3.5 | Effects of physiological structure of the host GIT on the gut microbiome
To investigate the relationship between the physiological structure of the host GIT and their gut microbiome in host dietary adaptation, we divided the above 12 species into ruminant animals, SNMs (ruminant-like animals) and monogastric animals according to their GIT physiological structures. First, LEfSe test was used to detect the taxonomic and functional (carbohydrate active enzyme families) differences among the three groups. At the genus level, Ruminococcus , Treponema and Clostridium were significantly enriched in SNMs, and Fibrobacter ,Butyrivibrio and Prevotella were significantly enriched in ruminant animals (LDA>4, p <0.05) (Figure 4a, Figure S5). The functions of these genera are all related to the fermentation of complex carbohydrates such as cellulose (Palevich et al., 2019; Ransom-Jones, Jones, McCarthy, & McDonald, 2012; Yang Gu & Jiang, 2010). However, in the monogastric animals, Bacteroides ,Faecalibacterium , Roseburia and Phocaeicola were significantly enriched, which were associated with the degradation of fat and protein (LDA>4, p <0.05) (Figure 4a; Figure S5). Carbohydrate active enzyme analysis showed that GHs, which significantly enriched in SNMs (GH78, GH13, GH109) and ruminant animals (GH25, GH5), were related to the degradation of structural polysaccharides. However, GHs that were significantly enriched in monogastric animals (GH43, GH2, GH92, GH97, GH105, GH29, GH28, GH32, GH20) were related to the degradation of oligosaccharides (LDA>3, p <0.05) (Figure 4b; Table S13). These results suggested that the composition and function of the gut microbiome are related to the host’s dietary adaptation, and the structure of gut microbes is more similar between SNMs and ruminants.
In addition, we found that the relative abundance of more than 50% (1859) of genera in the SNMs gut microbiome were higher than that in monogastric animals, but lower than that in ruminant animals (Table S14). Bacillus (Firmicutes, Bacilli), Butyrivibrio(Firmicutes, Clostridia) and Fibrobacter (Fibrobacteres, Fibrobacterales) had the highest relative abundance among these genera in the SNMs gut microbiome. Most of these 1859 genera belonged to Firmicutes (129 genera, average relative abundance in SNMs gut microbes was 1.44%), Bacteroidetes (245 genera, average relative abundance in SNMs gut microbes was 0.62%), Proteobacteria (866 genera, average relative abundance in SNMs gut microbes was 0.41%%), Fibrobacteres (3 genera, average relative abundance in SNMs gut microbes was 0.24%), Actinobacteria (264 genera, average relative abundance in SNMs gut microbes was 0.26%), and Tenericutes (4 genera, average relative abundance in SNMs gut microbes was 0.10%). Bacteria in these phyla have the ability to degrade complex carbohydrates, especially in Firmicutes (Yang Gu & Jiang, 2010) and Fibrobacteres (Ransom-Jones et al., 2012). We further found that the relative abundance of 37 GHs in SNMs was higher than that in monogastric animals but lower than that in ruminants. Most of these GHs are associated with the degradation of structural carbohydrates such as cellulose and starch (Figure S6; Table S13). Analysis of the correlations between these genera and these GHs showed that most bacteria correlated positively with these GHs (Table S15). We also found that with the adaptive evolution of the host GIT structure to herbivory, the diversity and abundance of GHs related to the fermentation of structural carbohydrates also increased, and the relationship between these genera and GHs are more complex. (Table S15), because the host needed a stronger fermentation capacity to obtain nutrients.
In summary, the structure of the SNMs gut microbiome was more similar to that of ruminants, both in taxonomy and function. Moreover, the relative abundance of some bacteria and carbohydrate enzymes in SNMs was intermediate to that those of ruminants and monogastric animals, suggesting that the physiological structure of the host GIT plays a regulatory role in the gut microbiome during the adaptation evolution of diet.