Unravelling functional capabilities of the human gut microbiota

The human gut microbiota is crucial for maintaining human health. Largely influenced by diet, its composition and subsequent function impact on a number of host processes such as nutrient absorption, immune function and mental health. As interest in gut microbiota-targeted interventions has grown, understanding the functional capacities of microbial communities has become essential. However, comprehensively understanding these complex interactions remains analytically challenging. The primary goal of this thesis was to unravel these complexities by monitoring selected small communities of bacteria using a combination of microbiology and analytical chemistry approaches. Through in vitro experiments with a nutrient-rich medium mimicking the gut environment, this research explored a simplified nine-gut microbial consortium representing the most abundant genera in the human gut. By dissecting the functional behaviour of these microbial species in various scenarios—pure cultures, co-cultures with a probiotic yoghurt, and mixed culture environments—valuable insights into microbial interactions, metabolic responses, and growth dynamics emerged. Particularly noteworthy was the potential of probiotic yoghurt as a promising dietary intervention strategy for gut microbiota-mediated health benefits. Metabolic profiling using 1H-NMR spectroscopy captured the complete metabolic profile of these bacteria, providing insight into microbial metabolic activity. The results showed that all bacteria studied in this thesis produced acetate, lactate, formate, ethanol, and methanol, while specific species like Bacteroides fragilis, Faecalibacterium prausnitzii, and Escherichia coli additionally produced propionate and succinate. Roseburia intestinalis synthesised butyrate, and Bacteroides fragilis and Clostridium perfringens generated gamma amino butyric acid (GABA), with inulin and yoghurt enhancing production of these metabolites. These findings contributed to the creation of an atlas of gut microbial function, offering insights for gut microbiota-targeted interventions. Furthermore, the thesis compared functional resemblance of the synthetic gut microbial community with human faeces. The novel synthetic gut microbial consortium comprising of the nine bacterial strains, including pathogenic species, was analysed using 1H-NMR spectroscopy to understand functional behaviour and flow cytometry-fluorescent in situ hybridisation (FC-FISH) enumeration to monitor the bacterial count. Results showed differences in substrate utilisation and metabolite production between the synthetic mix and human faecal samples, highlighting challenges in replicating the human gut microbiota's complexity. The study also investigated the effect of a probiotic yoghurt intervention on microbial populations and metabolic responses in a group of school children from South West Uganda, revealing significant increases in total bacterial counts post-intervention and distinct metabolic profiles. The objective was to provide a metabolic perspective on the outcomes observed in vivo by leveraging the in vitro data collected. This thesis has contributed to our understanding of gut microbial dynamics, dietary impacts, and therapeutic potentials. Future research directions include exploring diverse dietary substrates, refining synthetic models, and elucidating precise mechanisms underlying probiotic effects, aiming to optimise microbiota targeted interventions and improve human health outcomes.