ArticleScientific data2022
Benchmarking second and third-generation sequencing platforms for microbial metagenomics.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- An Acid-Oxidising Solution Containing Hypochlorous Acid Reduces Staphylococcus aureus and Improves Bacterial Diversity in Epidermolysis Bullosa Wounds.Experimental dermatology · 2025Trial
- DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.Briefings in bioinformatics · 2026Article
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential.World journal of microbiology & biotechnology · 2026Article
- Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.Nature biotechnology · 2026Article
- Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.Nature medicine · 2026Article
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.Nature communications · 2026Article
- Gastrointestinal microbial nitrogen metabolic landscape underlies nitrogen utilization efficiency of goats fed distinct dietary protein sources.Microbiome · 2026Article
- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- Lipid metabolic pathways and the roles of candidate transcription factors identified via lipidomic and transcriptomic analyses at various stages of seed development in Carya illinoinensis.BMC plant biology · 2026Article
- Innovative Single-Cell Sequencing Techniques for B cell Analysis and Their Implications for Rational HIV-1 Vaccine Design.Current HIV research · 2026Review
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Recent Insights on Dental Caries Microbiota in Pediatric Patients with Inborn Errors of Immunity.Advances in experimental medicine and biology · 2026Review
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.BMC oral health · 2025Article
- Key Challenges in Plant Microbiome Research in the Next Decade.Microorganisms · 2025Review
- LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.Nature communications · 2025Article
- HTS and PCR Methods Are the Most Used in the Diagnosis of Aspergillosis: Advantages over Other Molecular Methods.Journal of fungi (Basel, Switzerland) · 2025Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.
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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.