ArticleCommunications biology2024
Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.
Article in Communications biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Microbiome Profiling Reveals Prognostic Heterogeneity inmedRxiv : the preprint server for health sciences · 2026Article
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-age children.The Journal of allergy and clinical immunology · 2026Article
- Spatially resolved fetal and maternal cell contributions to severe preeclampsia across gestation.Science advances · 2026Article
- Empowering One Health with metagenomics.One health outlook · 2026Review
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 2026Article
- Gut virome-microbiome interactions across hosts and environments.NPJ biofilms and microbiomes · 2026Article
- TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- Review
- Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.Veterinary research communications · 2026Article
- Respiratory viral infection is associated with increasedERJ open research · 2026Article
- Clinical and Immunological Perspectives on the Nasal Microbiome's Role in Olfactory Function and Dysfunction.Microorganisms · 2026Review
- Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.Critical care (London, England) · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- Improved characterisation of coral-associated fungal communities using host DNA depletion and a novel ITS primer.ISME communications · 2026Article
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- The Human Respiratory Virome in Health and Disease: Interactions, Dysbiosis, and Methodological Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications.CHEST pulmonary · 2025Article
- Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.Environmental microbiome · 2025Article
- A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.Microbiology spectrum · 2025Article
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Abstract
Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.
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