ArticlePloS one2023
Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach.
Article in PloS one, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Gut Dysbiosis in Selected Gynecological Diseases Associated with Female Infertility: A Scoping Review.Journal of clinical medicine · 2026Review
- Article
- Distinct gut and oral microbiome patterns associated with dyslexia in a family-based cohort: A preliminary exploratory study.PloS one · 2026Article
- Evaluation of long-read 16S rRNA next-generation sequencing for identification of bacterial isolates in a clinical diagnostic laboratory.Journal of clinical microbiology · 2025Article
- Antimony resistant bacteria isolated from Budúcnosť adit (Pezinok-Kolársky vrch deposit) in western Slovakia.Heliyon · 2024Article
- Assessing the Risk of SpreadingAnimals : an open access journal from MDPI · 2024Article
- Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.International journal of molecular sciences · 2024Article
- 3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation.Scientific reports · 2024Article
- Multiple Sclerosis andBiomedicines · 2024Article
- Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.Microorganisms · 2024Review
- The gut microbiome modulates associations between adherence to a Mediterranean-style diet, abdominal adiposity, and C-reactive protein in population-level analysis.The American journal of clinical nutrition · 2024Article
- Comparative analysis of gut microbiota in children with obstructive sleep apnea: assessing the efficacy of 16S rRNA gene sequencing in metabolic function prediction based on weight status.Frontiers in endocrinology · 2024Observational
- Article
- Screening of heat-killed lactic acid bacteria based on inhibitory activity against oral bacteria and effects of oral administration of heat-killedJournal of oral microbiology · 2023Article
- Differences in the composition of the bacterial element of the urinary tract microbiome in patients undergoing dialysis and patients after kidney transplantation.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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