Molecular characterization of the dynamics and development of the human microbiota

Sammanfattning: The human body contains an enormous amount of bacteria, which are important in processes such as colonization resistance, digestion of food particles, and in the development of the immune system. Most host-microbe interactions are not harmful. Each individual harbors a unique and site-specific microbiota which is considered to be relatively stable within an individual over time. For many years, the indigenous microbiota was characterized using culture-based methods. The use of culture-based methods is quite time consuming and not completely comprehensive: a large fraction of the bacteria are not detected because of unknown growth conditions. Through the use of high-throughput sequencing technologies, based on analysis of the 16S rRNA gene, knowledge about the microbiota residing within human has increased. In this thesis the 454 pyrosequencing technology was used in order to characterize the human indigenous microbiota in infants and adults. By developing primers specific for a certain region of the 16S rRNA gene and by the addition of a 4-5 nucleotide long barcode to each primer the 454 pyrosequencing was developed to fit multiple samples in a single run. When the microbiota was analyzed in infants during the first two years of life, it was observed that mode of delivery had an impact on the early microbiota composition as well as chemokine levels. The diversity within the Bacteroidetes phylum was higher in vaginal delivered infants through the first six months of life and the major genus Bacteroides was detected significantly more frequently in the vaginally delivered infants. Moreover, a significant association between the presence of the genus Bacteroides in the infants’ stool at one and three months and high levels of the Th1- associated chemokines CXCL10 and CXCL11 was found. This thesis provide evidence that the Bacteroidetes are transferred from mother to child during vaginal delivery and that impaired colonization of this phylum may lead to an altered Th1/Th2 balance. The findings could help to explain the association between mode of delivery and allergy development in children. The etiology of allergy is, however, multifactorial, with many variables contributing to the final expression of atopic disease. The prevalence of allergic disease has increased markedly, especially in the Western world, and a combination of genetics and environmental factors has been proposed as a cause of this rise. Specific genera have been suggested to be part of this etiology, but with differing results. In this thesis, a specific genus was not correlated to allergic disease, but instead a low diversity of the total microbiota early in life was associated with development of allergic disease at two years of age. In this thesis, the stability of the gastrointestinal microbiota in healthy adults and following perturbation with antibiotics was also analyzed. A relatively, but not completely stable microbiota was found in adults. Following antibiotic treatment, dramatic short-term effects were observed in throat and fecal samples. Long-term perturbations were also observed in the microbiota and also a dramatic increase and persistence in antibiotic resistance genes causing macrolide resistance was seen.