Different gut microbial types were found in captive striped hamsters

Abstract

Background: Typing analysis has become a popular approach to categorize individual differences in studies of animal gut microbial communities. However, previous definitions of gut microbial types were more understood as a passive reaction process to different external interferences, as most studies involve diverse environmental variables. We wondered whether distinct gut microbial types can also occur in animals under the same external environment. Moreover, the role of host sex in shaping gut microbiota has been widely reported; thus, the current study preliminarily explores the effects of sex on potential different microbial types.

Methods: Here, adult striped hamsters Cricetulus barabensis of different sexes were housed under the same controlled laboratory conditions, and their fecal samples were collected after two months to assess the gut microbiota by 16S rRNA sequencing.

Results: The gut microbiota of captive striped hamsters naturally separated into two types at the amplicon sequence variant (ASV) level. There was a significant difference in the Shannon index among these two types. A receiver operating characteristic (ROC) curve showed that the top 30 ASVs could effectively distinguish each type. Linear discriminant analysis of effect size (LEfSe) showed enrichment of the genera Lactobacillus, Treponema and Pygmaiobacter in one gut microbial type and enrichment of the genera Turicibacter and Ruminiclostridium in the other. The former type had higher carbohydrate metabolism ability, while the latter harbored a more complex co-occurrence network and higher amino acid metabolism ability. The gut microbial types were not associated with sex; however, we did find sex differences in the relative abundances of certain bacterial taxa, including some type-specific sex variations.

Conclusions: Although captive animals live in a unified environment, their gut bacteria can still differentiate into distinct types, but the sex of the hosts may not play an important role in the typing process of small-scale captive animal communities. The relevant driving factors as well as other potential types need to be further investigated to better understand host-microbe interactions.

Keywords: 16S rRNA; Gut microbiota; Rodent; Sex; Typing analysis.

Figure 1. Identification of gut microbial types in captive striped hamsters.

(A) The two gut microbial types clustered at the ASV level. (B) Venn diagram of ASVs distribution among the two types. (C), (D) and (E) The Sobs indices, Pd indices and Shannon indices of the two types. Differences were assessed by Mann–Whitney U tests and are denoted as ^∗p < 0.05, ^∗∗p < 0.01 and ^∗∗∗p < 0.001.

Figure 2. Variations in gut microbiota between the two gut microbial types.

(A) LEfSe identification of gut microbial taxa with significant differences (LDA > 3, p < 0.05). (B) ROC curve calculated by the top 30 ASVs, and the area under the ROC curve (AUC) and 95% confidence intervals are also shown. (C) Six of 30 ASVs that showed significantly different relative abundances between the two types. Differences were assessed by Mann–Whitney U tests and are denoted as ^∗p < 0.05, ^∗∗p < 0.01 and ^∗∗∗p < 0.001.

Figure 3. Co-occurrence networks of the gut microbiota calculated by the top 30 ASVs.

Nodes represent each ASV, and their sizes indicate different degrees. Links represent significant (p < 0.05) and strong (Spearman’s correlation greater than 0.6 or lower than −0.6) correlations (green dotted lines: negative; red solid lines: positive).

Figure 4. Differences in gut microbial functions between the two gut microbial types.

(A) PCoA based on Bray–Curtis distances of KOs. (B) Significant differences in level-2 KEGG pathways between the two types (Welch t test, p < 0.05).

Figure 5. The role of sex in the differentiation of gut microbial types.

(A) Distribution of male and female individuals in gut microbial types; differences were assessed by Fisher’s exact test. (B) ROC curve calculated by the top 30 ASVs, and the area under the ROC curve (AUC) and 95% confidence intervals are also shown. (C) The Sobs indices, Pd indices and Shannon indices of males and females. Differences were assessed by Mann–Whitney U tests and are denoted as ^∗p < 0.05, ^∗∗p < 0.01 and ^∗∗∗p < 0.001. (D), (E) and (F) PCoA based on Bray–Curtis, unweighted UniFrac and weighted UniFrac distances calculated using ASVs.

Figure 6. Sex-specific differences of gut microbiota in captive striped hamsters.

LEfSe identification of gut microbial taxa with significant sex-specific differences in all individuals (A), Type 1 (B) and Type 2 (C) (LDA > 2, p < 0.05).