Metagenomic insights into taxonomic and functional shifts under chronic exposure to hypobaric hypoxia induced microbial communities

Alterations in the gut immune axis under hypobaric hypoxia (HH) exposure may be a consequence of microbial dysbiosis. The mechanism of induction of gut inflammation by alterations in gut bacterial and viral populations has not been discovered meticulously. Here we used whole-genome and 16S rRNA sequencing to characterize the taxonomic and functional shifts in the faecal microbiome after HH exposure. Ten faecal samples from unexposed and HH exposed (3 days, 7 days and 14 days) Sprague–Dawley rats were analyzed. 16S rRNA sequencing was conducted on Illumina MiSeq platform using universal primers and analysed using QIIME (Greengenes database). WGS sequencing was done on Illumina HiSEQ 2500 platform and analysed using MOCAT2 (eggNOG database). HH exhibited an overarching effect on taxonomic and functional gene composition. A significant change in α-diversity at phylum level and β-diversity at phylum and genus level were observed between control and HH exposed groups. Significant (p < 0.05) alterations in the taxonomic profiles of bacterial populations and functional metabolic pathways were observed post HH exposure was observed. Further, we hypothesized gut virome influencing bacterial diversity under HH to be a key determinant of intestinal inflammation and thus virome populations analyzed in unexposed and exposed groups showed seven families of Caudovirales to be significantly altered in terms of abundance and diversity. Caudovirales may alter the abundance of beneficial bacteria under HH exposure and thus, changing the intestinal bacterial diversity, initiate intestinal inflammation. This study provided new insights into taxonomic and functional shifts in the faecal microbiome and these findings can aid in future for using bacteriophages for the treatment of different intestinal related inflammatory disorders.