ArticleMicrobiome2018
Improving saliva shotgun metagenomics by chemical host DNA depletion.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers, 1 of them a synthesis that pooled it.
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Who cites it
217 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Clinical values of metagenomic next-generation sequencing in patients with severe pneumonia: a systematic review and meta-analysis.Frontiers in cellular and infection microbiology · 2023Pooled it
- Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial.Frontiers in cellular and infection microbiology · 2021Trial
- Review
- Functional Metagenomics Reveals Gut Microbial Biosynthetic Potential for Essential Nutrients in Juvenile Chum Salmon.Environmental microbiology · 2026Article
- The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.Molecular and cellular pediatrics · 2026Review
- Exploring the Oral Resistome: From Metagenomics to Precision Oral Health.Microorganisms · 2026Review
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Pre-sampling conditions affect salivary genomic DNA yield and human DNA fraction: a single-donor pilot study.Genomics & informatics · 2026Article
- Nucleosome-targeted host DNA depletion enables automated plasma metagenomic sequencing for sensitive detection of bloodstream pathogens.Journal of translational medicine · 2026Article
- Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.Microbiology spectrum · 2026Article
- Rapid and modular workflows for same-day sequencing-based detection of bloodstream infections and antimicrobial resistance determinants using culture-enriched samples.Microbiology spectrum · 2026Article
- Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.Current opinion in ophthalmology · 2026Review
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 2026Article
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
- Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.mSystems · 2026Article
- Targeting intratumoral Streptococcus mitis suppresses the progression of esophageal squamous cell carcinoma.Science China. Life sciences · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- A discriminative primer design workflow enables selective metabarcoding, demonstrated using long-read sequencing of endophytic fungi.FEMS microbiology ecology · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
157 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundShotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits.
resultsThree commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples.
conclusionOsmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.
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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.