ArticleMicrobiome2021
Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
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- Clinical application of metagenomic next-generation sequencing (mNGS) in children with suspected bloodstream infection.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Clinical characteristics and prognostic factors in non-HIV patients withFrontiers in public health · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Baricitinib Augments Lonafarnib Therapy to Preserve Colonic Homeostasis and Microbial Balance in a Mouse Model of Progeria.Aging cell · 2025Article
- Clinical application and impact of metagenomic next-generation sequencing for the diagnosis of infectious diseases in severely immunocompromised pediatric patients.BMC pediatrics · 2025Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Differences in Non-Pathogenic Lung-Colonizing Bacteria Among Patients with Different Types of Pneumonia: A Retrospective Study.Microorganisms · 2025Article
- Airway microbiota and immunity associated with chronic obstructive pulmonary disease severity.Journal of translational medicine · 2025Article
- Comparative diagnostic performance of metagenomic and two targeted sequencing methods in lower respiratory infection.Scientific reports · 2025Article
- Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.NPJ biofilms and microbiomes · 2025Article
- Primary and Re-exposure effects of D-enantiomeric peptide on metabolism, diversity, and composition of oral biofilms at different stages of recovery.Bioactive materials · 2025Article
- Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.Scientific reports · 2025Article
- Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study.Clinical and translational medicine · 2025Article
- Comparison of microbial culture, metagenomic next-generation sequencing and droplet digital polymerase chain reaction methods for pathogen detection in patients with neurosurgical central nervous system infection.Frontiers in cellular and infection microbiology · 2025Article
- Biliary microbiota in disease-free, obstructive and post-drainage biliary tracts.Frontiers in cellular and infection microbiology · 2025Article
- Metagenomic next-generation sequencing and galactomannan testing for the diagnosis of invasive pulmonary aspergillosis.Scientific reports · 2024Article
- Advances in preparation of acellular human dermis for tissue banking and transplantation.Cell and tissue banking · 2024Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities.
resultsWe investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 10
conclusionsThe BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.
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