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Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing

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Abstract

In addition to a wide variety of anaerobic and facultative anaerobic bacteria, camel rumen also harbors a diverse of eukaryotic organisms. In the present study, the eukaryotic communities of camel rumen were characterized using 18S rRNA amplicon sequencing. Metagenomic DNA was isolated from rumen samples of fourteen adult Bikaneri and Kachchhi breeds of camel fed different diets containing Jowar, Bajra, Maize, and Guar. Illumina sequencing generated 27,161,904 number of reads corresponding to 1543 total operational taxonomic units (OTUs). Taxonomic classification of community metagenome sequences from all the samples revealed the presence of 92 genera belonging to 16 different divisions, out of which Ciliophora (73%), Fungi (13%) and Streptophyta (9%) were found to be the most dominant. Notably, the abundance of Ciliophora was significantly higher in the case of Guar feed, while Fungi was significantly higher in the case of Maize feed, indicating the influence of cellulose and hemicellulose content of feedstuff on the composition of eukaryotes. The results suggest that the camel rumen eukaryotes are highly dynamic and depend on the type of diet given to the animal. Pearson’s correlation analysis suggested the ciliate protozoa and fungi were negatively correlated with each other. To the best of our knowledge, this is first systematic study to characterize camel rumen eukaryotes, which has provided newer information regarding eukaryotic diversity patterns amongst camel fed on different diets.

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The sequences for this study have been deposited in the NCBI-SRA under the BioProject PRJNA603266.

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Acknowledgements

This research work was financially supported by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, New Delhi; Reference No.: BT/PR15586/AAQ/1/651/2015.

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Authors and Affiliations

  1. Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India

    Priyaranjan Mishra

  2. Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India

    Nilam J. Tulsani, Subhash J. Jakhesara & Prakash G. Koringa

  3. Environmental Genomic Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440020, India

    Nishant A. Dafale & Hemant J. Purohit

  4. ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh, 334001, India

    Niteen V. Patil

  5. Gujarat Biotechnology Research Center, MS Building, Block B & D, 6th Floor, GH Road, Sector-11, Gujarat, Gandhinagar, 382001, India

    Chaitanya G. Joshi

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  1. Priyaranjan Mishra
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Contributions

HJP and CGJ conceptualised the experimental design, NVP performed the feeding experiment, SJJ and NAD performed sample collection. NJT and PM performed DNA isolation, sequencing, bioinformatics analysis, and initial manuscript writing; SJJ, PGK and NAD improved the manuscript.

Corresponding author

Correspondence to Subhash J. Jakhesara.

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The experiment was performed under the approval of the institutional animal ethics committee of the National Research Center on Camel, Bikaner, Rajasthan.

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The authors declare that they have no conflict of interest.

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Communicated by Erko Stackebrandt.

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Mishra, P., Tulsani, N.J., Jakhesara, S.J. et al. Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing. Arch Microbiol 202, 1861–1872 (2020). https://doi.org/10.1007/s00203-020-01897-w

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