BARRON PASTOR, HELI JAIME
Description
Host-microbe interactions are now considered essential for
maintaining host health. It is known that short and long term
dietary interventions influences the structure and activity of
gut bacterial communities. However, our understanding of the
forces shaping the gut microbiota is still limited and
controversial, and most of the studies of the gut microbiota use
the microbiota from faeces as a proxy for the intestinal tract
populations. As such, the...[Show more] overarching aim of this thesis is to
contribute to the understanding of host-microbiome interactions
using an animal model.
In this thesis I describe the effect of diet changes on microbial
community structure and host-microbiome interactions following 14
weeks on one of the three experimental diets. The diets
consisted of a basal diet low in fibre (LF); the basal diet
together with 26 % cellulose; a difficult to ferment fibre (HF);
and the basal diet together with 50% dried cooked red kidney
beans (B); a diet relatively high in easily fermentable fibre.
These diets were fed to 45, 21 day old female Wistar rats
originating from 6 litters for 14 weeks.
Diet had little effect on rat growth rates or adult body mass.
However, diet had profound effects on gastro-intestinal
morphology and dynamics. Caecum size was smallest in animals fed
the LF diet, and caecums were about 2x as large in animals fed
the B diet, while animals on the HF diet had intermediate-sized
caecums. Food transit times were slowest in animals on the B and
LF diets and fastest in animals on the HF diets. At the end of
the diet experiment, colon and caecum contents were collected
when the animals were killed and short chain fatty acids,
nitrogen, carbon, as well fibre concentrations were determined.
These data showed that the ‘chemical’ environment of the
hindgut varied substantially among animals fed the different
diets.
E. coli diversity and dynamics were described by characterizing
more than three thousand isolates. E. coli diversity was low,
and more than 97% of the isolates were represent by three
strains: one phylogroup B2 strain and two phylogroup B1 strains.
A decline of the frequency of the B2 strain in the animals fed on
the bean diet was observed.
The faecal microbiota was characterized when the animals were 21
days old, while faecal, caecal and rectal microbial communities
characterized at the end of the experiment. 16S amplicon
sequencing of the V4 region on the Ion Torrent platform was the
approach used to characterize the microbiota.
Members of 23 microbial families were detected in communities of
the animals before and after 14 weeks on the experimental diets.
At the start of the experiment there were significant litter
membership effects on the structure of the faecal microbial
communities. After 14 weeks on the experimental diets, both
litter and diet explained a significant amount of the variation
in microbial community structure. There were substantial
differences in the microbial communities of the caecum and rectum
and the extent of these differences depended on diet and on the
time taken for material to move through the hindgut.
The outcomes of the present study make a contribution to our
understanding of the factors that shape gut microbial
communities. Microbial characterization of faecal samples is
frequently used as proxy of gut microbiota. However, stool
samples are probably most likely representative of the microbial
communities in the rectum than other parts of the
gastrointestinal tract. Indeed, the findings also throw doubt on
the value of faecal community characterization as a means to
understand community structure and function in the
gastro-intestinal tract. Further, the results of these
experiments suggest that efforts attempting to achieve positive
health outcomes through diet manipulation may have limited
success in general due to among individual differences in
microbial community composition, and in how these different
communities respond to dietary manipulation.
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