Metagenomic investigation of the rumen and caecum microbial communities of the Saharan dromedary camel

The metagenomic bacterial profile of dromedary camel from Algerian Sahara was carried out by exploring 16S rRNA gene amplicon sequencing of the 16S V3-V4 region of bacterial communities of a pregastric (rumen) and post-gastric (caecum) segments in three young camels aged between 2–3 years fed on straw and native vegetation. The generated valid reads were 188,237 and 201,385 for the rumen and caecum respectively, with an average number of OTUs reaching 140 and 170 for the rumen and cecum respectively. The good average ranged from 96.29% to 97.73%. The sequencing analysis revealed 313 bacterial genera distributed in 19 phyla. Taxonomic analysis of metagenomic reads revealed Bacteroidetes and Firmicutes as dominant taxa with significant variation between GIT segments confirmed with principal component analysis. The Bacteroidetes reached 46.92% in the rumen versus 30.70% in the caecum, whereas the Firmicutes attained 55.15% in the caecum against 36.26% in the caecum. Verrucomicrobia taxa ranged from 0.08 (rumen) to 7.17% (caecum) and TM7 distinct specifically the caecum microbiota. Prevotella (26.75%) and Akkermansia (<0.01%) represent respectively the main and lowest dominant genus in the rumen; however, the unclassified Ruminococcaceae (18.82%) and Fibrobacter (1.01%) are successively the highest and lowest dominant genera in the caecum segment. In addition, interdromedaries variation was recorded by UniFrac unweighted and UniFrac weighted distances which was less important than that observed between rumen and caecum segments. The current research provides useful information on the diversity and variation of the microbiota in the gastrointestinal tracts of dromedary camels living in the Algerian Sahara, which can constitute fundamental data to comprehend the interrelationships of these bacterial communities to the performance and productivity of the Saharan dromedary.