High diversity, close genetic relatedness, and favorable living conditions benefit species co-occurrence of gut microbiota in Brandt's vole

Abstract

Introduction: Revealing factors and mechanisms in determining species co-existence are crucial to community ecology, but studies using gut microbiota data are still lacking.

Methods: Using gut microbiota data of 556 Brandt's voles from 37 treatments in eight experiments, we examined the relationship of species co-occurrence of gut microbiota in Brandt's voles (Lasiopodomys brandtii) with genetic distance (or genetic relatedness), community diversity, and several environmental variables.

Results: We found that the species co-occurrence index (a larger index indicates a higher co-occurrence probability) of gut microbiota in Brandt's voles was negatively associated with the genetic distance between paired ASVs and the number of cohabitating voles in the experimental space (a larger number represents more crowding social stress), but positively with Shannon diversity index, grass diets (representing natural foods), and non-physical contact within an experimental space (representing less stress).

Discussion: Our study demonstrated that high diversity, close genetic relatedness, and favorable living conditions would benefit species co-occurrence of gut microbiota in hosts. Our results provide novel insights into factors and mechanisms that shape the community structure and function of gut microbiota and highlight the significance of preserving the biodiversity of gut microbiota.

Keywords: biodiversity; density dependency; phylogenetic relatedness; social stress; species co-occurrence.

FIGURE 1

Community composition and diversity of the gut microbiota in Brandt’s vole. (A) Abundance of each genus of gut microbiota in each individual of Brandt’s vole. Only genera with an average abundance above 1% were shown. (B) Variation in phylum composition of gut microbiota in Brandt’s voles among different treatment groups. Different colors indicate different phyla. (C) Function composition of gut microbiota in Brandt’s voles among different treatment groups. Different colors indicate different enzyme classes (level 1 classification). (D) Shannon diversity of microbiota of Brandt’s voles in each treatment. (E) Functional diversity of microbiota of Brandt’s voles in each treatment. For Simpson diversity, see Supplementary Figure 3.

FIGURE 2

(A) Co-occurrence network of pooled ASVs of the gut microbiota in Brandt’s voles under different treatments. (B) Distribution of degree, positive degree (i.e., the Spearman correlation coefficient is positive), and negative degree (i.e., the Spearman correlation coefficient is negative) of network nodes in each phylum.

FIGURE 3

Relationship between co-occurrence index and genetic distance between ASVs of gut microbiota in Brandt’s voles in the eight experiments. The co-occurrence index represents Spearman correlation coefficient, and the scatter points indicate the pooled ASV pairs for each experiment. The red line indicates the linear fitting line. The coefficients of the regression are shown in Supplementary Table 4. (A–H) indicate Experiments 1–8 (see “Materials and methods” and Table 1).