A Comprehensive Hamster Gut Bacterial Genome Catalog via Integrated Metagenomics and Culturomics
Hamsters are emerging as a valuable model organism for studying metabolic diseases due to their high physiological and metabolic similarities to humans. However, research on the composition of the hamster gut microbiota and its reference genomes remains limited. In particular, the gut microbiota characteristics of hamsters as an animal model for coronary heart disease remain unclear. Consequently, establishing a comprehensive and high-quality reference genome catalog is essential. In this study, we performed metagenomic sequencing on 381 fecal samples from hamsters and conducted microbial cultivation and isolation on selected samples. As a result, we constructed a reference genome catalog comprising 1,693 representative genomes, among which 1,378 (81%) are novel bacterial genomes. The establishment of this reference genome catalog significantly enhanced the mapping rate and data utility of hamster gut microbiota, enabling a more accurate characterization of the species composition, influencing factors, and functional diversity of the hamster gut microbiota. This study also revealed the unique characteristics of the hamster gut microbiota. Compared with mice and human, the functional composition of the hamster gut microbiota, particularly in lipid metabolism, shows greater similarity to that of humans, highlighting its value as a cardiovascular disease model. Furthermore, we investigated the gut microbiota of LDLR-KO and ApoC3-KO hamsters compared with wild-type controls. Gene knockout not only altered their blood lipid levels but also affected the composition and functional profile of their gut microbiota. Notably, changes in the functional characteristics of the hamster gut microbiome were consistent with alterations in host gene function, providing evidence for a correlation between host genetic function and gut microbial functionality. These results suggesting a potential synergistic effect on the onset and progression of atherosclerosis. In summary, this comprehensive reference genome catalog provides a valuable resource for future studies of the hamster gut microbiota and enhances our understanding of its role in health and disease.