Jose V Lyju, More Ravi P, Appoothy Thulasi, Arun A Sha
Rumen Microbiology Laboratory, Animal Nutrition Division, National Institute of Animal Nutrition and Physiology, Bangalore, India; Department of Biotechnology, Jain University, Bangalore, India.
Bioinformatics Laboratory, Division of Molecular Entomology, National Bureau of Agricultural Insect Resources, Bangalore, India.
Syst Appl Microbiol. 2017 Apr;40(3):160-170. doi: 10.1016/j.syapm.2017.02.003. Epub 2017 Feb 28.
Rumen houses a plethora of symbiotic microorganisms empowering the host to hydrolyze plant lignocellulose. In this study, NGS based metagenomic approach coupled with bioinformatic analysis was employed to gain an insight into the deconstruction of lignocellulose by carbohydrate-active enzymes (CAZymes) in Indian crossbred Holstein-Friesian cattle. Cattle rumen metagenomic DNA was sequenced using Illumina-MiSeq and 1.9 gigabases of data generated with an average read length of 871 bp. Analysis of the assembled sequences by Pfam-based Carbohydrate-active enzyme Analysis Toolkit identified 17,164 putative protein-encoding CAZymes belonging to different families of glycoside hydrolases (7574), glycosyltransferases (5185), carbohydrate-binding modules (2418), carbohydrate esterases (1516), auxiliary activities (434) and polysaccharide lyases (37). Phylogenetic analysis of putative CAZymes revealed that a significant proportion of CAZymes were contributed by bacteria belonging to the phylum Bacteroidetes (40%), Firmicutes (30%) and Proteobacteria (10%). The comparative analysis of HF cross rumen metagenome with other herbivore metagenomes indicated that Indian crossbred cattle rumen is endowed with a battery of CAZymes that may play a central role in lignocellulose deconstruction. The extensive catalog of enzymes reported in our study that hydrolyzes plant lignocellulose biomass, can be further explored for the better feed utilization in ruminants and also for different industrial applications.
瘤胃中存在大量共生微生物，使宿主能够水解植物木质纤维素。在本研究中，采用基于二代测序（NGS）的宏基因组学方法并结合生物信息学分析，以深入了解印度杂交荷斯坦 - 弗里生牛中碳水化合物活性酶（CAZymes）对木质纤维素的解构作用。使用Illumina - MiSeq对牛瘤胃宏基因组DNA进行测序，产生了1.9千兆碱基的数据，平均读长为871 bp。通过基于Pfam的碳水化合物活性酶分析工具包对组装序列进行分析，鉴定出17164个推定的蛋白质编码CAZymes，它们属于不同的糖苷水解酶家族（7574个）、糖基转移酶家族（5185个）、碳水化合物结合模块家族（2418个）、碳水化合物酯酶家族（1516个）、辅助活性家族（434个）和多糖裂解酶家族（37个）。对推定的CAZymes进行系统发育分析表明，很大一部分CAZymes由拟杆菌门（40%）、厚壁菌门（30%）和变形菌门（10%）的细菌贡献。对杂交荷斯坦 - 弗里生牛瘤胃宏基因组与其他食草动物宏基因组的比较分析表明，印度杂交牛瘤胃拥有一系列可能在木质纤维素解构中起核心作用的CAZymes。我们研究中报道的水解植物木质纤维素生物质的大量酶类目录，可进一步探索用于提高反刍动物的饲料利用率以及不同的工业应用。
