Metagenomic Analysis of Microbial Community in a Microbial Fermentation-bed for Pig Raising
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摘要: 养猪微生物发酵床分解猪粪、消除恶臭，将猪粪形成生物菌肥，实现了养猪污染的微生物治理和猪粪的资源化利用，微生物起到关键作用。然而，关于发酵床微生物群落的种类、数量、结构等方面系统研究鲜见报道。课题组采用高通量宏基因组学方法，系统地开展了微生物发酵床的微生物组研究，揭示不同空间、不同深度、不同发酵程度、不同垫料组成、不同季节发酵床中的微生物组成及其区系演替规律。本文就相关的宏基因组测序的样本采集、样本处理、测序原理、分析模型、数据统计、结果表述等分析流程和方法进行了归纳，阐明微生物组操作分类单元（OTU）鉴定，物种累积曲线，核心微生物组，种类丰度主成分分析，种类秩-多度曲线，物种组成丰度柱状图、热图、星图等分析的原理与方法，列举微生物组种类复杂度-多样性分析、-多样性分析、种类显著性差异LEfSe分析，冗余分析等实例，为深入研究发酵床微生物群落提供了完整的分析思路和范例。Abstract: The microbial community can decompose pig feces and eliminate funk odor in the microbial fermentation-bed for pig raising. Thus, the pig raising technology in the microbial fermentation-bed can not only achieve zero release of the pig raising pollutants, but also carry out resourceful utilization of the pig feces resources. Moreover, some key techniques in the microbial fermentation-bed for pig raising are directly or indirectly related to microorganisms. However, very few researches have been done on the microbial species, quantity, structure, and other aspects of the microbial fermentation-bed. Our group had comprehensively and systematically performed the microbiomics analysis of the microbial fermentation-bed to reveal its microbial community and the ecological succession in different space and depth with different fermenting degrees and litter composition in different seasons. In this paper, we summarized the analytical methods and procedures for sample collection, sample processing, and data analysis of the microbial fermentation-bed metagenomic analysis, of which included bacterial operational taxonomic units (OTUs) identification; species accumulation curve; core microbiome; principal component analysis of bacterial abundance; rank-abundance curve; histogram, heatmap, star analyses of bacterial species composition and abundance; - and -diversity analyses of bacterial species complexity; linear discriminative analysis (LDA) coupled with effect size measurement for significant difference, and bacterial species redundancy analysis (RDA). Our work could provide the complete analytical methods and ideas for more deep and broad researches on the microbial community in microbial fermentation-bed.
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