Species-Level Resolution of Female Bladder Microbiota from 16S rRNA Amplicon Sequencing.
16S sequencing
algorithms
bioinformatics
bladder
microbiome
taxonomic classification
urobiome
Journal
mSystems
ISSN: 2379-5077
Titre abrégé: mSystems
Pays: United States
ID NLM: 101680636
Informations de publication
Date de publication:
26 Oct 2021
26 Oct 2021
Historique:
pubmed:
15
9
2021
medline:
15
9
2021
entrez:
14
9
2021
Statut:
ppublish
Résumé
The human bladder contains bacteria, even in the absence of infection. Interest in studying these bacteria and their association with bladder conditions is increasing. However, the chosen experimental method can limit the resolution of the taxonomy that can be assigned to the bacteria found in the bladder. 16S rRNA amplicon sequencing is commonly used to identify bacteria in urinary specimens, but it is typically restricted to genus-level identification. Our primary aim here was to determine if accurate species-level identification of bladder bacteria is possible using 16S rRNA amplicon sequencing. We evaluated the ability of different classification schemes, each consisting of combinations of a reference database, a 16S rRNA gene variable region, and a taxonomic classification algorithm to correctly classify bladder bacteria. We show that species-level identification is possible and that the reference database chosen is the most important component, followed by the 16S variable region sequenced.
Identifiants
pubmed: 34519534
doi: 10.1128/mSystems.00518-21
pmc: PMC8547459
doi:
Types de publication
Journal Article
Langues
eng
Pagination
e0051821Subventions
Organisme : HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
ID : K01DK116706
Organisme : NCATS NIH HHS
ID : UL1 TR002369
Pays : United States
Organisme : HHS | NIH | National Institute on Aging (NIA)
ID : R03AG060082
Organisme : NIDDK NIH HHS
ID : K01 DK116706
Pays : United States
Organisme : NIA NIH HHS
ID : R03 AG060082
Pays : United States
Organisme : HHS | NIH | National Center for Advancing Translational Sciences (NCATS)
ID : UL1TR002369
Organisme : NIA NIH HHS
ID : P30 AG028716
Pays : United States
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