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Volume 7, Issue 8

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

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): carbohydrate active enzymes , co-assembly , gut microbiome , post-weaning , shotgun metagenomics and time series
Funding
This study was supported by the:
  • Australian Research Council (Award LP150100912)
    • Principle Award Recipient: DanielaGaio
  • Australian Research Council (Award LP150100912)
    • Principle Award Recipient: ToniA Chapman
  • Australian Research Council (Award LP150100912)
    • Principle Award Recipient: AaronE Darling
  • Australian Research Council (Award LP150100912)
    • Principle Award Recipient: StevenP Djordjevic
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2021-08-09
2024-04-23
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Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes
M Gen 7, 000501 (2021); https://doi.org/10.1099/mgen.0.000501
/content/journal/mgen/10.1099/mgen.0.000501
/content/journal/mgen/10.1099/mgen.0.000501
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