The role of hydrogenotrophic microbiota in the human gut

It has been widely acknowledged that the gut microbiota plays an important role in human health. Maintaining a healthy gut microbiota protects us from microbiota related diseases, while a distorted one may contribute to chronic gut disorders. Therefore, it is fundamental to understand the mechanisms determining gut microbiota composition and function to maintain a healthy gut microbiota and to assist in the development of microbiota-based therapeutics for gut disorders/diseases. External drivers that impact microbiota composition and function, such as diet, host physiology and genotype, have been widely studied, whereas the internal ones, such as the interactions among and between the microorganisms remain largely unknown. Hydrogen metabolism plays a central role in regulating overall microbial fermentation in anaerobic ecosystems and is hypothesised to serve as one of the important internal drivers in shaping gut microbiota composition and function. Here the hydrogenotrophic microbiota plays an essential role by disposing of the accumulated hydrogen in gut ecosystems. This thesis aimed to investigate the role of the hydrogenotrophic microbiota in overall gut microbiota composition and function as well as the interactions between different hydrogenotrophic microbes. In terms of the external drivers, we firstly summarized and discussed the impact of diet on the gut microbiota in adulthood. Afterwards, we investigated the microbial signatures associated with irritable bowel syndrome (IBS) and its severity in a longitudinal study (two timepoints with 4 weeks in between). We found that the overall microbiota composition did not differ between IBS patients and healthy subjects, but that IBS patients had a consistently lower relative abundance of Bifidobacterium and a higher relative abundance of Terrisporobacter and Turicibacter compared to healthy subjects. In addition, this study observed large dynamics in stool patterns, symptom severity, and their associations with microbiota composition over time which argues that insights obtained from cross-over studies with single sampling points is limited. To investigate the role of the hydrogenotrophic microbiota in the human gut, we firstly assessed the distribution and stability of the three major hydrogenotrophic functional groups (methanogens, sulphate-reducing bacteria and reductive acetogens) in both healthy adults and IBS patients over time, as a distorted hydrogen metabolism is suggested to be associated with IBS. Interestingly, we found methanogen abundance showed a bimodal distribution, and methanogen levels were significantly associated with microbiota alpha diversity and composition. However, the three hydrogenotrophic functional groups showed co-occurrences rather than anti-occurrences in healthy adults and IBS patients, suggesting that these microbes coexist in the human gut. To further investigate the interactions between the hydrogenotrophic functional groups, the representative isolates (Methanobrevibacter smithii for methanogens; Desulfovibro piger for sulphate-reducing bacteria; Blautia hydrogenotrophica for reductive acetogens) were cocultured in vitro under hydrogenotrophic conditions. We observed that the three hydrogenotrophic species not only coexisted with each other under hydrogenotrophic conditions, but also that D. piger and B. hydrogenotrophica shortened the growth lag phase of M. smithii. Moreover, we noticed that a high hydrogen sulfide concentration, produced by D. piger likely inhibited the growth and metabolite production of B. hydrogenotrophica and M. smithii. To obtain insights into the impact of hydrogenotrophic microbiota on overall microbiota composition and function,  we modulated gut microbiota composition and function via altering hydrogenotrophic activities in vitro in which faecal inocula of subjects characterised as either methane excretors with a high level of methanogens or non-methane excretors with a low level of methanogens were used. Methanogenesis was inhibited by adding 2‐bromoethanesulfonate to the incubations in methane excretors, or stimulated by adding M. smithii as inoculum to incubations in non-methane excretors, and sulphate was added to the incubations in both methane excretors and non-methane excretors to stimulate sulphate reduction. We observed that sulphate was not consumed in any of the incubations while the genus Desulfovibrio was detected in four of the six inocula, suggesting that this genus did not use hydrogen for its metabolism under the conditions used for these experiments. Although altering the methanogenic activities did not change overall microbiota composition and SCFA profiles, M. smithii was able to sustain and produce methane in a faecal community of non-methane excretors. Overall, this thesis concluded that 1) longitudinal studies are crucial to understanding the links between microbiota and host physiology and health in IBS, 2) the hydrogenotrophic microbiota is stongly associated with overall microbiota composition and function, 3) the hydrogenotrophic species coexist and their interactions vary depending on the gut environment conditions, and 4) that faecal communities are resilient ecosystems in which methanogenesis is a specialized but optional niche.