ArticleMicrobial genomics2021
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Microbiota in the Early Lives of Sheep: A Short Overview on the Rumen Microbiota.Animals : an open access journal from MDPI · 2025Review
- Integrating Machine Learning to Identify Key Microbiota of Gut Community Changes Across Different Stages in Dahe Black Pigs.Microorganisms · 2025Article
- Gut Microbiota of Ruminants and Monogastric Livestock: An Overview.Animals : an open access journal from MDPI · 2025Review
- Temporal changes in fecal swine microbiome primarily reflectFrontiers in veterinary science · 2025Article
- Bile acid pathways in Caprinae gut microbiota: adaptive shifts in microbial metabolism and community structure.Frontiers in microbiology · 2025Article
- Genome-centric investigation of bile acid-metabolizing microbiota in chickens and their association withFrontiers in veterinary science · 2025Article
- Article
- Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes.mSystems · 2024Article
- Massive expansion of the pig gut virome based on global metagenomic mining.NPJ biofilms and microbiomes · 2024Article
- Swine Gastrointestinal Microbiota and the Effects of Dietary Amino Acids on Its Composition and Metabolism.International journal of molecular sciences · 2024Review
- Impact of Early Weaning on Development of the Swine Gut Microbiome.Microorganisms · 2023Review
- The gut microbiome and resistome of conventionally vs. pasture-raised pigs.Microbial genomics · 2023Article
- Metagenomic analysis fecal microbiota of dysentery-like diarrhoea in a pig farm using next-generation sequencing.Frontiers in veterinary science · 2023Article
- Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives.Animals : an open access journal from MDPI · 2022Review
- Environmental and maternal factors shaping tonsillar microbiota development in piglets.BMC microbiology · 2022Article
- Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes.Microbiology spectrum · 2022Article
- Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification.Microbial genomics · 2021Article
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6 authors.
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No grant is acknowledged in the PubMed record.
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.
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