Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

Abstract

This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level). Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

Keywords: 16S rRNA Gene; Duroc; Fecal Microbiota; Pigs; Pyrosequencing.

Figure 1

Bacterial composition and abundance of the fecal microbiota of Duroc (n = 17) pigs at the phylum (A) and class levels (B). The bar graph depicts the mean relative abundance of each taxonomic group in the pigs. Taxonomic groups with a calculated abundance <0.3% were pooled and labeled as ETC. The error bars represent standard deviations.

Figure 2

Mean relative abundance of the observed genera (A) and unclassified bacteria (B) in the pig fecal samples. Only bacterial phylotypes that had >0.1% of the total sequence reads are shown in the graph. Bacterial phylotypes that had <0.1% were pooled and labeled as ETC. The error bars represent standard deviations.

Figure 3

Heat map showing the relative abundance of the five most abundant taxonomic groups in the pigs. Depicted in the plot are individual pigs (n = 17) containing the most abundant groups from the phylum to the genus level. The relative levels of abundance are depicted visually from black to white; black represents the lowest abundance (min = 0%), while white (max = 100%) represents the highest level of abundance.