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Gut Microbial Genes Profiled in Pigs From Diverse Breeds, Locations

NEW YORK (GenomeWeb) – An international team led by investigators in China, France, and Denmark has characterized the collection of gut microbial genes present in hundreds of pigs from three countries, developing a resource that's expected to inform pig production methods as well as efforts to blunt the distribution of antibiotic resistance gene.

"Combined with the recently published pig genome, the pig gut gene catalogue will accelerate research that aims at deciphering the complex interactions between microbiota and hosts," co-corresponding author Jun Wang, former BGI-Shenzhen CEO, and his colleagues wrote. "Integration of phenotypic, genomic, and metagenomic data will provide key biological information for future biomedical research, as well as in translational research towards more sustainable knowledge-based pig farming."

As they reported in Nature Microbiology today, Wang and his co-authors used metagenomic sequencing to profile microbial genes in fecal samples from 287 pigs in France, Denmark, and China. From these sequence data, they uncovered almost 8 million microbial genes, including genes with many of the same predicted functions as microbial genes previously detected in the human gut microbiome.

"[T]he overlap between the human and pig gut microbiome is modest at the gene level," they wrote, "but high at the [Kyoto Encyclopedia of Genes and Genomes orthology] function level."

The researchers used Illumina GAIIx or HiSeq 2000 to do paired-end metagenomic sequencing on microbial DNA found in fecal samples from 100 pigs apiece from farms in France and Denmark, and 87 pigs from China. They noted that the pigs selected for the study came from almost a dozen farms and represented 17 different breeds.

From more than 6 billion bases of sequence per sample, on average, the team detected just shy of 7.7 million non-redundant microbial genes, including 4,430 genes found in gut samples from all of the pigs considered and 88,261 genes present in samples from at least 90 percent of the pigs.

All but 2 percent of the non-redundant genes appeared to stem from bacteria, while the remaining genes were predicted to come from archaea and eukaryotes. Among the genes that could be classified taxonomically, the researchers saw an over-representation of genes from the Firmicutes and Bacteroidetes phyla, though they assigned less than 8 percent of the genes to specific bacterial genera.

Almost 500 of the 719 metagenomic species they identified coincided with annotated bacterial species, the team noted, while 222 appeared to represent previously undescribed microbial species.

The researchers went on to explore shifts in gut microbial gene repertoire that appeared to coincide with the breed, age, or sex hormone production of the pigs considered, along with the gut microbial genes related to geographic location and exposure to antibiotics. For example, they saw high levels of antibiotic resistance genes and lower overall species richness in gut samples from pigs in China, which were raised on low doses of prophylactic antibiotics, though certain antibiotic resistance genes were more common in pigs from France or Denmark — patterns that appear to be related to the antibiotics that are permitted or routinely used in each country.

The team noted that the pig gut microbe gene had more pronounced gene and functional richness than has been reported in mouse and human gut microbiomes. And while fewer than 10 percent of the specific genes in the pig and human gut microbiomes overlapped, the microbiomes appeared to be functionally similar and were more closely related than the human and mouse gut microbiomes.

"[Ninety-six percent] of the [Kyoto Encyclopedia of Genes and Genomes orthology pathways] found in the human gut metagenome are present in the pig gut metagenome based on the taxonomically annotated [non-redundant] genes," the authors wrote, "supporting the use of the pig as a model for functional studies on the role of the microbiome in health and disease."