Metagenomic Analysis of Microbial Community in a Microbial Fermentation-bed for Pig Raising

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.