Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages

Ankit T Hinsu,Hemant J Purohit,Nilam J Tulsani,Chaitanya G Joshi,Subhash J Jakhesara,Ketankumar J Panchal,Niteen V Patil,Basanti Jyotsana,Nishant A Dafale,Ramesh J Pandit

doi:10.1038/s41598-021-88943-9

Abstract

In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.

Highlights

In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants
After all steps of DADA2 pipeline, 6.51 million clean paired-reads (63.75% of reads generated) with an average of 54,290 paired-reads per sample were assigned to 14,978 amplicon sequence variant (ASV) (Amplicon Sequence Variants) (Table S1)
Observed ASVs ranged from 356 to 2,250 with significant differences among liquid and solid fraction samples (Kruskal–Wallis, BH p-value = 0.026) and five collections (Kruskal–Wallis, BH p-value < 0.0001), while no significant differences observed between different feeds (Kruskal–Wallis, BH p-value = 0.83) and different breeds (Kruskal–Wallis, BH p-value = 0.38) (Fig. 1)

Summary

Introduction

In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. Previous studies on dromedary camel rumen microbiome employed 16S rRNA based a pproaches[8,11,12,13] as well as shotgun metagenomics a pproach[14]. These studies have explored microbiota under different feeding conditions from free ranging and controlled environments. The present study was undertaken with the aim of characterizing the microbiota of camel rumen when fed with different roughage feeds namely Bajra, Jowar and Makai (Figure S1). 16S rRNA amplicon sequencing and shotgun metagenomics were used for phylogenetic and functional profile characterization of rumen microbial communities, respectively

Methods

Results

Discussion

Conclusion