A Literature Review of Metagenomics and Culturomics of the Peri-implant Microbiome: Current Evidence and Future Perspectives
Notice bibliographique
Résumé
Background and objectives: In recent years, many different culture-independent molecular techniques have been developed with the aim of investigating the not yet cultivated part of the resident flora of the oral cavity and of analyzing the peri-implant and periodontal flora both in healthy and diseased sites. The most used technologies are Roche 454 pyrosequencing, Illumina HiSeq/MiSeq, ABI SOLiD and Ion Torrent. Due to these methods, two different approaches are available: Metagenomics and the 16S gene analysis. A complementary strategy was also recently developed: Culturomics. Culturomics consists of different culture conditions that allow a very rapid bacterial identification. The focused question of this review was developed in PICO format in order to investigate the role of metagenomics, 16S gene analysis and culturomics (interventions) in the differential study (comparison) of the peri-implant and periodontal microbiome (outcome) in humans (participants). The secondary aim was the characterization of currents limits and future applications of the three techniques. Methods: The authors performed a literature search on three databases (Web of Science, Scopus and PubMed) from 01/01/2003 to 31/06/2019. Date of last search was: 25/08/19. Any type of article dealing with the analysis of periodontal and peri-implant flora with metagenomic, culturomic or 16S gene analysis was included. No language restrictions were applied. Risk of bias for RCT was assessed using the Cochrane collaboration’s tool whereas case-control and cohort studies were evaluated through the Newcastle–Ottawa scale. Results: The initial search resulted in 330 titles in total. After careful evaluation of all results no studies were found to satisfy the primary outcome of the present review. Hence a narrative review dealing with the secondary aim was performed. Conclusions: Metagenomic and 16S gene analysis approaches contributed in clarifying some crucial aspects of the oral microbiome. Based on the reported evidence some bacteria could be found around teeth and implants even in the absence of signs of inflammation and other species are more frequently found in supragingival peri-implant biofilm. Teeth and implants (even if adjacent) seem not to share the same microbiome and healthy teeth have a more diversified one. The same analyses also highlighted that the oral biofilm of smokers is composed by more periodontopathogen bacteria compared to non-smokers and that geographical location and ethnicity seem to play a role in bacterial composition. Culturomics, which has not yet been applied to the study of oral microbiota, consists of the use of different culture conditions and of the identification by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI–TOF MS) with the aim of increasing the bacterial repertoire and avoiding the limits of molecular methods. In order to better evaluate perspectives and limits of the all presented approaches further studies comparing the different molecular techniques are encouraged. This review received no funding.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,005 | 0,017 |
| Méta-épidémiologie (sens strict) | 0,002 | 0,001 |
| Méta-épidémiologie (sens large) | 0,005 | 0,003 |
| Bibliométrie | 0,022 | 0,025 |
| Études des sciences et des technologies | 0,001 | 0,001 |
| Communication savante | 0,003 | 0,004 |
| Science ouverte | 0,002 | 0,002 |
| Intégrité de la recherche | 0,002 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,006 | 0,001 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».