41-Title: Comparative metagenomic analysis of samples from footrot-affected sheep and healthy sheep
Authors: Apurva Gupta, Anil Taku, MA Bhat, Indica Sharma, Deep Shikha, Ufaq Aijaz, GA Badroo and Faizan Javid
Source: Ruminant Science (2022)-11(1):203-208.
How to cite this manuscript: Gupta Apurva, Taku Anil, Bhat MA, Sharma Indica, Shikha Deep, Aijaz Ufaq, Badroo GA and Javid Faizan (2022). Comparative metagenomic analysis of samples from footrot-affected sheep and healthy sheep. Ruminant Science 11(1):203-208.
The present study aimed to analyse the metagenome associated with ovine footrot based on 16S rRNA gene by next-generation sequencing methodology. Two samples were collected, one from footrot-affected sheep and one from healthy sheep and both were compared for their associated microbial diversity. Footrot was detected in the affected sample by 16S rRNA gene-based PCR for D. nodosus which showed an amplicon size of 783 bp. Metagenomic analysis of the samples was done using Oxford Nanopore Technology GridION done by Biokart India Pvt. Ltd.(Bangalore) and obtained reads were clustered into Operational Taxonomic Units (OTU’s). The top ten genera found in footrot-affected sheep were Treponema (27%), Acinetobacter (26%), Brevundimonas (17%), Staphylococcus (13%), Candidatus (6%), Agrobacterium (4%), Mycoplasma (2%), Corynebacterium (2%) Ralstonia (2%) and Megasphaera (1%). In the healthy sheep, the top ten genera were Stenotrophomonas (27%), Achromobacter (24%), Brevundimonas (19%), Staphylococcus (14%), Comomonas (5%), Candidatus (3%), Ralstonia (3%), Agrobacterium (2%), Megasphaera (2%) and Rhizobium (1%). Although Brevundimonas and Staphylococcus were also abundant in apparently healthy sheep samples, we envisage that extrinsic and intrinsic factors might affect their niche, producing an imbalance in the bacterial community from healthy to diseased feet. Dichelobacter nodosus, which is the main causative agent of the disease was among the top ten enriched organisms in the footrot-affected sheep sample and was completely absent from apparently healthy sheep. Thus, footrot can be considered a polymicrobial disease as several taxa other than Dichelobacter nodosus are linked to footrot lesions in sheep. To the best of our knowledge, this is the first such study from India.
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