ArticleGenome biology2020
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers, 1 of them a synthesis that pooled it.
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Who cites it
168 citing papers in PubMed, 1 synthesis or guideline pooled it, 249 citations in OpenAlex.
- Exploring Oral Microbiome in Healthy Infants and Children: A Systematic Review.International journal of environmental research and public health · 2022Pooled it
- Steroid hormones produced by coral-associated Endozoicomonas influence coral immune response during thermal stress.Nature microbiology · 2026Article
- Emerging food- and waterborne pathogenMicrobiology spectrum · 2026Article
- Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.Microbiology spectrum · 2026Article
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- Comparative genomics approaches to identify genomic regions associated with the antimicrobial activity ofMicrobial genomics · 2026Article
- Associations between the oral microbiome, age, and cumulative dental caries experience: a cross-sectional study.Clinical oral investigations · 2026Article
- Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery.Microbiome · 2026Article
- Pangenomes of the human oral microbiome.Microbiology resource announcements · 2026Article
- Genomic and phenotypic insights into the novel speciesMicrobiology spectrum · 2026Article
- Phylogenetically diverse MucoralesMicrobial genomics · 2026Article
- Dental Calculus Formation Is Linked to Diet and Phylogeny in Mammals.Ecology and evolution · 2026Article
- Site-specialization of human oralbioRxiv : the preprint server for biology · 2026Article
- Ancient Species Diversity and Niche Adaptation in Tannerella and Porphyromonas Revealed Through Pangenomics.Genome biology and evolution · 2026Article
- Molecular identification ofOpen veterinary journal · 2026Article
- From genome to lifestyle: adaptive strategies ofApplied and environmental microbiology · 2026Article
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- The genomic history of Streptococcus mutans from the Mesolithic until modern times.Genome biology · 2026Article
- Kun-peng enables scalable and accurate pan-domain metagenomic classification.Briefings in bioinformatics · 2026Article
- Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.bioRxiv : the preprint server for biology · 2026Article
108 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
16 authors at 8 institutions in 2 countries.
Funding
Abstract
introductionMicrobial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life.
resultsHere, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.
conclusionsOur data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.
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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.