Deep litter system is widely applied to pig production. The beddings have complex microbial communities which play an important role in fermentation efficiency. To obtain the bacterial community in pig deep litter system, we utilized the traditional culture-dependent method and molecular biology technique. Using plate count method Microbacterium (35.33%) and Arthrobacter (20.30%) were remarkable in total culturable bacteria. By 16S rRNA gene library method, the sequences are mostly distributed in 3 phyla: Proteobacteria (38.40%), Firmicutes (28.18%), Bacteroidetes (16.57%) and affiliated to 10 genera: Clostridium (19.89%), Castellaniella (4.70%), Comamonas (2.76%), Rhodanobacter (2.21%), Acinetobacter (1.38%), Planctomyces (1.38%), Nitrosomonas (1.10%), Devosia (1.10%), Gemmatimonas (1.10%), and Steroidobacter (1.10%). In addition, an Illumina next generation sequencing named MiSeq was used to observe the V4/V5 hypervariable region of 16S rDNA sequence. Proteobacteria, Firmicutes, and Bacteroidetes accounted for 83.7% of all sequences. The 10 genera described above were also presented and new 4 genera were added. Clostridium was increased to 25.5% as the predominant bacteria. The results were consistent with that of 16S rRNA gene library analysis in general. It is the first report which provides information on bedding microbiota in pig deep litter system taking advantage of culture and culture-independent approaches.
Bacteria community, Deep litter system, MiSeq, 16S rRNA gene
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