Abstract
Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.
Highlights
Gut microbiota plays an important role in pig health and production
We show gene catalogs of the pig gut microbiome consisting of 48,697,887 (PIGC100), 17,237,052 (PIGC90), and 7,246,447 (PIGC50) nonredundant genes at 100%, 90%, and 50% amino acid identity, respectively
Compared with the core species, there were significantly higher percentages of KEGG orthologous groups (KOs) (45%), KEGG pathways (91%), eggNOG orthologous (22%), and carbohydrate-active enzymes (CAZymes) (72%) found in more than 90% of the 500 samples (Fig. 3c), implying the functional redundancy of the gut microbiota
Summary
Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Several studies have reported an association between gut microbiota and pig feed efficiency[5,6], growth[7], and diarrhea resistance in early-weaned piglets[8] Most of these studies relied on the available annotation information of microbes that are often connected to partial genome sequences. It is still difficult to profile those uncharacterized microbes using the assembly-free approaches The deficiency of both annotated genes and reference genomes severely restricts the mining and use of metagenomic sequencing data and presents a major challenge for metagenomic sequencing analysis. As for the genome catalog of the gut microbiome, several studies have reconstructed large numbers of microbial genomes from metagenomic sequencing data in both human[9,30,31,32] and agricultural animal species[33,34] using metagenomic assembly approach. A comprehensive genomic catalog of uncultivated microbiota is useful to the studies of gut microbiome their corresponding microbial entities of MAGs need to be further confirmed by culture-based approaches
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
