Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach.
ITS
metagenomics
profiling
Journal
mSystems
ISSN: 2379-5077
Titre abrégé: mSystems
Pays: United States
ID NLM: 101680636
Informations de publication
Date de publication:
28 Jul 2020
28 Jul 2020
Historique:
entrez:
30
7
2020
pubmed:
30
7
2020
medline:
30
7
2020
Statut:
epublish
Résumé
16S small-subunit (SSU) rRNA gene-based bacterial profiling is the gold standard for cost-effective taxonomic reconstruction of complex bacterial populations down to the genus level. However, it has been proven ineffective in clinical and research settings requiring higher taxonomic resolution. We therefore developed a bacterial profiling method based on the internal transcribed spacer (ITS) region employing optimized primers and a comprehensive ITS database for accurate cataloguing of bacterial communities at (sub)species resolution. Performance of the microbial ITS profiling pipeline was tested through analysis of host-associated, food, and environmental matrices, while its efficacy in clinical settings was assessed through analysis of mucosal biopsy specimens of colorectal cancer, leading to the identification of putative novel biomarkers. The data collected indicate that the proposed pipeline represents a major step forward in cost-effective identification and screening of microbial biomarkers at (sub)species level, with relevant impact in research, industrial, and clinical settings.
Identifiants
pubmed: 32723792
pii: 5/4/e00404-20
doi: 10.1128/mSystems.00404-20
pmc: PMC7394355
pii:
doi:
Types de publication
Journal Article
Langues
eng
Informations de copyright
Copyright © 2020 Milani et al.
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