ArticlePLoS genetics2009
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 1 of them a synthesis that pooled it.
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
91 citing papers in PubMed, 1 synthesis or guideline pooled it, 177 citations in OpenAlex.
- A gut microbial signature for combination immune checkpoint blockade across cancer types.Nature medicine · 2024Pooled it
- Bifidobacteria: biogeography, host adaptation and ecological functions.Nature reviews. Microbiology · 2026Review
- The oral cavity of chronically homeless adults is home for unusual extremophile environmental bacteria.iScience · 2026Article
- Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study.Frontiers in microbiology · 2026Article
- Gut oralisation signatures in Parkinson's disease: an integrative multi-study analysis.Journal of oral microbiology · 2026Article
- Insights into toxin-antitoxin systems in the genusApplied and environmental microbiology · 2025Review
- Probing the adhesion potential of Bifidobacterium animalis subsp. lactis MCM-B-2007 via in vitro and in silico analyses.Archives of microbiology · 2025Article
- Metabolic insights of lactic acid bacteria in reducing off-flavors and antinutrients in plant-based fermented dairy alternatives.Comprehensive reviews in food science and food safety · 2025Review
- Gene-trait matching amongFrontiers in microbiology · 2025Article
- The Oral Microbial Ecosystem in Age-Related Xerostomia: A Critical Review.International journal of molecular sciences · 2024Review
- Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.Nature communications · 2024Article
- Diversity Analysis of Intestinal Bifidobacteria in the Hohhot Population.Microorganisms · 2024Article
- Influence of gender, age, and body mass index on the gut microbiota of individuals from South China.Frontiers in cellular and infection microbiology · 2024Article
- Evaluation of Human Dental Plaque Lactic Acid Bacilli for Probiotic Potential and Functional Analysis in Relevance to Oral Health.Indian journal of microbiology · 2023Article
- Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans.Foods (Basel, Switzerland) · 2023Article
- Identification of conserved genomic signatures specific to3 Biotech · 2023Article
- Cryptic Oral Microbiota: What Is Its Role as Obstructive Sleep Apnea-Related Periodontal Pathogens?International journal of environmental research and public health · 2023Article
- Identification and structural basis of an enzyme that degrades oligosaccharides in caramel.Biophysics and physicobiology · 2023Article
- Study of the binding of ΔFN3.1 fragments of theMicrobiome research reports · 2023Article
- Stress Response in Bifidobacteria.Microbiology and molecular biology reviews : MMBR · 2022Review
31 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
23 authors at 8 institutions in 7 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bifidobacteria, one of the relatively dominant components of the human intestinal microbiota, are considered one of the key groups of beneficial intestinal bacteria (probiotic bacteria). However, in addition to health-promoting taxa, the genus Bifidobacterium also includes Bifidobacterium dentium, an opportunistic cariogenic pathogen. The genetic basis for the ability of B. dentium to survive in the oral cavity and contribute to caries development is not understood. The genome of B. dentium Bd1, a strain isolated from dental caries, was sequenced to completion to uncover a single circular 2,636,368 base pair chromosome with 2,143 predicted open reading frames. Annotation of the genome sequence revealed multiple ways in which B. dentium has adapted to the oral environment through specialized nutrient acquisition, defences against antimicrobials, and gene products that increase fitness and competitiveness within the oral niche. B. dentium Bd1 was shown to metabolize a wide variety of carbohydrates, consistent with genome-based predictions, while colonization and persistence factors implicated in tissue adhesion, acid tolerance, and the metabolism of human saliva-derived compounds were also identified. Global transcriptome analysis demonstrated that many of the genes encoding these predicted traits are highly expressed under relevant physiological conditions. This is the first report to identify, through various genomic approaches, specific genetic adaptations of a Bifidobacterium taxon, Bifidobacterium dentium Bd1, to a lifestyle as a cariogenic microorganism in the oral cavity. In silico analysis and comparative genomic hybridization experiments clearly reveal a high level of genome conservation among various B. dentium strains. The data indicate that the genome of this opportunistic cariogen has evolved through a very limited number of horizontal gene acquisition events, highlighting the narrow boundaries that separate commensals from opportunistic pathogens.
Indexed as
Identifiers
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.