ArticleGenomics, proteomics & bioinformatics2022
Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies.
Article in Genomics, proteomics & bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 18 citations in OpenAlex.
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- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- The impact of DNA extraction methods on species quantification and apparent community composition of in vitro oral biofilms.FEMS microbiology letters · 2026Article
- Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.Nutrients · 2025Article
- Rapid Nanopore Sequencing of Positive Blood Cultures Using Automated Benzyl-Alcohol Extraction Improves Time-Critical Sepsis Management.Antibiotics (Basel, Switzerland) · 2025Article
- Assessment of the biofilm formation capacities of Staphylococcus aureus strains Newman and Newman D2C in vitro and in vivo.Scientific reports · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- The differential gut microbiota and their MetaCyc pathways in IBRV infected Angus calves.Frontiers in microbiology · 2025Article
- Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes.Nature communications · 2024Article
- Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.Nature communications · 2024Article
- Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics.Nucleic acids research · 2024Article
- Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept.One health outlook · 2024Article
- 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
- Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions.Foods (Basel, Switzerland) · 2023Review
- The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis.Nutrients · 2023Article
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Authors and funding
19 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.
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