摘要
Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P 0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P 0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.
摘要译文
Zebu（Bos indicus）是一种源自印度次大陆的家养牛，现在在几个大陆广泛驯化。在这个研究中，我们特别感兴趣的是在不同的饮食方案下了解一个重要的瘤牛品种Gir的功能活跃的瘤胃微生物群。在不同的分类水平上比较了种子组学数据，以阐明不同粗饲料日粮条件下Gir牛瘤胃中的微生物种群及其功能动态。不同比例的粗饲料而不是粗饲料（干燥或绿色）调节的微生物组组成和其基因库的表达。纤维降解菌（即梭菌属，与液体部分相比，瘤胃固体部分中的Ruminococcus，Eubacterium，Butyrivibrio，Bacillus和Roseburia）更高（P 0.01），而被认为是降解产物（即普氏菌，拟杆菌，拟除虫菊酯，Paludibacter和Victivallis）的利用者的细菌在液体部分中占优势（P 0.05）。同样，纤维降解酶和相关碳水化合物结合模块（CBM）的表达发生在固体部分中。当比较宏基因组和元变性数据时，结果发现，虽然它们的丰度很低，但是一些属和物种的转录活性更高。对纤维降解及其在瘤胃中的进一步代谢作出重要贡献。该研究还鉴定了一些转录活性属，例如Caldicellulosiruptor和Paludibacter，其在瘤胃中的潜力较少。总体，与传统的宏基因组分析相比，宏基因组霰弹枪和元转录组测序的比较似乎是更丰富的信息来源。
Ramesh J.Pandit[a];Ankit T.Hinsu[a];Shriram H.Patel[a];Subhash J.Jakhesara[a];Prakash G.Koringa[a];FossoBruno[b];AndronikiPsifidi[c][d];S.V.Shah[e];Chaitanya G.Joshi[a];. Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches[J]. Systematic and Applied Microbiology, 2018,41(4): 374-385