Community composition and development of the post-weaning piglet gut microbiome

Abstract

BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. Studies have previously investigated the effects of probiotics as alternatives to antibiotic treatment for the prevention of post-weaning diarrhea. In order to describe the post-weaning gut microbiota, and the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we processed over 800 faecal time-series samples from 126 piglets and 42 sows, generating over 8Tbp of metagenomic shotgun sequence data. Here we describe the animal trial procedures, the generation of our metagenomic dataset and the analysis of the microbial community composition using a phylogenetic framework.ResultsFactors such as age, litter effects, and breed, by significantly correlating with gut microbial community shifts, can be major confounding factors in the assessment of treatment effects. Intramuscular antibiotic treatment and probiotic treatments were found to correlate with alpha and beta diversity, as well as with a transient establishment of Mollicutes and Lactobacillales, respectively. We found the abundance of certain taxa to correlate with weight gain.ConclusionsOur findings demonstrate that breed, litter, and age, are important contributors to variation in the community composition, and that treatment effects of the antibiotic and probiotic treatments were subtle, while host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The current study shows, by means of a phylogenetic diversity framework, that the post-weaning pig gut microbiome appears to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life.

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

“…The second method applies clustering via taxonomic assignment using the most comprehensive bacterial and archaeal taxonomic database that is currently available. Based on GTDB clustering of MAGs derived from positive control samples (three positive control types; eight replicates within each), MAG taxonomic assignments matched the expected profile and the profile obtained from analysis of the reads with MetaPhlAn2 [ 82 ] reported in our previous study [ 21 ] (Fig. S4).…”

“…In fact, over 80 % of the GTDB clustered MAGs that showed significant abundance shifts during the first week of post-weaning were showing positive fc. This is also reflected by the major increase in microbial richness we measured by community composition analysis of the GTDB clustered MAGs, as well as by phylogenetic diversity analysis of the metagenomic reads in our previous study [21]. Nearly 40 % of the species that increased during the first week of the trial ( t 0– t 2) continued to increase during the following week ( t 2– t 4), reflecting the fact that these species kept taking up a larger portion of the microbial community.…”

“…Below, we briefly summarize the origin of the samples, but we refer to our previous report [ 21 ] for a thorough description of the animal trial and the sample processing workflow. Subjects were post-weaning piglets ( n =126) from which faecal samples were collected between 1 and 10 times during a 40 day period.…”

“…In total, mothers were sampled once, while piglets were sampled between 1 and 10 times (median=6.0; mean=6.11). As previously described [ 21 ], samples were homogenized immediately after collection and stored at −80 °C until thawed for further processing. Extraction of DNA was performed with the PowerMicrobiome DNA/RNA EP kit (Qiagen) and libraries were prepared from genomic DNA using the Hackflex method [ 22 ].…”

“…The present work builds upon a large collection of post-weaning porcine gut samples for which we previously described the microbial community composition using an assembly-free phylogenetic profiling technique [ 21 ]. We reconstruct genomes from this large sample collection and analyse how those genomes change in abundance across time and treatment cohorts.…”