The intestinal microbiota in early life plays a major role in infant health and development, impacting on maturation of the immune system, protection against pathogens, and influencing the long-term metabolic welfare of the host. The acquisition of microbial strains from mother to infant may occur through multiple different pathways, including the birth canal (and the proximity of the birth canal to the anus), contact between mothers and infant during parental care and through breast milk. From birth through to the initial stages of weaning, microbial composition has a significant impact on the infant gut. Recent advances in culture-independent sequencing technologies has allowed for the identification of key microbial species involved in the initial colonization process, including those facultative anaerobes such as Streptococcus, Staphylococcus and Enterobacter spp. Thus, the microbiome of vaginally born, exclusively breast fed infants at term, with no previous exposure to antibiotics either directly or indirectly from the mother, could be considered the "gold standard". Breast milk, a natural prebiotic source provides the optimal active ingredients for the growth of beneficial microbial species. A disturbance in the balance of microbial inhabitants can affect human host biology in many ways. Immune, endocrine, cognitive, as well as metabolic functions can be influenced by the microbial communities present; subsequently implicating future health outcomes such as insulin resistance, allergic diseases, depression and perhaps even autism. Beneficial microbial species and its associated bioactive compounds, which may restore overall gut health are thus of interest for infant nutrition, which when administered, may help treat or prevent a microbial disturbance in the gastrointestinal environment and have long term health benefits.

The gut microbiota appears to influence the development of emotional behaviour, stress- and pain-modulation systems, and brain neurotransmitter systems. Additionally, microbiota perturbations by probiotics and antibiotics exert modulatory effects on some of these measures have been seen in adult animal models. Current evidence suggests that multiple mechanisms, including endocrine and neurocrine pathways, may be involved in gut microbiota-to-brain signalling and that the brain can in turn alter microbial composition and behaviour via the autonomic nervous system. Therefore, another aspect of the work will involve studies addressing microbe to brain signalling to identify and develop commensal probiotic consortium (mixed strains and possibly mixed strains/ingredient mixes) products underpinned by the necessary science suitable for development of probiotics targeted at the microbiota-gut-brain axis, a bidirectional communication between the gastrointestinal system and the brain, which regulates brain function and plays a crucial role in mood control. It is well established that probiotic intervention, at least in mice, can improve mood and reduce anxiety in various models of stress. Despite confounding evidence, the mood enhancing impact of probiotic intervention observed in murine studies are not always translated in humans.

Babies born by C-section get the greatest benefit from breastfeeding, and often these mothers are taking antibiotics for 1-2 weeks post-delivery. Antibiotics are administered at time of incision (for both elective and emergency sections) to prevent internal wound infection. While human milk itself could be a source of bacteria for the developing infant, thereby influencing microbial intestinal colonization following birth, many questions remain about the impact of nutrition during pregnancy and lactation, source of the 'milk microbiome' and its impact on the establishment of the infant gut microbiota. A limited number of studies have examined the microbial communities present within breast milk and tracked alterations in microbial diversity throughout the lactation period. However, in a recent study, the investigator's group reported the presence of a core breast milk microbiome using Illumina MiSeq sequencing to detect 12 dominant genera in lactating mothers (n=10), constituting 81% of the taxa present over the first 6 weeks of life. A number of frequently shared taxa, including Bifidobacterium, Lactobacillus, Staphylococcus and Enterococcus were common in both breast milk and infant faeces during the first 3 months of life, and culture-dependent analysis identified identical strains of Bifidobacterium breve and Lactobacillus plantarum present in both breast milk and infant faeces, confirming the concept of maternal-infant transmission. Similar findings have been reported using randomly amplified polymorphic DNA (RAPD) and/or multi-locus sequence typing (MLST) to identify identical genomic patterns of Bifidobacterium and Lactobacillus present in breast milk and corresponding infant faeces.

Antibiotic treatment throughout pregnancy accounts for 80% of prescribed medications during pregnancy. The Mayo Clinic describes amoxicillin, ampicillin, clindamycin, erythromycin, penicillin and nitrofurantoin as being generally considered safe during pregnancy. Tetracyclines can damage a woman's liver during pregnancy, and trimethoprim + sulfamethoxazole (commonly used together to treat UTIs) may be linked with an increased risk of birth defects. Considering that it is now accepted that optimal establishment of the gut microbiota is highly desirable for normal human development, the risk is that antibiotic usage during pregnancy may have undesirable effects on the maternal vaginal and milk microbiome, with knock-on negative impact on the early infant microbiome. It is estimated that one in five pregnant women in Europe is prescribed at least one course of antibiotics during pregnancy; in the United States, this rate is double. In the case of proven maternal infection, narrow spectrum antibiotics should be preferred due to their less extensive effects on the microbiome, taking into account the association of prenatal antibiotics with increased risk of childhood atopic disease, epilepsy, and obesity.