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Molecular analysis of the bacterial microbiome in the forestomach fluid from the dromedary camel (Camelus dromedarius)

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Abstract

Rumen microorganisms play an important role in ruminant digestion and absorption of nutrients and have great potential applications in the field of rumen adjusting, food fermentation and biomass utilization etc. In order to investigate the composition of microorganisms in the rumen of camel (Camelus dromedarius), this study delves in the microbial diversity by culture-independent approach. It includes comparison of rumen samples investigated in the present study to other currently available metagenomes to reveal potential differences in rumen microbial systems. Pyrosequencing based metagenomics was applied to analyze phylogenetic and metabolic profiles by MG-RAST, a web based tool. Pyrosequencing of camel rumen sample yielded 8,979,755 nucleotides assembled to 41,905 sequence reads with an average read length of 214 nucleotides. Taxonomic analysis of metagenomic reads indicated Bacteroidetes (55.5 %), Firmicutes (22.7 %) and Proteobacteria (9.2 %) phyla as predominant camel rumen taxa. At a finer phylogenetic resolution, Bacteroides species dominated the camel rumen metagenome. Functional analysis revealed that clustering-based subsystem and carbohydrate metabolism were the most abundant SEED subsystem representing 17 and 13 % of camel metagenome, respectively. A high taxonomic and functional similarity of camel rumen was found with the cow metagenome which is not surprising given the fact that both are mammalian herbivores with similar digestive tract structures and functions. Combined pyrosequencing approach and subsystems-based annotations available in the SEED database allowed us access to understand the metabolic potential of these microbiomes. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the rumen microbiota regardless of rumen type. The present study provides a baseline for understanding the complexity of camel rumen microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments.

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Abbreviations

MG-RAST:

Metagenome rapid annotation using subsystem technology

GS-FLX:

Genome sequencer flexible

SSU:

Small subunit

COG:

Clusters of orthologous groups

KO:

KEGG orthology

NOG:

Non-supervised orthologous group

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Acknowledgments

Authors are thankful to the LSF Unit, NRCC, Bikaner for the facilities of rumen fluid collection. Authors are thankful to Professor D.S. Nauriyal, who carefully read the early manuscript, corrected some errors, and made many valuable suggestions for improvement.

Conflict of interest

None of the authors has any financial or personal relationships that could inappropriately influence or bias the content of the paper.

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Authors and Affiliations

  1. Department of Animal Biotechnology, College of Veterinary Science and A. H., Anand Agricultural University, Anand, 388 001, Gujarat, India

    Vaibhav D. Bhatt & Chaitanya G. Joshi

  2. National Research Centre on Camel, P.O. Box 07, Jorbeer, Bikaner, 334001, Rajasthan, India

    Suchitra S. Dande & Nitin V. Patil

Authors
  1. Vaibhav D. Bhatt
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  2. Suchitra S. Dande
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  3. Nitin V. Patil
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  4. Chaitanya G. Joshi
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Correspondence to Chaitanya G. Joshi.

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Bhatt, V.D., Dande, S.S., Patil, N.V. et al. Molecular analysis of the bacterial microbiome in the forestomach fluid from the dromedary camel (Camelus dromedarius). Mol Biol Rep 40, 3363–3371 (2013). https://doi.org/10.1007/s11033-012-2411-4

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  • DOI: https://doi.org/10.1007/s11033-012-2411-4

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