ArticlemSystems2020
Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines.
Article in mSystems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
36 citing papers in PubMed, 62 citations in OpenAlex.
- Evaluating Sequencing Strategies for Endometrial Microbiome Profiling in Endometrial Cancer: A Comparative Study of Short- and Long-Read 16S rRNA Approaches.Cancer reports (Hoboken, N.J.) · 2026Article
- Standardized and batch effect-independent technologies enable global collaboration in microbiome research.The ISME journal · 2026Article
- Methodological bias shapes the interpretation of the urinary microbiome in low-biomass systems.Frontiers in microbiology · 2026Review
- Decoding the Tumor-Associated Microbiota: From Origins to Nanomedicine Applications in Cancer Therapy.Biology · 2025Review
- De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation.Microbiome · 2025Article
- Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.Phenomics (Cham, Switzerland) · 2025Article
- Key features and guidelines for the application of microbial alpha diversity metrics.Scientific reports · 2025Article
- The gut-kidney axis in urolithiasis: roles of gut microbiota, metabolites, and therapeutic implications.Frontiers in microbiology · 2025Review
- Position statement of the Microbiota International Clinical Society.Frontiers in microbiomes · 2025Article
- Cross-comparison of gut metagenomic profiling strategies.Communications biology · 2024Article
- Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome.Clinical and experimental dental research · 2024Article
- Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem.Scientific reports · 2024Article
- Article
- Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses.Scientific reports · 2024Article
- Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data.BMC biology · 2023Article
- Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.BMC genomics · 2023Article
- Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem.Scientific reports · 2023Article
- Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples.Future science OA · 2023Article
- Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions.Journal of microbiological methods · 2022Article
- Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast.BMC microbiology · 2022Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
When studying the microbiome using next-generation sequencing, the DNA extraction method, sequencing procedures, and bioinformatic processing are crucial to obtain reliable data. Method choice has been demonstrated to strongly affect the final biological interpretation. We assessed the performance of three DNA extraction methods and two bioinformatic pipelines for bacterial microbiota profiling through 16S rRNA gene amplicon sequencing, using positive and negative controls for DNA extraction and sequencing and eight different types of high- or low-biomass samples. Performance was evaluated based on quality control passing, DNA yield, richness, diversity, and compositional profiles. All DNA extraction methods retrieved the theoretical relative bacterial abundance with a maximum 3-fold change, although differences were seen between methods, and library preparation and sequencing induced little variation. Bioinformatic pipelines showed different results for observed richness, but diversity and compositional profiles were comparable. DNA extraction methods were successful for feces and oral swabs, and variation induced by DNA extraction methods was lower than intersubject (biological) variation. For low-biomass samples, a mixture of genera present in negative controls and sample-specific genera, possibly representing biological signal, were observed. We conclude that the tested bioinformatic pipelines perform equally, with pipeline-specific advantages and disadvantages. Two out of three extraction methods performed equally well, while one method was less accurate regarding retrieval of compositional profiles. Lastly, we again demonstrate the importance of including negative controls when analyzing low-bacterial-biomass samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.