Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes

Abstract

Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic ‘signatures’ that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

“…Since 2004, advances in the sequencing of entire microbial communities comprising uncultivated organisms combined with new bioinformatics methodologies [45] revealed hitherto unknown taxa and led to a burst of new bacterial genomes [46–49]. However, as large proportions of the proteins encoded by these genomes are of unknown functions, the automated annotation of these genomes remains challenging.…”

Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes

“…To determine how widely distributed the species/strains represented by the MAGs in the present study are among pigs from other studies in different geolocations, the presence and relative abundance of these MAGs within publicly available swine gut metagenomic data sets was assessed. These metagenomic sequences were from 626 fecal and cecal content samples within nine studies representing 13 different counties ( 14 – 22 ) (Table S6). On average, 45.5% ± 0.4% SEM of these metagenomic sequences mapped to one of the MAGs from the present study (Table S7).…”

“…These included MAGs enriched in postweaning pigs that were assigned to uncultured genera or species and were also identified as potential butyrate producers such as CAG-83 sp., Aphodosoma sp900769035, Copromorpha sp., Egerieousia sp004561775, and UMGS1668 sp004556975. Some of these placeholder names represent bacterial taxa that have been previously reported in swine gut metagenomes and await further characterization ( 14 , 41 ). One MAG classified as E. faecalis was relatively abundant in the nursing pig samples (0.25 ± 0.07%) but was not detected in any of the postweaning fecal samples.…”

Novel insights into the pig gut microbiome using metagenome-assembled genomes

“…These included MAGs enriched in post-weaning pigs that were assigned to uncultured genera or species and were also identified as potential butyrate producers such as CAG-83 sp., Aphodosoma sp900769035, Copromorpha sp., Egerieousia sp004561775, and UMGS1668 sp004556975. Some of these placeholder names represent bacterial taxa that have been previously reported in swine gut metagenomes and await further characterization (32, 33). One MAG classified as E. faecalis was relatively abundant in the nursing pig samples (0.25 ± 0.07%) but was not detected in any of the post-weaning fecal samples.…”