Microbiome Analysis Reveals the Attenuation Effect of Lactobacillus From Yaks on Diarrhea via Modulation of Gut Microbiota

Abstract

Domestic yaks (Bos grunniens) are indigenous to the Tibetan Plateau and display a high diarrhea rate due to poor habitat and husbandry conditions. Lactobacillus has been shown to exert beneficial effects as antimicrobial, growth promotion, and gut microbiota in humans and/or murine models, but the relevant data regarding Lactobacillus isolated from yaks was unavailable. Therefore, this study aimed to investigate the effects of Lactobacillus from yaks on the intestinal microbial community in a mouse model and determine whether Lactobacillus supplementation contributed in alleviating diarrhea by modulating gut microbiota. A total of 12 ileac samples from four groups were collected for 16S rRNA gene amplicon sequencing of V3-V4 region. Results revealed that although Lactobacillus supplementation did not change the diversity of gut microbiota in mice, the proportion of some intestinal microbiota significantly changed. Specifically, the proportion of Lactobacillus and Sphingomonas in the Lactobacillus treated-group (L-group) were increased as compared to control group (C-group), whereas Pantoea, Cutibacterium, Glutamicibacter, Turicibacter, Globicatella, Microbacterium, Facklamia, unidentified_Corynebacteriaceae, Brachybacterium, and Staphylococcus were significantly decreased in the L-group. In contrast, Escherichia coli (E. coli) infection significantly decreased the proportion of beneficial bacteria such as Globicatella, Acinetobacter, Aerococcus, and Comamonas, while loads of pathogenic bacteria significantly increased including Roseburia and Megasphaera. Interestingly, Lactobacillus administration could ameliorate the microbial community structure of E. coli-induced diarrheal mice by reducing the relative abundance of pathogenic bacteria such as Paenibacillus, Aerococcus, Comamonas, Acinetobacter, Corynebacterium, Facklamia, and Globicatella. Results in this study revealed that Lactobacillus supplementation not only improved the gut microbiota but also alleviated diarrhea in mice, which may be mediated by modulating the composition and function of gut microbiota. Moreover, this study is expected to provide a new theoretical basis for the establishment of a preventive and treatment system for diarrhea in yaks.

Keywords: Escherichia coli; Lactobacillus; Tibet Plateau; gut microbiota; yak.

Figure 1

Venn diagrams and sample feasibility analysis. Venn diagrams for bacterial OTUs compositions in C (A), L (B), E (C) and EL (D) groups. (E) Venn diagram for unique and shared bacterial OTUs in four groups. (F) Venn diagrams for core OTUs compositions. The rarefaction (G) and species accumulation curve (H) and rank abundance curve (I) were used to assess the adequacy, evenness and richness of sequencing of each sample. Each curve with a different color shown in the figures indicates a sample.

Figure 2

Comparison of alpha diversity of mice gut microbiota in different groups. Four indices such as Good's coverage (A), Chao1 (B), ACE (C), and Simpson (D) were used to assess the alpha diversity of gut microbiota. The data used in this study were expressed as the mean ± SD.

Figure 3

Principal coordinate (PCoA) analysis of gut microbiota in different groups. (A, B) represent PCoA map based on unweighted and weighted uniFrac distance, respectively. Each colored point indicates one sample and the difference in the different groups can be evaluate by the distance between the points.

Figure 4

Relative abundance of the most preponderant (top 10 and 30) gut microbial taxa at phylum (top 10) and genus (top 30) levels for bacteria among four groups. (A, C) Relative abundance of gut microbiota in each sample at the phylum and genus levels. (B, D) Relative abundance of gut microbiota on the basis of the average number of each subfamily at the phylum and genus levels.

Figure 5

Heatmap of the relative abundance of bacterial communities at the genus level in each sample. Each color-block in the heatmap indicates the relative abundance of a bacterial genus in a sample.

Figure 6

Differentially abundant phylotypes in different groups on the basis of LEfSe analysis. Cladogram obtained from LEfSe analysis displayed the different taxa in microbiota of different groups of mice. (A) Cladogram indicating the phylogenetic distribution of microbiota correlated with the C and L groups. (B) Cladogram indicating the phylogenetic distribution of microbiota correlated with the C and E groups. (C) Cladogram indicating the phylogenetic distribution of microbiota correlated with the E and EL groups. (D) Cladogram indicating the phylogenetic distribution of microbiota correlated with the C, E, EL and L groups. The colored circles from the inside to the outside represent different taxonomic levels (phylum, class, order, family, and genus levels). The yellow circles in the cladogram indicate the taxa with no evident differences.

Figure 7

The differences in abundance between the different groups were evaluated using LDA scores. (A) The differences in abundance between the C and L groups. (B) The differences in abundance between the C and E groups. (C) The differences in abundance between the E and EL groups. (D) The differences in abundance between the C, E, EL and L groups. LDA scores > 2 was considered statistically significant.