ArticleNPJ biofilms and microbiomes2021
Assessing saliva microbiome collection and processing methods.
Article in NPJ biofilms and microbiomes, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 25 citations in OpenAlex.
- Evaluation of Salivary Biomarkers of Periodontal Disease Based on Smoking Status: A Systematic Review.International journal of environmental research and public health · 2022Pooled it
- Multi-omics profiling of oral microbial functional signatures and systemic immune-metabolic features in perinatal depression.Brain, behavior, & immunity - health · 2026Article
- Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.Molecular ecology resources · 2025Article
- Recent advancements in artificial intelligence-powered cancer prediction from oral microbiome.Periodontology 2000 · 2025Review
- Examining the healthy human microbiome concept.Nature reviews. Microbiology · 2025Review
- Functional profiling of the oral microbiome reveals microbial and oncogenic signatures in never-smoking female patients with oral squamous cell carcinoma.Journal of oral microbiology · 2025Article
- Dysbiosis of the Saliva Microbiota in Patients with Psoriasis: A Case-Control Study.Journal of inflammation research · 2025Article
- Alterations in the Salivary Microbiome and Metabolism in Patients With Carotid Atherosclerosis from Rural Northeast China.Journal of the American Heart Association · 2024Article
- Effects of Mint Oils on the Human Oral Microbiome: A Pilot Study.Microorganisms · 2024Article
- Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis.Clinical proteomics · 2024Article
- Microbiomic association between the saliva and salivary stone in patients with sialolithiasis.Scientific reports · 2024Article
- Microbes for lung cancer detection: feasibility and limitations.Frontiers in oncology · 2024Review
- Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics.Frontiers in microbiology · 2024Article
- Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.Biomolecules · 2023Article
- Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults.EBioMedicine · 2023Article
- Factors influencing oral microbiome analysis: from saliva sampling methods to next-generation sequencing platforms.Scientific reports · 2023Article
- Pharmacologic improvement of CFTR function rapidly decreases sputum pathogen density, but lung infections generally persist.The Journal of clinical investigation · 2023Observational
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.
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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.