ArticleiScience2021
Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples.
Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.Cell reports · 2026Article
- Ageing processes in the bonobo gut microbiome mirror human patterns.NPJ biofilms and microbiomes · 2026Article
- Considerations for the design of impactful citizen-science projects in microbiome research.Nature protocols · 2026Review
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 2026Article
- Practical lessons from microbiome citizen-science projects.Nature microbiology · 2026Article
- Article
- 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
- Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.BMC microbiology · 2026Article
- Improved characterisation of coral-associated fungal communities using host DNA depletion and a novel ITS primer.ISME communications · 2026Article
- Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.ISME communications · 2026Article
- Article
- Article
- Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.Microbiome · 2025Article
- Freezing of Vaginal Swabs Prior to DNA Purification Does Not Statistically Significantly Affect Microbiome Composition.MicrobiologyOpen · 2025Article
- Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.Cell reports · 2025Article
- Shallow metagenomic shotgun sequencing improves detection of pathogenic species in cystic fibrosis respiratory samples.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2025Article
- A comprehensive atlas of the bonobo gut bacteriome and its associated host and exposome factors.Cell reports · 2025Article
- Toward standardized methods in canine vaginal microbiome research: evaluation of storage, host DNA depletion, and database selection.Microbiology spectrum · 2025Article
- Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.NPJ biofilms and microbiomes · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Few validated protocols are available for large-scale collection, storage, and analysis of microbiome samples from the vagina, skin, and mouth. To prepare for a large-scale study on the female microbiome by remote self-sampling, we investigated the impact of sample collection, storage, and host DNA depletion on microbiome profiling. Vaginal, skin, and saliva samples were analyzed using 16S rRNA gene amplicon and metagenomic shotgun sequencing, and qPCR. Of the two tested storage buffers, the eNAT buffer could keep the microbial composition stable during various conditions. All three tested host DNA-depletion approaches showed a bias against Gram-negative taxa. However, using the HostZERO Microbial DNA and QIAamp DNA Microbiome kits, samples still clustered according to body site and not by depletion approach. Therefore, our study showed the effectiveness of these methods in depleting host DNA. Yet, a suitable approach is recommended for each habitat studied based on microbial composition.
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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.