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

Gaio, D; DeMaere, MZ; Anantanawat, K; Chapman, TA; Djordjevic, SP; Darling, AE

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

Gaio, D

DeMaere, MZ Anantanawat, K

Chapman, TA Djordjevic, SP Darling, AE

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Publisher:: Microbiology Society
Publication Type:: Journal Article
Citation:: Microbial Genomics, 2021, 7, (8)
Issue Date:: 2021-08-09

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Field	Value	Language
dc.contributor.author	Gaio, D https://orcid.org/0000-0002-7695-3145
dc.contributor.author	DeMaere, MZ
dc.contributor.author	Anantanawat, K https://orcid.org/0000-0002-7862-0969
dc.contributor.author	Chapman, TA
dc.contributor.author	Djordjevic, SP
dc.contributor.author	Darling, AE
dc.date.accessioned	2022-01-06T00:32:40Z
dc.date.available	2022-01-06T00:32:40Z
dc.date.issued	2021-08-09
dc.identifier.citation	Microbial Genomics, 2021, 7, (8)
dc.identifier.issn	2057-5858
dc.identifier.issn	2057-5858
dc.identifier.uri	http://hdl.handle.net/10453/152716
dc.description.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.
dc.format	Print
dc.language	eng
dc.publisher	Microbiology Society
dc.relation	http://purl.org/au-research/grants/arc/LP150100912
dc.relation.ispartof	Microbial Genomics
dc.relation.isbasedon	10.1099/mgen.0.000501
dc.rights	This is an open- access article distributed under the terms of the Creative Commons Attribution License.
dc.rights	info:eu-repo/semantics/restrictedAccess
dc.subject	0604 Genetics, 0605 Microbiology
dc.title	Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes.
dc.type	Journal Article
utslib.citation.volume	7
utslib.location.activity	England
utslib.for	0604 Genetics
utslib.for	0605 Microbiology
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - ithree - Institute of Infection, Immunity and Innovation
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	recently_added	*
dc.date.updated	2022-01-06T00:32:34Z
pubs.issue	8
pubs.publication-status	Published
pubs.volume	7
utslib.citation.issue	8

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.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/152716