Pyrosequencing-based analysis of the complex microbiota located in the gastrointestinal tracts of growing-finishing pigs

The commensal gut microbial communities play an important role in the health and production efficiency of growing-finishing pigs. This study aimed to analyse the composition and diversity of the microbiota in the gastrointestinal tract sections (stomach, duodenum, jejunum, ileum, caecum, colon and rectum) of growing-finishing pigs. This analysis was assessed using 454 pyrosequencing targeting the V3-V6 region of the 16S rRNA gene. Samples were collected from 20, healthy pigs aged 24 weeks and weighing 115.9 +/- 5.4 kg. The dominant bacterial phyla in the various gastrointestinal tract sections were Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria. At the genus level, Prevotella, unclassified Lachnospiraceae, Ruminococcus, unclassified Ruminococcaceae and Oscillospira were more abundant in the large intestine than in the stomach and the small intestine. Unclassified Peptostreptococcaceae and Corynebacterium were more abundant in the small intestine than in the stomach and the large intestine. Shuttleworthia, unclassified Veillonellaceae and Mitsuokella were more abundant in the stomach than in the small and large intestines. At the species level, M. el.s.d.enii and M. multacida were predominant in the stomach. In addition, P. stercorea, P. copri, C. butyricum, R. flavefaciens and R. bromii were significantly more abundant in the large intestine than in the stomach and the small intestine. B. pseudolongum and B. thermacidophilum were significantly more abundant in the small intestine than in the stomach and the large intestine. Principal coordinates analysis showed that the overall composition of the pig gastrointestinal microbiota could be clustered into three groups: stomach, small intestine (duodenum, jejunum and ileum) and large intestine (caecum, colon and rectum). Venn diagrams illustrated the distribution of shared and specific operational taxonomic units among the various gastrointestinal tract sections.