Evidence map›Paper›PMID 25171331›Full record

ArticleThe ISME journal2015

Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease.

Akiko Endo, Takayasu Watanabe, Nachiko Ogata, Takashi Nozawa, Chihiro Aikawa, Shinichi Arakawa, Fumito Maruyama, Yuichi Izumi, Ichiro Nakagawa

Abstract readComparative Study
In one paragraph

Article in The ISME journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

22 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Trial
  3. Article
  4. Review
  5. Review
  6. CRISPRJournal of oral microbiology · 2025
    Article
  7. Article
  8. Review
  9. Article
  10. Phylogenomic analysis of theFrontiers in microbiology · 2023
    Article
  11. Contribution of -Omics Technologies in the Study ofInternational journal of molecular sciences · 2022
    Review
  12. Review
  13. Article
  14. Article
  15. Article
  16. Journal of oral microbiology · 2019
    Review
  17. Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Akiko EndoDepartment of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Takayasu WatanabeSection of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Nachiko OgataSection of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Takashi Nozawa1] Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan [2] Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Chihiro Aikawa1] Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan [2] Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Shinichi ArakawaDepartment of Lifetime Oral Health Care Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Fumito Maruyama1] Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan [2] Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan [3] Section of Microbial Genomics and Ecology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Yuichi IzumiDepartment of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
Ichiro Nakagawa1] Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan [2] Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. Periodontitis represents a polymicrobial disease; Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia, called 'the red complex', have been recognized as the causative agents of periodontitis. Although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are unknown. In this study, we uncovered novel interactions in comparative genome analysis among the red complex species. Clustered regularly interspaced short palindromic repeats (CRISPRs) of T. forsythia might attack the restriction modification system of P. gingivalis, and possibly work as a defense system against DNA invasion from P. gingivalis. On the other hand, gene deficiencies were mutually compensated in metabolic pathways when the genes of all the three species were taken into account, suggesting that there are cooperative relationships among the three species. This notion was supported by the observation that each of the three species had its own virulence factors, which might facilitate persistence and manifestations of virulence of the three species. Here, we propose new mechanisms of bacterial symbiosis in periodontitis; these mechanisms consist of competitive and cooperative interactions. Our results might shed light on the pathogenesis of periodontitis and of other polymicrobial diseases.

Indexed as

Genome, BacterialBacteroidetesHumansPeriodontitisPhylogenyPorphyromonas gingivalisSymbiosisTreponema denticola

Identifiers

PMID25171331
PMCPMC4331577

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.