Bifidobacteria on the spot: a genomics approach on population dynamaics and interactions in the intestinal tract

This thesis combines comprehensive microarray-based studies contributing to a better understanding of the role of bifidobacteria in relation to the human host. It reviews recently described modes of interaction between bifidobacteria and human gastrointestinal cells and highlights the unique characteristics of the genus Bifidobacterium that are indicative for its role in our gut. A microarray platform has been developed that enables genomic comparison of Bifidobacterium species originating from our gastrointestinal tract (GIT). Based on the obtained high-resolution data, species-unique genomic sequences could be identified. A large fraction of these predicted genes encode proteins belonging to the bifidobacterial glycobiome. An unique ability of the microarray platform is to zoom in on the strain level. Direct mapping of genomic hybridization patterns was applied on different B. breve isolates. This revealed a relatively high genomic variation, testifying for the existence of various subspecies within the species B. breve. Clustering of the same hybridization patterns resulted in clear grouping of isolates originating from the same infant, indicating specific niche adaption. Additionally, DNA extracts from Bifidobacterium populations from different infant fecal samples were analyzed. This enabled the analysis of the bifidobacterial population dynamics in breast- and formula-fed infants. The applied microarray platform showed the potential to monitor temporal development and effects of dietary regimens. The observed differences in the composition of bifidobacterial populations could be linked to dietary effects. Additionally, mapping of hybridization patterns enabled monitoring shifts in genomic content within one bifidobacterial species in time. Sequence analysis of DNA fragments showing discriminating hybridization characteristics, resulted in the selection of genes that are either conserved or strain-specific within the species B. breve. Next to studying genomic variation, transcript profiling experiments in both bifidobacterial cells and human intestinal epithelial cell lines were performed. Analysis of bifidobacterial transcriptional responses provided clear proof of transcriptional activity in bifidobacterial cells isolated from infant feces. To the best of our knowledge, this is the first demonstration of in situ activity of bifidobacteria in the human GIT. Furthermore, our results indicate a link between transcription patterns and the infants’ diet, as bifidobacteria in fecal samples from breast-fed infants showed differential transcriptional responses in comparison to those in fecal samples from formula-fed infants. Additionally, transcript sequence analysis revealed expression of genes that are homologous to genes known to be involved in folate production, testifying for the production of this important vitamin in early life. Finally, transcriptome analysis on human intestinal epithelial cells (HIECs) showed species-specific suppression by B. breve M-16V of genes upregulated by TNF-α. Other B. breve strains showed an extreme mild or no effect on TNF-α stimulation. Although we did not observe complete suppression of the TNF effect, we could show that apoptotic and immune regulatory pathways were affected by incubation with cells of B. breve M-16V. In conclusion, the work presented in the thesis, which formed part of a larger IOP Genomics project, contributed to an advanced insight in the interaction between bifidobacteria and the human host. Furthermore, it resulted in the development of genome-based molecular platforms suited for analyzing genomic diversity between and within species, as well as population dynamics in complex microbial communities. We anticipate that the molecular approaches pioneered in this thesis will be instrumental in the further elucidation of the host-microbe interactions in the GIT of human an other animals.