MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.
CP: Microbiology
MetaPhlAn
diet
metagenomics
mouse microbiome
uncharacterized microbial species
Journal
Cell reports
ISSN: 2211-1247
Titre abrégé: Cell Rep
Pays: United States
ID NLM: 101573691
Informations de publication
Date de publication:
30 05 2023
30 05 2023
Historique:
received:
28
12
2022
revised:
10
03
2023
accepted:
17
04
2023
medline:
5
6
2023
pubmed:
4
5
2023
entrez:
4
5
2023
Statut:
ppublish
Résumé
Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.
Identifiants
pubmed: 37141097
pii: S2211-1247(23)00475-8
doi: 10.1016/j.celrep.2023.112464
pmc: PMC10242440
pii:
doi:
Types de publication
Meta-Analysis
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
112464Subventions
Organisme : NCI NIH HHS
ID : U01 CA230551
Pays : United States
Informations de copyright
Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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