Development of molecular approaches for the identification and characterization of oral treponeme bacteria
Notice bibliographique
Résumé
Elevated populations of oral treponeme bacteria are associated with periodontal\n\ndiseases. Furthermore, genetic analyses of oral bacterial populations using 16S rRNAbased\n\napproaches have previously shown that deeply-infected periodontal pockets\n\ncontain a large diversity of oral treponeme species (or species level phylotypes).\n\nHowever, the diversity of treponeme populations present within ‘healthy’ dental\n\nplaque has been relatively poorly investigated. In this thesis, I used a 16S rRNA-based\n\nmolecular approach to analyze the diversity of treponeme ‘species’ within human\n\nsubjects with chronic periodontitis, versus periodontally-healthy controls. I found that\n\nsimilar levels of oral treponeme phylotype diversity were present in both subject\n\ngroups, but there were notable significant differences in the composition of treponeme\n\nphylotypes present. Within both groups, oral phylogroup 1 treponemes had the highest\n\nlevels of phylotype diversity; phylogroup 2 treponemes had similar levels of diversity;\n\nwhilst phylogroup 6 treponemes were more abundant and exhibited greater phylotype\n\ndiversity in the healthy group. As has been previously found, T. denticola was\n\nassociated with periodontal disease.\n\nOver the past few decades, numerous T. denticola strains have been isolated from\n\npatients with periodontal diseases. However, their genetic diversity has never been\n\nsystematically analyzed. Here I describe the formulation of a multilocus sequence\n\nanalysis (MLSA) scheme for the characterization of T. denticola isolates. The\n\nsequences of seven conserved genes (flaA, recA, pyrH, ppnK, dnaN, era and radC)\n\nwere determined within 16 diverse reference strains and clinical isolates of T.\n\ndenticola from China, Japan, Canada, the Netherlands and the USA. Results showed\n\nthat all 16 T. denticola strains were monophyletic, and formed at least 5 well-defined\n\nclades, with OTK, ATCC 700768 and ATCC 700771 being the most diverse strains.\n\nNo geographical relationships could be established, but several strains isolated from\n\ndifferent continents appear to be very closely related. Whilst the use of the\n\nconcatenated seven-gene sequence dataset (6,769nt) had the highest straindiscriminatory\n\npower, the concatenated sequence of the recA, pyrH and flaA genes\n\n(3,150 nt) also had excellent strain-discriminatory abilities.\n\nThe recently-discovered oral phylogroup II treponeme, T. putidum shares many\n\nbiological similarities with T. denticola. Here, I used a small-scale MLSA-type\n\napproach based on the recA and pyrH genes to systematically characterize five T.\n\nputidum isolates. Results revealed that these T. putidum strains clustered together with\n\nT. denticola ATCC 700768, and were well-separated from other T. denticola strains. T.\n\nputidum cell morphology was investigated using electron microscopy and fluorescence\n\nin situ hybridization (FISH) techniques. In addition, oral phylogroup II treponeme\n\npopulations present in a clinical sample of subgingival plaque were analyzed by\n\nsurveying the diversity of pyrH genotypes present. A diverse population of T.\n\ndenticola strains was revealed.\n\nIn conclusion, the MLSA approach developed in this study was shown to be a very\n\nuseful tool for the identification and characterization of oral treponeme isolates\n\nbelonging to phylogroup II (e.g. T. denticola, T. putidum). In future studies, this\n\npowerful molecular approach may be further developed for the analysis of other oral\n\ntreponeme phylogroups, or for the analysis of spirochete populations within related\n\nanimal infections.
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 | 0,002 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,001 |
| Méta-épidémiologie (sens large) | 0,001 | 0,001 |
| Bibliométrie | 0,002 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,001 |
| Communication savante | 0,001 | 0,001 |
| Science ouverte | 0,001 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,002 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 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 ».