title: Unravelling functional capabilities of the human gut microbiota
Creators: name: Dalukdeniya Arachchilage, Choshani
Publisher: name: University of Reading
Year: 2025

description: 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.