Large-scale pig gut microbial gene set to build scientific research results

February 17th, the research team of Jiangxi Agricultural University, led by China's
Huang Lusheng, published a major scientific research achievement in Nature Communications, the world's top academic journal, providing the largest collection of pig gut microbial genes and genomes assembled based on macro genomes. The results provide an important extension resource for the research of pig gut microbiome.
pig is the main meat eaten by humans and an animal model for biomedical research. Pigs have trillions of bacteria in their gastrointestinal tracts that play a vital role in the host's metabolism, immunity and even behavior. In the study of causation between the intestinal bacteriobiosis and the important economics of pigs, reference genes and high-quality microbial genomes are essential resources for understanding the functional role of specific microorganisms and their quantification, but in the current database, only the genomes of some microorganisms and related functional genes are annotated, and about 40-50% of gut microorganisms lack reference genomes.
It is understood that macrogenome sequencing can be used to infer the biological function of the microbiome compared to the 16S rRNA gene sequencing, which is prone to bias, low sensitivity and lack of functional information in the gut microbiome, and has been gradually used in studies to explore the correlation between the gut microbiome and the host esotype based on macro genome association analysis. However, when macro genome sequencing data analysis is performed using the commonly used assembly methods, misalmed and nested overlap groups may be produced, and obvious biases may be introduced into the results. Therefore, there is an urgent need for a complete microbial gene catalog and reference genome sequence information to study the gut microbiome.
Huang Lusheng
team collected 500 samples of different ages, genders, breeds, geographical regions, different intestinal sites and different wild boar sources for deep macro genome sequencing, and integrated the existing pig gut bacteria genome to build and integrate Pig Gut Microbial Gene Catalog (PIGC), which contains 17,237,052 complete genes from 787 gut metagenomes, are clustered with 90 percent protein ismogeneity, 28 percent of which are unknown proteins. At the same time, 6,339 microbial genomes (MAGs) assembled based on macro genomes were constructed using a case-by-case analysis model, which was clustered into 2,673 species-level genomic silos, of which more than 86% were genome sequences that were not available in the current database.
In this study, Huang Lusheng
and Chen Zhiying, lead professor at Jiangxi Agricultural University, compared the differences between wild boars and the highly commercialized Dulock pig gut microbiome using the built-up PIGC and MAG, and found significant differences in the composition of the gut bacteriomes between the two. In order to analyze the resistance of wild boars and the high growth rate and high feed utilization of commercial pig species from the perspective of intestinal bacteria, the use of samples of wild boar intestinal virlobes and samples of empty intestines, return intestines and blind intestines has greatly enhanced the broad representation of PIGC and MAG.