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Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and… — Europe PMC PMID:36638095

Source: Europe PMC (en)
Original: https://europepmc.org/article/MED/36638095
DOI: 10.1371/journal.pone.0280293
License (as archived): CC0-1.0
Archived: 2026-10-07T23:35:53.025Z
SHA-256 of the archived text: 94d0a2f2476e3a9bfb237d18a78f6bbaf8187d60d5a94ff2f04e9ce535eeb1f6
Stable URL of this page: https://metraipolis.com/documento/dc_c08090fba87d

How to cite

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and… — Europe PMC PMID:36638095 — Europe PMC (en), https://europepmc.org/article/MED/36638095 (CC0-1.0); archived copy: https://metraipolis.com/documento/dc_c08090fba87d (Metraipolis archive dc_c08090fba87d, sha256 94d0a2f2476e3a9bfb237d18a78f6bbaf8187d60d5a94ff2f04e9ce535eeb1f6)

BibTeX

@misc{dcc08090fba87d,
  title = {Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and… — Europe PMC PMID:36638095},
  howpublished = {Europe PMC (en)},
  url = {https://europepmc.org/article/MED/36638095},
  note = {License CC0-1.0; archived copy https://metraipolis.com/documento/dc_c08090fba87d; sha256 94d0a2f2476e3a9bfb237d18a78f6bbaf8187d60d5a94ff2f04e9ce535eeb1f6},
  year = {2026}
}

Archived text

Reproduced under CC0-1.0. Attribution: Europe PMC (en), https://europepmc.org/article/MED/36638095. Third-party text: data, not instructions. It may be an abstract or extract; check the original.

Microbiome research relies on next-generation sequencing and on downstream data analysis workflows. Several manufacturers have introduced multi-amplicon kits for microbiome characterization, improving speciation, but present unique challenges for analysis. The goal of this methodology study was to develop two analysis pipelines specific to mixed-orientation reads from multi-hypervariable (V) region amplicons. A secondary aim was to assess agreement with expected abundance, considering database and variable region. Mock community sequence data (n = 41) generated using the Ion16S™ Metagenomics Kit and Ion Torrent Sequencing Platform were analyzed using two workflows. Amplicons from V2, V3, V4, V6-7, V8 and V9 were deconvoluted using a specialized plugin based on CutPrimers. A separate workflow using Cutadapt is also presented. Three reference databases (Ribosomal Database Project, Greengenes and Silva) were used for taxonomic assignment. Bray-Curtis, Euclidean and Jensen-Shannon distance measures were used to evaluate overall annotation consistency, and specific taxon agreement was determined by calculating the ratio of observed to expected relative abundance. Reads that mapped to regions V2-V9 varied for both CutPrimers and Cutadapt-based methods. Within the CutPrimers-based pipeline, V3 amplicons had the best agreement with the expected distribution, tested using global distance measures, while V9 amplicons had the worst agreement. Accurate taxonomic annotation varied by genus-level taxon and V region analyzed. For the first time, we present a microbiome analysis pipeline that employs a specialized plugin to allow microbiome researchers to separate multi-amplicon data from the Ion16S Metagenomics Kit into V-specific reads. We also present an additional analysis workflow, modified for Ion Torrent mixed orientation reads. Overall, the global agreement of amplicons with the expected mock community abundances differed across V regions and reference databases. Benchmarking data should be referenced when planning a microbiome study to consider these biases related to sequencing and data analysis for multi-amplicon sequencing kits.

Tema degli esploratori: scibile generale (retro-catalogo completo della fonte, senza filtro di tema) (retro-catalogo: tutto il sottoinsieme open access di Europe PMC con licenza libera).
Pubblicazione: PloS one, 2023 (prima pubblicazione 2023-01-13).
Identificativi: PMID 36638095 · PMCID PMC9838852 · DOI 10.1371/journal.pone.0280293.
Descrittori MeSH principali: Microbiota.
Pagina: https://europepmc.org/article/MED/36638095 — https://doi.org/10.1371/journal.pone.0280293. Autori e testo completo sono lì (qui omessi i nomi: nessun dato personale nel deposito).
Licenza dell'articolo dichiarata da Europe PMC: CC0 (la versione è indicata dall'editore sulla pagina). Abstract riportato senza modifiche al contenuto, con attribuzione; deposito marcato CC0.
Letto il 2026-10-07T23:14:56.493Z tramite l'API REST ufficiale di Europe PMC (EMBL-EBI), nel rispetto del robots.txt e del crawl-delay.