Bacterial community composition in faeces from pigs in an outdoor production system without prophylactic or growth-promoting antibiotics

Abstract

A 16S rRNA gene library-based study was performed to determine the diversity and composition of faecal bacteria from pigs reared outdoors. Fresh faeces were obtained at two different instances from outdoor-reared Berkshire pigs weighing approximately 30 kg (October 2006 and June 2007) or 80 kg (June 2007); samples collected in each instance were labelled EF06-30, EF07-30 and EF07-80, respectively. Fresh faeces from a group of LWD (Landrace × Large White × Duroc) pigs conventionally reared in a pig barn were used as a control. After constructing 16S rRNA gene clone libraries from each sample, taxonomic identification of the sequences, diversity and compositional comparison among the libraries was conducted using BLAST, DOTUR, web-LIBSHUFF and the Library Compare tool of the Ribosomal Database Project. From the four libraries, 90 clones in the control, 93 clones in EF06-30, 94 clones in EF07-30 and 94 clones in EF07-80 were analyzed. Faecal bacterial diversity (Chao1) was higher in pigs reared outdoors than in the control pigs. The bacterial community composition significantly differed between the libraries, except for EF07-30 and EF07-80. The taxonomic assignment in EF06-30 was similar to that in control than the other outdoor groups (EF07-30 and EF07-80). These results indicated that the pigs reared outdoors had obtained a higher intestinal diversity in response to the feeding environments such as location and diet.