Comparative Analysis of Structural Composition and Function of Intestinal Microbiota between Chinese Indigenous Laiwu Pigs and Commercial DLY Pigs

SIMPLE SUMMARY: The intestinal microbiota produces essential products as well as forms a barrier against pathogens, which has an important impact on pig phenotypes. Recent studies mainly focused on the microbiota of the feces and worldwide farmed commercial pigs, while research on the microbiota of various intestinal sections and indigenous pig breeds is very limited. Laiwu pigs, a precious Chinese indigenous pig breed, are distinguished by their good meat quality, especially their high intramuscular fat (IMF) content, and they also have high resistance to certain infectious diseases. In recent years, people’s demand for meat consumption has transformed from quantity to quality. In this study, intestinal microbiota in the six intestinal segments of Laiwu pigs and the worldwide farmed crossbred, Duroc × Landrace × Yorkshire (DLY) pigs were sequenced by 16S rRNA sequencing and comparatively analyzed to understand the composition and function of microbiota in each intestinal segment, and to explore the influence of intestinal microbiota to phenotypic traits, such as high IMF, high utilization rate of crude fiber, and strong tolerance of Laiwu pigs. This study can help us better understand the microbial characteristics of indigenous pigs and lay a foundation for the potential influence of the host’s genetic background on variation in microbiota composition and diversity. ABSTRACT: Intestinal microbiota has an important impact on pig phenotypes. Previous studies mainly focused on the microbiota of feces and worldwide farmed commercial pigs, while research on the microbiota of various intestinal sections and indigenous pig breeds is very limited. This study aimed to characterize and compare the biogeography of intestinal microbiota in pigs of one Chinese indigenous breed and one commercial crossbred. In this study, we sequenced the microbiota of six intestinal segments in the grown-up pigs of a Chinese indigenous breed, Laiwu pigs, and the worldwide farmed crossbred Duroc × Landrace × Yorkshire (DLY) pigs by 16S rRNA sequencing, characterized the biogeography of intestinal microbiota, and compared the compositional and functional differences between the two breeds. The results showed that there were obvious differences in microbial structure and abundance between the small and large intestines. Laiwu pigs had higher large intestinal diversity than DLY pigs, while DLY pigs had higher small intestinal diversity than Laiwu pigs. Moreover, some specific bacterial taxa and Kyoto Encyclopedia of Genes and Genomes pathways were found to be related to the high fat deposition and good meat quality of Laiwu pigs and the high growth speed and lean meat rate of DLY pigs. This study provides an insight into the shifts in taxonomic composition, microbial diversity, and functional profile of intestinal microbiota in six intestinal segments of Laiwu and DLY pigs, which would be essential for exploring the potential influence of the host’s genetic background on variation in microbiota composition and diversity.