Novel insights into fibre and lipid substrates on the microbiome

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Strain, Ronan
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University College Cork
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Since the turn of the millennium, advances in sequencing technology have uncovered a plethora of microorganisms that live with and inside us. There are some indications that a considerable part of the environmental influence on human health and disease is mediated by this microbial community and it is recognised that diet massively dictates the structure and function of these symbionts. Identifying dietary components, therefore, that impact this internal community can reveal novel insights into how these symbionts affect and promote human health and well-being. This thesis investigated the effects of dietary fibre and lipid components on the human gut microbiota using in vitro, in vivo and in silico methods. Attempts were made to characterise the effects of these dietary components on gut microbiota composition from an alternative perspective in relation to human health; how they impact colonisation resistance against pathogens, influence bacterial taxa associated with metabolic disease and how they affect an overlooked proportion of the microbiota, the human gut virome. An extensive literature review was undertaken in Chapter 1 to examine how diet may impact colonisation resistance against invading pathogens, exploring how different food components and metabolites either protect or promote gastrointestinal pathogen colonisation. In Chapter 2 and Chapter 3, it was found that dietary fibres have differential effects on colonisation resistance against pathogens by employing an ex vivo model of the distal colon and assessing pathogen growth following 24-hour faecal fermentation. Glucose was used as a positive control to compare the success of pathogen growth in the presence of various pre-digested dietary fibres. Pathogen abundance was evaluated by 16S rDNA sequencing, qPCR and the effects on metabolic activity by short chain fatty acid (SCFA) analysis. We found that SCFA concentrations were increased in the presence of pathogens. The same ex vivo model was implemented, as described in Chapter 4 to study the effects of various dietary fibres and lipids on gut microbiota, using faecal samples collected from subjects with various stages of metabolic syndrome. Effects of microbial composition and diversity were assessed by 16S rDNA sequencing and SCFA analysis was performed for some of the treatments. Dietary fibre supplementation increased bacterial taxa negatively associated with metabolic disease including Bacteroides and Faecalibacterium. Fish oil treatment exhibited a decrease in pro-inflammatory Enterobacteriaceae and an increase in Bifidobacterium and Veillionella. A pilot study, described in Chapter 5, using faecal samples taken from a randomised controlled trial (RCT) on a dietary oily fish intervention was used to study dietary relationships with the human gut virome. The purpose was to evaluate how diet might influence this overlooked proportion of the microbiota and if oily fish intake selects for viral taxa negatively associated with autoimmune disorders. Metagenomic shotgun sequencing was performed on faecal samples taken from the RCT at baseline and at 8 weeks for 2 different fish types (sardine & tuna) eaten at either one portion or two portions of fish per week; these data were compared with a no fish intake group. The analysis was limited to diversity and viral load assessments, owing to the fact that a large fraction of our sequences had no matches in the viral database. There was a trend towards oily fish intake having a transient association with the human gut virome, which may be an artefactual signal from the high degree of inter-individual variation observed in humans. In conclusion, these results highlight the potential of dietary fibre and lipid food components in modulating microbiota composition. Further research is required to assess whether these changes in microbiota composition have a beneficial effect on human health.
Strain, R. 2022. Novel insights into fibre and lipid substrates on the microbiome. PhD Thesis, University College Cork.
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