ArticleFrontiers in microbiology2020
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline.
Article in Frontiers in microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 182 papers, 3 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
182 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Fire Limits Soil Microbial Dispersal and Differentially Impacts Bacterial and Fungal Communities.Global change biology · 2025Pooled it
- Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis.Scientific reports · 2021Pooled it
- Identification of microbial markers across populations in early detection of colorectal cancer.Nature communications · 2021Pooled it
- Effect of Short-Term Grape Powder Supplementation in Patients with Crohn's Disease: A Pilot Study.Nutrients · 2026Trial
- Gut microbial dynamics and antibiotic resistance during rifaximin therapy in severe cirrhosis: a ProPILA-Rifax ancillary study.Frontiers in cellular and infection microbiology · 2026Trial
- Effects of Early Emollient Use in Children at High Risk of Atopic Dermatitis: A German Pilot Study.Acta dermato-venereologica · 2023Trial
- Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV.Frontiers in immunology · 2022Trial
- Early antibiotic exposure and vaccine immune responses in preterm infants: potential sex-specific differences.Gut microbes · 2026Observational
- DNA-based monitoring uncovers contrasting salinity-driven diversity patterns of bacterial and protist plankton in the Baltic Sea area.Communications biology · 2026Article
- Photohydrogenotrophic Cultivation of Purple Non-Sulfur Bacteria in an Open Bioreactor: Enhanced Selectivity Through Light Cycling and Ammonium Limitation.Biotechnology and bioengineering · 2026Article
- Article
- Changes in bacterial and metabolic profiles in breastfed infants during dietary transition to solids.Pediatric research · 2026Article
- Can the leafhopper microbiome unlock new strategies for its control?Journal of economic entomology · 2026Review
- Short-Term Stability of the Fecal Microbiota in WildMicroorganisms · 2026Article
- Versatile microbial community responsible for nitrate turnover in a carbonate aquifer in southwest Germany.FEMS microbiology ecology · 2026Article
- Environmental Gradients Shape the Distribution of Free-Living and Host-Associated Syndiniales Life Stages.Microbial ecology · 2026Article
- Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.BMC microbiology · 2026Article
- Experiences from national biodiversity data infrastructures in Europe: advancing data integration and community engagement.Bioscience · 2026Article
- Not All Microbiomes Reflect Chronic Pain: Evidence from the Urinary Tract in a Case-Control Study.Journal of clinical medicine · 2026Article
- Multi-Year Biofilm Formation on Granitic Surfaces Reveals Dynamic Microbial Communities in Fennoscandian Shield Deep Groundwaters.Microbial ecology · 2026Article
122 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the
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