Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes
Citation
Holman, D.B., Kommadath, A., Tingley, J.P., Abbott, D.W. (2022). Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes. Microbiology Spectrum, [online] 10(4), http://dx.doi.org/10.1128/spectrum.02380-22
Plain language summary
Many of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from
fecal samples collected from pigs at multiple time points during the swine production cycle. We recovered 1,150 high-quality MAGs from fecal metagenomes of pre- and post-weaned pigs. The MAGs described here demonstrate the vast potential of the pig gut microbiome to degrade and metabolize various glycans and of certain members to provide beneficial short-chain fatty acids to the host. In addition, the significant number
of antimicrobial resistance genes found associated with MAGs assigned to bacterial species that are typically commensals in the gut, may explain why resistance to macrolides and tetracyclines persists in the absence of antimicrobial selective pressure. The large majority of the MAGs were assigned to poorly characterized taxa and thus, there still exists a large fraction of the swine gut microbiome that has yet to be cultured. This included many bacterial species that appear to be widely disseminated among pigs from different geolocations.
Abstract
Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g., Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g., Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs, such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes.