Characteristics of gut microbiota in representative mice strains: Implications for biological research

Abstract

Background: Experimental animals are used to study physiological phenomena, pathological mechanisms, and disease prevention. The gut microbiome is known as a potential confounding factor for inconsistent data from preclinical studies. Although many gut microbiome studies have been conducted in recent decades, few have focused on gut microbiota fluctuation among representative mouse strains.

Methods: A range of frequently used mouse strains were selected from 34 isolation packages representing disease-related animal (DRA), immunity defect animal (IDA), or gene-editing animal (GEA) from the BALB/c and C57BL/6J backgrounds together with normal mice, and their microbial genomic DNA were isolated from mouse feces to sequence for the exploration of gut microbiota.

Results: Mouse background strain, classification, introduced source, introduced year, and reproduction type significantly affected the gut microbiota structure (p < 0.001 for all parameters), with background strain contributing the greatest influence (R² = 0.237). In normal groups, distinct gut microbiota types existed in different mouse strains. Sixty-four core operational taxonomic units were obtained from normal mice, and 12 belonged to Lactobacillus. Interestingly, the gut microbiota in C57BL/6J was more stable than that in BALB/c mice. Furthermore, the gut microbiota in the IDA, GEA, and DRA groups significantly differed from that in normal groups (p < 0.001 for all). Compared with the normal group, there was a significantly higher Chao1 and Shannon index (p < 0.001 for all) in the IDA, GEA, and DRA groups. Markedly changed classes occurred with Firmicutes and Bacteroidetes. The abundances of Helicobacter, Blautia, Enterobacter, Bacillus, Clostridioides, Paenibacillus, and Clostridiales all significantly decreased in the IDA, GEA, and DRA groups, whereas those of Saccharimonas, Rikenella, and Odoribacter all significantly increased.

Keywords: Bacteroidetes; Firmicutes; BALB/c mice; C57BL/6J; disease-related animal; gene-editing animal; gut microbiota; immunity defect animal; strains.

FIGURE 1

Bacterial community structures in normal mouse strains. (A) NMDS analysis of gut microbiota composition in normal mouse strains. (B) Chao1 and Shannon index in normal mouse strains. (C) Relative abundance of gut bacteria at the phylum level in normal mice strains. (D) Relative abundance of gut bacteria at the genus level in normal mice strains. (E) Flower plot. (F) 64 core of OTUs. (G) Correlation of 10 filtered key OTUs.

FIGURE 2

Robustness of the bacterial community in BALB/c (including packages BALB.cJ, BALB.c, and B.C.S.) and C57BL/6J (C57 including packages C57B.J, C57BLS, and C57BL6J) strains. (A) NMDS analysis of gut microbiota communities in BAL and C57 mice. (B) Comparison of inner Bray–Curtis distance in BAL and C57 mice. (C) Chao1 index of gut microbiota in three packages belonging to BAL and C57 mice. (D) Shannon index of gut microbiota in three packages belonging to BAL and C57 mice. (E,F) Venn diagram of three individual packages in BAL and C57 mice, ***p < 0.001.

FIGURE 3

Characteristics of the bacterial community in diseased animal models of different types of disease. (A) NMDS analysis of gut microbiota communities. (B) Comparison of inner Bray–Curtis distance in normal, DRA, IDA, and GEA groups. (C) Chao1 index. (D) Shannon index. (E) Phylogenetic diversity (PD) index. (F) Cluster analysis based on the relative abundance of taxa at the phylum level. (G) Relative abundance of Firmicutes and Bacteroidetes. (H) Heatmap of changed genus in the DRA, IDA, and GEA groups compared with that in the normal group. Red: significantly decreased in all DRA, IDA, and GEA groups compared with the normal group; green: significantly increased in all DRA, IDA, and GEA groups compared with the normal group.