Topological and spatial heterogeneity of gut microbiota co-abundance networks in pigs revealed by using large-scale samples.

Fecal samples have often been used as a proxy for studying the gut microbiota. However, the fecal microbiota does not fully reflect the gut microbiota composition. To elucidate the biogeographical characteristics and interaction networks of porcine gut microbiota, we systematically determined the compositions and co-abundance networks of gut microbiota from small to large intestine using 2,955 microbial samples from ileum, cecum, and feces of F6 (715) and F7 (687) pigs which were slaughtered at the age of 240 days from an experimentally designed heterogeneous pig population by crossing eight divergent breeds using 16S rRNA gene sequencing. The gut microbial composition showed significant spatial heterogeneity. The diversity of the gut microbiota progressively increased along the intestinal tract. Significantly spatial heterogeneity was also observed in the co-abundance networks. The numbers of OTUs showing co-abundance correlations with other OTUs were increased from ileum to cecum and feces. We found that the stronger the co-abundance correlation, the higher the gut location specificity of the co-abundance relationships. Only 644 (0.2%) co-abundance relationships among OTUs existed in all three gut locations.