Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages

Abstract

Tibetan animals have several unique advantages owing to the harsh ecological conditions under which they live. However, compared to Tibetan mammals, understanding of the advantages and underlying mechanisms of the representative high-latitude bird, the Tibetan chicken (Gallus gallus, TC), remains limited. The gut microbiota of animals has been conclusively shown to be closely related to both host health and host environmental adaptation. This study aimed to explore the relationships between the cecal microbiome and the advantages of TCs based on comparisons among three populations: native TCs residing on the plateau, domestic TCs living in the plain, and one native plain species. Metatranscriptomic sequencing revealed a significant enrichment of active Bacteroidetes but a loss of active Firmicutes in native TCs. Additionally, the upregulated expression of genes in the cecal microbiome of native TCs showed enriched pathways related to energy metabolism, glycan metabolism, and the immune response. Furthermore, the expression of genes involved in the biosynthesis of short-chain fatty acids (SCFAs) and secondary bile acids (SBAs) was upregulated in the cecal microbiome of native TCs. Data from targeted metabolomics further confirmed elevated levels of certain SCFAs and SBAs in the cecum of native TCs. Based on the multi-omics association analysis, we proposed that the higher ratio of active Bacteroidetes/Firmicutes may be attributed to the efficient energy metabolism and stronger immunological activity of native TCs. Our findings provide a better understanding of the interactions between gut microbiota and highland adaptation, and novel insights into the mechanisms by which Tibetan chickens adapt to the plateau hypoxic environment.

Importance: The composition and function of the active cecal microbiome were significantly different between the plateau Tibetan chicken population and the plain chicken population. Higher expression genes related to energy metabolism and immune response were found in the cecal microbiome of the plateau Tibetan chicken population. The cecal microbiome in the plateau Tibetan chicken population exhibited higher biosynthesis of short-chain fatty and secondary bile acids, resulting in higher cecal content of these metabolites. The active Bacteroidetes/Firmicutes ratio in the cecal microbiome may contribute to the high-altitude adaptive advantage of the plateau Tibetan chicken population.

Keywords: active Bacteroidetes/Firmicutes ratio; active microbiome; innate immune activity; multi-omics; secondary bile acids; short-chain fatty acids.

Fig 1

The composition of the active cecal microbiome between the plateau Tibetan chicken population and the plain chicken population. (A) Relative abundance of top 10 abundant active cecal bacterial phyla among the samples studied. (B) Differences in the relative abundance of active cecal bacterial genera among the three chicken populations. The size and color of the points represent the average abundance of active cecal bacterial genera in samples from the same population. Different lowercase letters inside the points in the same column represent significant differences (P-value of Tukey’s HSD test <0.05) between different populations.

Fig 2

Expression levels of COG terms and CAZymes in the cecal microbiome between the plateau Tibetan chicken population and the plain chicken population. Differences in the expression levels of COG terms (A) and CAZymes (B) in the cecal microbiome of the three chicken populations. Different lowercase letters above the boxes in the same subFig represent significant differences (P-value of Tukey’s HSD test <0.05) between different populations.

Fig 3

DGEs and enrichment analysis in the cecal microbiomes between the plateau Tibetan chicken population and the plain chicken population. Venn diagrams for upregulated (A) and downregulated (B) DEGs among the three comparisons. (B) KEGG enrichment analysis of upregulated genes in the cecal microbiomes of chickens residing in the plateau and plain regions.

Fig 4

Biosynthesis of SCFAs and immune activity in the cecal microbiome of In-TCs. (A) Expression levels of genes associated with SCFA biosynthesis in the cecal microbiome of different chicken populations. (B) Host composition of SCFA biosynthesis genes differentially expressed among different chicken populations. (C) Expression levels of genes related to the biosynthesis of innate immune factors in the cecal microbiome of different chicken populations. (D) Host composition of innate immune factor biosynthesis-related genes differentially expressed among different chicken populations. Color and values represent the fold change of gene expression levels in each population compared to that in the In-TC group. Red points represent significant differences in gene expression levels among the different groups.

Fig 5

Targeted metabolomic analysis of SCFAs and BAs in the cecum among the three chicken populations. PCoA shows differences in the composition of SCFAs (A) and BAs (B) in the cecum among the three chicken populations studied. (C) Comparison of SCFA and BA concentrations in the cecum of different chicken populations. Colors and values represent the fold-change in metabolites in each population compared with those in the In-TC group. The red points represent significant differences in metabolite concentrations among the different groups.

Fig 6

Differences in the ratio of active Bacteroidetes/Firmicutes in the cecal microbiome between chickens residing in plateau and plain areas and their correlations with gene expression levels and metabolite contents related to SCFAs and BAs. Different lowercase letters above the boxes in the boxplot represent statistically significant differences (P-value of Tukey’s HSD test <0.05) between different populations. The color of the blocks in the heatmaps represents the correlation coefficient of Spearman correlations. “+” and “++” represent P-values Spearman correlations lower than 0.05 and 0.01, respectively.

Fig 7

Framework for the ratio of active Bacteroidetes/Firmicutes regulating the biosynthesis of SCFAs and SBAs in chickens residing in plateau and plain regions.