ArticlePloS one2014
The prevalence of species and strains in the human microbiome: a resource for experimental efforts.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 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
80 citing papers in PubMed.
- Chemical suppression of a bacterial immune system revives repressed phages.bioRxiv : the preprint server for biology · 2026Article
- Microbiota-derived D-amino acids in intestinal homeostasis and inflammatory bowel disease.Inflammation and regeneration · 2026Review
- Cell surface polysaccharides in the gut microbiota: occurrence, structure and role.Gut microbes · 2025Review
- Polypeptides synthesized by common bacteria in the human gut improve rodent metabolism.Nature microbiology · 2025Article
- Impact of Diquat on the Intestinal Health and the Composition and Function of the Gut Microbiome.Antioxidants (Basel, Switzerland) · 2025Review
- Where Do Milk Microbes Originate? Traceability of Microbial Community Structure in Raw Milk.Foods (Basel, Switzerland) · 2025Article
- Ruminococcus gnavus in the gut: driver, contributor, or innocent bystander in steatotic liver disease?The FEBS journal · 2025Review
- Distribution of Bacillota in Water and Sediments from Aquatic Environments.Microbial ecology · 2025Article
- Health Effects and Therapeutic Potential of the Gut MicrobeNutrients · 2025Review
- Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.Nature communications · 2025Article
- Correlation Analyses of the Consumption of Artificial Sweeteners During Pregnancy and the Incidence of Gestational Diabetes Mellitus.Diabetes, metabolic syndrome and obesity : targets and therapy · 2025Article
- Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology.Cell host & microbe · 2024Article
- Article
- Improved mouse models of the small intestine microbiota using region-specific sampling from humans.bioRxiv : the preprint server for biology · 2024Article
- Hemophore-like proteins of the HmuY family in the oral and gut microbiome: unraveling the mystery of their evolution.Microbiology and molecular biology reviews : MMBR · 2024Review
- Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota.Cell host & microbe · 2024Article
- An Update on the Role and Potential Molecules in Relation toDiabetes, metabolic syndrome and obesity : targets and therapy · 2024Review
- Article
- Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilizedmSystems · 2023Article
- Identification of donor Bacteroides vulgatus genes encoding proteins that correlate with early colonization following fecal transplant of patients with recurrent Clostridium difficile.Scientific reports · 2023Article
20 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
5 authors.
Funding
Abstract
Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. Here, we report an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.
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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.