CSIR - National Environmental Engineering Research Institute, Nagpur, India.
Arch Microbiol. 2019 Dec;201(10):1385-1397. doi: 10.1007/s00203-019-01706-z. Epub 2019 Jul 23.
Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.
瘤胃微生物群落蕴藏着独特的遗传潜力，能够高效地对植物生物质进行解构，其中包含大量碳水化合物活性酶（CAZyme）。基于这一前提，本研究采用宏基因组学方法对牛和水牛的瘤胃微生物群落进行了特征分析，并鉴定了其碳水化合物活性基因，这些牛和水牛分别以绿色或干草粗饲料为食。本研究生成了来自四个样本（以绿色粗饲料喂养的牛（NDC_GR）、水牛（NDB_GR）、以干草粗饲料喂养的牛（NDC_DR）和水牛（NDB_DR））的元数据。系统发育分析表明，所有四个样本中都存在厚壁菌门、拟杆菌门、变形菌门、放线菌门和纤维杆菌门的优势，这些细菌占据了总细菌群的 90-96%。在更精细的分辨率下，在 NDB_DR 中观察到更多的细菌属，如纤维杆菌属、拟杆菌属、梭菌属、普雷沃氏菌属和瘤胃球菌属，这些菌与植物生物质水解有关。使用 dbCAN 注释算法对功能进行注释后，鉴定出 NDC_GR、NDB_GR、NDC_DR 和 NDB_DR 对应的总基因中，分别有 28.13%、8.08%、10.93%和 12.53%的基因被推测具有碳水化合物活性。进一步对 CAZymes 进行分析后发现，以干草粗饲料喂养的动物中存在大量的糖苷水解酶（GHs），其中 GH2、GH3、GH13 和 GH43 家族的基因显著富集。GH45、GH12、GH113、GH128、GH54 和 GH27 家族的 GHs 仅在 NDB_DR 宏基因组中被观察到。NDB_DR 宏基因组中纤维素酶、半纤维素酶、支链酶和寡糖水解酶的丰度较高。因此，可以得出结论，水牛瘤胃微生物组在植物生物质水解方面更为高效。本研究深入了解了瘤胃微生物组在应对饲料类型和宿主动物变化时，在微生物群落和植物多糖解构能力方面的变化。从这些动物中获得的具有特定活性的微生物群落可进一步用于高效的植物生物质水解。本研究还确立了利用瘤胃微生物组作为挖掘多样化木质纤维素酶的独特资源的可行性。
