In:
PLOS ONE, Public Library of Science (PLoS), Vol. 18, No. 2 ( 2023-2-16), p. e0280870-
Abstract:
The use of NGS-based testing of the bacterial microbiota is often impeded by inconsistent or non-reproducible results, especially when applying different analysis pipelines and reference databases. We investigated five frequently used software packages by submitting the same monobacterial datasets to them, representing the V1-2 and the V3-4 regions of the 16S-rRNA gene of 26 well characterized strains, which were sequenced by the Ion Torrent™ GeneStudio S5 system. The results obtained were divergent and calculations of relative abundance did not yield the expected 100%. We investigated these inconsistencies and were able to attribute them to failures either of the pipelines themselves or of the reference databases they rely on. On the basis of these findings, we recommend certain standards which should help to render microbiome testing more consistent and reproducible, and thus useful in clinical practice.
Type of Medium:
Online Resource
ISSN:
1932-6203
DOI:
10.1371/journal.pone.0280870
DOI:
10.1371/journal.pone.0280870.g001
DOI:
10.1371/journal.pone.0280870.t001
DOI:
10.1371/journal.pone.0280870.t002
DOI:
10.1371/journal.pone.0280870.t003
DOI:
10.1371/journal.pone.0280870.t004
DOI:
10.1371/journal.pone.0280870.s001
DOI:
10.1371/journal.pone.0280870.s002
DOI:
10.1371/journal.pone.0280870.s003
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2023
detail.hit.zdb_id:
2267670-3
Permalink