ArticleNature microbiology2016
Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.
Article in Nature microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
64 citing papers in PubMed, 104 citations in OpenAlex.
- Probiotics Partly Suppress the Impact of Sugar Stress on the Oral Microbiota-A Randomized, Double-Blinded, Placebo-Controlled Trial.Nutrients · 2023Trial
- Effects of Probiotics and Vitamin D Deficiency Correction on Clinical, Inflammatory, Metabolic, and Microbiota Profiles in Older Adults with Oral Lichen Planus: A Multi-Omics Study.International journal of molecular sciences · 2026Article
- Put your money where your mouth is: surveillance of antibiotic resistance within the commensalMicrobiology spectrum · 2026Article
- Put your money where your mouth is: Surveillance of antibiotic resistance within the commensalbioRxiv : the preprint server for biology · 2026Article
- Comparative machine learning analysis of saliva and plaque microbiomes in Kuwaitis with type 1 diabetes.Frontiers in microbiology · 2026Article
- Peritoneal dialysis peritonitis due toRenal failure · 2025Review
- Development of the Breastfed Infant Oral Microbiome Is Associated with Concentrations and Intakes of Human Milk Oligosaccharides.Nutrients · 2025Article
- Metabolic strategies that enable oral commensal persistence in a lower airway environment.mBio · 2025Article
- CommensalAnnual review of microbiology · 2025Review
- Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients.BMC microbiology · 2025Article
- An in vitro model demonstrating homeostatic interactions between reconstructed human gingiva and a saliva-derived multispecies biofilm.Microbiome · 2025Article
- The metagenome and metabolome signatures of dental biofilms associated with severe dental fluorosis.Journal of oral microbiology · 2025Article
- Article
- Commensal Neisseria Inhibit Porphyromonas Gingivalis Invasion of Gingival Epithelial Cells.Oral health & preventive dentistry · 2024Article
- The Impact of Prevotella on Neurobiology in Aging: Deciphering Dendritic Cell Activity and Inflammatory Dynamics.Molecular neurobiology · 2024Review
- Upper respiratory microbial communities of healthy populations are shaped by niche and age.Microbiome · 2024Article
- Unveiling the immune dynamics ofInfection and immunity · 2024Article
- Peptidoglycan fragment release and NOD activation by commensalInfection and immunity · 2024Article
- Upper respiratory microbial communities of healthy populations are shaped by niche and age.bioRxiv : the preprint server for biology · 2024Article
- Rolling the evolutionary dice:Microbiology spectrum · 2024Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
Abstract
Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes. We applied these tools to 520 oral metagenomes from the Human Microbiome Project, finding evidence of site tropism and temporal intra-subject strain retention. Although the opportunistic pathogen Neisseria meningitidis is enriched for colonization in the throat, N. flavescens and N. subflava populate the tongue dorsum, and N. sicca, N. mucosa and N. elongata the gingival plaque. The buccal mucosa appeared as an intermediate ecological niche between the plaque and the tongue. The resulting approaches to metagenomic strain profiling are generalizable and can be extended to other organisms and microbiomes across environments.
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What OpenQuestion holds
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.