Characterizing the diversity and complexity of the human gut microbiome through the combination of culture and culture-independent methods

Abstract

The human gut microbiome is the collection of all organisms and their genetic content that inhabit the gastrointestinal tract. An overwhelming number of studies have associated the gut microbiota with health and disease, but with little consensus on which specific bacterial groups are important for causing or maintaining either state. A majority of microbiome studies only identify associations between the gut microbiome and health status, and determining causation requires the isolation and growth of bacterial isolates for further experiments. The goal of this thesis is to demonstrate that the combination of culture-based and culture-independent methods describes greater complexity and diversity in the human gut microbiota than observed by either approach alone. In the first study, a method of culture-enriched molecular profiling could capture the majority of bacterial groups found in fecal samples. Additionally, when compared to culture-independent 16S rRNA gene sequencing, culture detected more bacterial taxa. This method was applied to the targeted culture of the commensal Lachnospiraceae family. The second study explored the diversity in the isolated Lachnospiraceae strains, and compared the genetic diversity of the strains to reference genomes, revealing functional and genetic heterogeneity within the bacterial family. The third study characterized the intra-species phenotypic and genetic diversity in Escherichia coli. E. coli diversity was extensive between individuals, but also within-individuals, in both the phenotypes and genetic profiles. Lastly, a method of culture-enriched metagenomics was applied to a murine IBS microbiota transfer model to identify bacterial members of the microbiota and their functional pathways that may be responsible for the development of gastrointestinal and behavioural IBS phenotypes, although no bacterial groups could be conclusively associated with symptoms. Together, the work described demonstrates that culture and culture-independent methods are complementary, and provides more resolution into the structure and diversity of the human gut microbiome than either approach in isolation.