To Örebro University

Human gut microbiota plays a vital role in maintaining host health. This thesis aims to investigate the gut microbial population and function using next generation sequencing (NGS) data from faecal samples. Paper I examines the influence of sequencing depth and analysis methods in microbiota profiling using NGS whole genome sequencing (WGS) data. By subsampling the metagenomic data, the influence of varying sequencing depths on different phylogenetic classification methods is investigated. This suggests that necessary sequencing depth would be dependent on the individual research plan. This paper recommends the need for a consensus approach and an informed choice of NGS analysis method selection for a reliable prediction. Paper II relates the gut microbiota to general health, nutrient intake, physical activity, medications, and psychological distress in community-dwelling older adults and senior orienteers. A higher abundance of F. prausnitzi in the faecal microbiota of senior orienteers confirms the hypothesis that senior orienteers can be seen as a model for healthy ageing in the perspective of the microbiota. Paper III focuses on assessing the validity of function prediction using LC-MS at multiple annotation levels. Predicted and quantified protein-pathway profiles were subjected to correlation analyses, which showed statistically significant association between predicted and quantified proteins as well as predicted and quantified pathways. This study also showed a direct relation between protein abundance and correlation for predicted and quantified proteins at higher function levels. Paper IV investigates the effects of faecal microbiota transfer (FMT) on functional microbiota profiles. This study showed that allogenic FMT did not alter the metabolite profiles, but it seems to disturb the gut microbiota-metabolite interactions when compared to autologous FMT.

This thesis reiterates the need for carefully selecting prediction tools and methods for microbiome analysis. The findings of this thesis could stimulate more focused studies using NGS in medicine and aid in better understanding of host-microbe interactions.