The human gastrointestinal tract is colonised by trillions of microbes that actively impact the health of the host. This ecosystem, known as the gut microbiota, varies in composition between individuals and is associated with outcomes of many diseases. However, the underlying physiology of these associations remains largely unknown, preventing development of targeted microbiota therapeutics and clinical interventions. Animal models are essential for studying these host-microbiota interactions and for causally linking them to health outcomes; mice are the most widely used models for achieving this. Despite this, the mouse gut microbiota is poorly characterised compared to humans, limiting translation of research between these hosts.

This thesis describes the generation of the largest and most comprehensive catalogue of high-quality mouse gut-derived genomes to date: the Mouse Gastrointestinal Bacteria Catalogue (MGBC). By facilitating the comparison of the human and mouse gut microbiotas, the MGBC demonstrates that only 2.58% of species are shared between these biomes, although over 80% of predicted functions are conserved. Application of species-level taxonomic mapping of these functions to predict the closest functionally-related species between the gut microbiotas of humans and mice demonstrates that these taxa are not necessarily the same as the closest genetically-related species. These analyses were implemented as a bioinformatic toolkit to enable other researchers to identify functionally equivalent species according to their functions of interest, with the aim of improving translation of gut microbiome research between the clinical and laboratory contexts.

The MGBC improves coverage of the mouse gut microbiota, yielding metagenome classification rates of over 95%, and enables better resolution for mouse gut metagenomic studies. Nearly 2,500 mouse gut-derived shotgun metagenomes were used to characterise the taxonomic structure of the global mouse gut microbiota and identify factors associated with variation between studies. These analyses found that virtually every species of the mouse gut microbiota varied significantly between study institutes, therefore potentially representing an underlying basis for the irreproducibility crisis observed between mouse studies.

This thesis further investigates the role of the gut microbiota in determining outcomes of bacterial enterocolitis caused by Salmonella Typhimurium and Clostridioides difficile. Through this work, Enterocloster clostridioformis was identified as a novel resistance-inducing microbe against Salmonella infection. This phenotype is potentially mediated through induction of protective epithelial responses and expansion of regulatory T cells in the caecal mucosa. Furthermore, by applying the MGBC to explore the association of intra-institutional microbiota variation with outcomes of C. difficile infection, this work identifies taxonomic and functional correlates of resistance and susceptibility. These findings validate the importance of the MGBC for facilitating shotgun metagenomic analyses in mice and highlight the impact of the gut microbiota on outcomes of health and disease.

Mouse models will continue to be essential for developing microbiota-directed diagnostic and therapeutic interventions as well as enabling their introduction to clinical practice. This thesis therefore represents multiple advances towards understanding and tackling the obstacles posed by host-specific microbiotas. To this end, I have provided a starting point for efficient and informed translation of gut microbiota research between humans and mice, as well as the means for experimental validation of these analyses.