The human gut is home to an enormous number of microbes that play an important role in host physiology, metabolism, nutrition and immune function. Deviations in initial human gut microbiota development have been associated with a number of immune-mediated diseases including inflammatory bowel diseases, atopy and allergies, as well as obesity, which are reaching epidemic proportions in the westernized world. However, gut microbiota dysbiosis has also been linked to health problems common in the developing world including malnutrition. The aim of this thesis was to unravel the impact of specific factors, including environment, geographical location, diet and mother’s microbiota, on the gut microbiota development in early infancy. 

Analysis of gut microbiota composition of six-month-old infants from Malawi and Finland, representing developing and westernized countries, revealed that the Malawians had a distinct Lactobacillus microbiota that was richer and more diverse compared to their Finnish counterparts. Interestingly, we detected L. rhamnosus GG, a widely used probiotic in Finland, in a third of the Finnish infants even though the infants or their mothers did not receive any probiotic products. For the detection, we used a L. rhamnosus GG strain-specific detection system, whose specificity was confirmed in this thesis. In addition, we noted that lipid-based nutrient supplements do not have an impact on gut microbiota development in Malawian infants. These dietary supplements have been used in several clinical trials to promote growth of children from developing countries, but their impact on the gut microbiota has been previously unknown. In addition to environment and diet, a number of host factors may have an impact on the gut microbiota development. Here, we assessed how mother’s microbiota influences the gut microbiota development in early infancy by comparing samples of maternal feces, placenta, amniotic fluid, colostrum, meconium and infant feces from mother-infant pairs. Our results suggest that the microbial colonization may begin already during fetal life. After birth, colostrum seems to influence the gut microbiota development of the neonate by serving as a source of microbes and microbiota modulating factors, such as human milk oligosaccharides. We also noted that human milk oligosaccharides and microbiota of the colostrum are interrelated. 

Taken together, this thesis provides further knowledge on how different factors influence gut microbiota development in early life. Modification of gut microbiota composition during its development may be a viable strategy to prevent or treat inflammatory non-communicable diseases in the future.