 mmol/L) and after (>5.6 mmol/L) pregnancy.

Further, at 12 months post-partum, the risk of central adiposity, which is an indicator of metabolic syndrome, was lower in the group receiving dietary counselling and probiotics. The overall purpose of this study was to reduce the risk of infant sensitisation. Skin prick test positivity was reduced by half in infants by the introduction of probiotics to their mothers.


Therefore, this is a very critical period of life that can influence long-term health. Pregnancy, mother's health (nutritional status, immunological health) and also the mode of delivery, breastfeeding and breast milk composition, all determine infant general health. Along with the food matrix in our weaning diet, these all influence our gut's health and the composition of gut microbiota, which have many functions in our body and for our health later in life.


The author was invited by Nestle Australia Pty Ltd to speak at the combined 17th Congress of the Federation of Asian and Oceania Perinatal Societies (FAOPS) and the 16th Annual Congress of the Perinatal Society of Australia and New Zealand (PSANZ) – FAOPS & PSANZ Sydney 2012. This supplement is a review article based on the presentation provided by the author at this meeting. The content for this article was presented by the author, and a medical writer, Rodrick Faulkner, undertook the writing of the first draft. The author contributed to reviewing and revising the manuscript with the medical writer coordinating the author amendments.

Multiple Choice Questions

  • 1Intestinal microbiota profiles in infants can be linked to risk of disease later in life by:
    • A Low colonies of Bifidobacterium
    • B Presence of clostridia and absence of Lactobacillus
    • C Absence of specific strains of Bifidobacterium
    • D Presence of unidentified microbiota
    • E Presence of B. longum and absence of B. adolescentis

Answer: C. Microbiota is made up of helpful, neutral and harmful bacteria. Many microbiota strains remain unidentified and so their harmfulness or otherwise is unknown. Absence or low colonies of bifidobacteria or Lactobacillus alone and/or presence of clostridia would be uncertain profiles for predicting later disease development without counts of specific strains of this microbiota. Thus, only the absence of specific bifidobacterial strains has been directly linked to later disease development.

  • 2Breastfeeding is important for the health of the infant in terms of:
    • A Duration of breastfeeding
    • B Ingestion of IgA and other compounds which the newborn infant lacks
    • C Provision of cytokines which stimulate growth of the infant immune system
    • D Both B and C
    • E Exposure to antigens and pathogens in order to promote immunity against later inflammation

Answer: D. Quality of breast milk is more important than duration of total breastfeeding because the newborn infant is dependent upon the supply of IgA and other compounds as well as cytokines and antigens, but not pathogens, in the healthy development of its own immune system.

  • 3Development of infant immunity is dependent upon:
    • A Exposure to antigens and pathogens
    • B Mode of delivery and presence of bifidobacteria in breast milk
    • C Lactating mother's education regarding probiotics
    • D Presence of high levels of bifidobacteria in the infant gut
    • E Mode of delivery, quality of breast milk and health of the mother

Answer: E. Healthy development of infant immunity is directly dependent upon several factors: mode of delivery and the presence of specific strains of microbiota (not just bifidobacteria per se), anti-inflammatory compounds, cytokines and antigens (quality) in breast milk, which in turn, is dependent upon the nutritional and immunological health of the lactating mother.


There is no potential conflict of interest, real or perceived, and no disclosures to be made.