摘要
Present study described rumen microbiome of Indian cattle (Kankrej breed) to better understand the microbial diversity and largely unknown functional capacity of the rumen microbiome under different dietary treatments. Kankrej cattle were gradually adapted to a high-forage diet (four animals with dry forage and four with green forage) containing 50 % (K1), 75 % (K2) to 100 % (K3) forage, and remaining concentrate diet, each for 6 weeks followed by analysis of rumen fiber adherent and fiber-free metagenomic community by shotgun sequencing using ion torrent PGM platform and EBI-metagenomics annotation pipeline. Taxonomic analysis indicated that rumen microbiome was dominated by Bacteroidetes followed by Firmicutes, Fibrobacter, Proteobacteria, and Tenericutes. Functional analysis based on gene ontology classified all reads in total 157 categories based on their functional role in biological, molecular, and cellular component with abundance of genes associated with hydrolase activity, membrane, transport, transferase, and different metabolism (such as carbohydrate and protein). Statistical analysis using STAMP revealed significant differences (P < 0.05) between solid and liquid fraction of rumen (in 65 categories), between all three treatments (in 56 categories), and between green and dry roughage (17 categories). Diet treatment also exerted significant difference in environmental gene tags (EGTs) involved in metabolic pathways for production of volatile fatty acids. EGTs for butyrate production were abundant in K2, whereas EGTs for propionate production was abundant during K1. Principal component analysis also demonstrated that diet proportion, fraction of rumen, and type of forage affected rumen microbiome at taxonomic as well as functional level.
摘要译文
印度牛瘤胃cribed微生物（Kankrej品种），以更好地了解微生物的多样性和不同的饮食治疗瘤胃微生物的主要是未知功能的能力。Kankrej牛被逐渐适应高草料日粮（四只动物的干饲料和四个绿色饲料）含有50％（K1），75％（K 2）至100％（K3）饲料，和剩余的精料日粮，每6周，然后瘤胃纤维粘附和无纤维宏基因组社区通过分析鸟枪测序用离子洪流PGM平台和EBI，宏基因组注释管道。分类分析表明，瘤胃微生物主要是由拟杆菌其次是厚壁菌门，Fibrobacter，变形菌和Tenericutes。基于基因本体功能分析归类的基础上的生物，它们的分子功能的作用，共157类别所有读取，并与丰度与水解酶活性，膜，运输，转移酶，和不同的代谢（例如碳水化合物和蛋白质）相关的基因的细胞成分。统计分析使用STAMP显示显著差异（P所有三种处理（56种），以及之间的绿色和干粗饲料（17类）之间。饮食治疗也施加在涉及生产挥发性脂肪酸代谢途径环境基因标记（EGTS）显著差异。EGTS的丁酸盐产生较丰富的K2，而K1在EGTS为丙酸产量丰富。主成分分析也表明，饮食中的比例，瘤胃的分数，和饲料类型的影响在瘤胃分类微生物以及功能级别。
Vilas Patel [1] Amrutlal K. Patel [1] Nidhi R. Parmar [1] Anand B. Patel [1] Bhaskar Reddy [1] Chaitanya G. Joshi [1]. Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet[J]. Applied Microbiology and Biotechnology, 2014,98(23): 9749-9761