Rumen, one of the most productive diverse microbial habitats plays a vital role in the breakdown of feed to produce energy for maintenance and milk production in cattle. Culture-based procedures could identify only 10% of microbial species present in the rumen. Kerala, one of the southern states of India, owns only one native cattle breed, the Vechur cattle, which is noted for its short stature, disease resistance and adaptability to hot humid climate. Lower population density and decreased milk production potential of Vechur cattle led to the development of crossbred cattle of Kerala, with higher milk yield. A study was conducted to assess the rumen microbial profile of low productive Vechur cattle and high productive crossbred cattle for a better understanding of the relationship between the host and microbial community. DNA isolated from rumen liquor of five cattle each from both genetic groups maintained on standard ration (forage, concentrate ratio of 50:50) was subjected to whole metagenome sequencing. Bioinformatics and statistical analysis revealed that bacteria followed by archaea and eukaryota dominated in the Vechur cattle as well as the crossbred cattle rumen. Bacterial community was dominated by Bacteroidetes and Firmicutes phyla in both genetic groups with a higher Firmicutes to Bacteroidetes ratio of 0.45 in Vechur cattle. Among archaea, Euryarchaeota was more abundant, which constitute methanogens, contributing 98% of total archaeal reads. Prevalent protozoal genus found in the Vechur cattle rumen was Entodinium and in crossbred cattle rumen was Entamoeba. In Vechur and crossbred cattle rumen, 1086 and 1262 microbial species were observed exclusively and 4731 species were shared between habitats. There was a significant difference in total microbial species abundance between the two genetic groups and Vechur cattle displayed significantly higher microbial diversity compared to crossbred. As per literature, this is presumably the first report of rumen metagenome profile of Vechur cattle, a unique short breed of India.

中文翻译：

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元基因组学分析，探索印度喀拉拉邦Vechur和杂交牛瘤胃微生物群落的分类学多样性。

瘤胃是生产力最高的多种微生物栖息地之一，在饲料分解中产生至关重要的作用，以产生维持和牛牛生产的能量。基于培养的程序只能识别瘤胃中存在的微生物种类的10％。喀拉拉邦（Kerala）是印度南部各州之一，仅拥有一种本土牛种Vechur牛，该种牛身材矮小，抗病能力强，并且对湿热气候适应能力强。Vechur牛的较低种群密度和降低的产奶潜力导致了喀拉拉邦杂交牛的发展，产奶量更高。进行了一项研究，以评估低产Vechur牛和高产杂种牛的瘤胃微生物特征，以更好地了解宿主与微生物群落之间的关系。从两个基因组的五头牛的瘤胃液中分离的DNA均以标准比例（草料，浓缩比为50:50）进行完整的基因组测序。生物信息学和统计分析表明，细菌，其次是古细菌和真核生物，在Vechur牛和杂种牛瘤胃中占主导地位。细菌群落由拟杆菌和厚壁菌门所用更高的两个遗传群厚壁菌门到拟杆菌在Vechur牛0.45比。在古细菌中，Euryarchaeota更为丰富，构成产甲烷菌，占古细菌总读取量的98％。在Vechur牛瘤胃中发现的原生动物属为Entodinium，在杂种牛瘤胃中发现为Entamoeba。在Vechur和杂交牛瘤胃中，仅观察到1086和1262种微生物，生境之间共有4731种。这两个遗传群体之间的总微生物物种丰度存在显着差异，与杂交品种相比，Vechur牛的微生物多样性更高。根据文献，这大概是印度唯一的短品种Vechur牛的瘤胃元基因组概况的首次报道。