Background Under anoxic conditions, the body will undergo a series of changes to compensate for the low oxygen environment. Changes in gut microbes are an important part of this. Currently, there are relatively few studies on the changes of intestinal microorganisms and metabolites in the low-oxygen environment of plateau. This study employed a non-targeted metabolomics approach coupled with shotgun metagenomic sequencing to analysis the changes of intestinal microorganisms and metabolites in rats under hypoxic environment. Results Significant difference in biodiversity were observed. At the genus level, the relative abundance of Lactobacillus, Alistipes in the hypoxic cohort were significantly increased, while Flavonifractor, Faecalibacterium and Dorea were significantly decreased(P < 0.05). Non-targeted metabolomics analysis showed significant differences in 4 metabolic pathways (pyrimidine metabolism, aminoacyl-tRNA biosynthesis, nicotinate and nicotinamide metabolism, thyroid hormone synthesis) between T group and C group (P < 0.05). Furthermore, correlation analysis of metagenomic and metabolomic data sets showed that there was a certain relative quantitative relationship between some bacterial genera and differential metabolites. Conclusions Our results indicate that a plateau hypoxic environment can significantly alter the composition of intestinal microbes in the host.Compared with the plain control group, the relative increase of some bacteria genera was accompanied by the increase of related metabolites, suggesting that these bacteria genera and metabolites were closely related to the low-oxygen environment in the plateau.It provides a certain foundation for the next research.
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