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. / Thesis / Doctor of Philosophy (PhD) / Bacteria that inhabit the human intestine are important for health, and are involved
in several diseases; therefore, it is critical to determine the roles of specific bacteria. I
describe a method that results in the growth and recovery of most bacteria in stool, which
allows them to be studied in detail. The differences, both in behaviour and in DNA
sequences, found within two different bacterial groups were characterized, and extensive
variability was observed between closely related bacteria. I studied which bacteria and
their functions might be important in Irritable Bowel Syndrome (IBS) by using our
method for growing stool bacteria combined with sequencing of all DNA in the stool, but
could not find strong support for specific bacteria causing IBS symptoms. This work
shows how the ability to grow and isolate bacteria, combined with studying their DNA,
allows for better understanding of their functions in the human intestine.
| Identifer | oai:union.ndltd.org:mcmaster.ca/oai:macsphere.mcmaster.ca:11375/22053 |
| Date | 11 1900 |
| Creators | Lau, Jennifer T. |
| Contributors | Surette, Michael G., Biochemistry |
| Source Sets | McMaster University |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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