Comparative metagenomics analysis reveals how the diet shapes the gut
microbiota in several small mammals
Abstract
The gut microbiomes of the host are large and complex communities, which
helps to maintain homeostasis, improves digestive efficiency, and
promotes the development of the immune system. The small mammals
distributed in Sichuan Province are the most popular species for
biodiversity research in Southwest China. However, the effects of
different diets on the structure and function of the gut microbial
community of these small mammals are poorly understood. In this study,
whole-metagenome shotgun sequencing has been used to analyze the
composition and functional structures of the gut microbiota of seven
small mammals in Laojunshan National Nature Reserve, Sichuan Province,
China. Taxonomic classification revealed that the most abundant phyla in
the gut of seven small mammals were Bacteroides, Proteobacteria and
Firmicutes. Moreover, Hafnia, Raoultella and Aeromonas were most
abundant genus in the gut microbiomes of these seven species. At the
functional level, we annotated a series of KEGG functional pathways, six
Cazy categories and 46,163 AROs in the gut microbiomes of the seven
species. Comparative analysis found that the difference in the gut
microbiomes between the Soricidea and Muridae concentrated on the
increase in the F/B (Firmicutes/Bacteroides) ratio in the Soricidea
group, probably driven by the high fat and calorie digestive
requirements due to their insectivorous diet. The comparative functional
profiling revealed that functions related to metabolism and
carbohydrates were significantly more abundant in Muridae group, which
may be attributed to their high carbohydrate digestion requirements
caused by their herbivorous diet. These data suggested that different
diets in the host may play an important role in shaping the gut
microbiota, and lay the foundation for teasing apart the influences of
heritable and environmental factors on the evolution of gut microbial
communities.