Bacterial Diversity of Deep Carious Lesions Analysed by Next-Generation Sequencing Approaches Associated With Different Pulp Diagnoses: A Systematic Review.

AIM: This systematic review aimed to synthesise evidence on the microbiome of deep or extremely deep caries associated with a range of different pulp conditions, by analysing studies using next-generation sequencing (NGS) approaches.

METHODOLOGY: The review reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines and protocol was registered prospectively at the Open Science Framework (https://osf.io/vnwjh/). A literature search was carried out in the following databases: MEDLINE via PubMed, Scopus, Cochrane Database for Systematic Reviews (CDSR), Web of Science, the clinicaltrials.gov, and the Open Science Framework, in English language without time restriction. The last search was performed on May 1st 2025. An additional online search of the four major journals in the field of endodontics (International Endodontic Journal, Journal of Endodontics, Australian Endodontic Journal and the European Endodontic Journal) was also carried out independently starting from January 1st, 2010 to May 1st 2025. Only original research articles that used an NGS approach and investigated the microbiome of deep or extremely deep caries associated with different pulp diagnoses, assessed preoperatively, were included. The Johanna Brigg's Institute (JBI's) Critical Appraisal Instrument for Studies Reporting Prevalence Data was used to assess the risk of bias of included studies.

RESULTS: Among 1914 articles initially identified, four were considered eligible for inclusion and further assessed for certain parameters. The overall risk of bias of the three and one included studies was characterised as 'unclear' and 'high'. Firmicutes were the most prevalent phylum in all cases. In cases of irreversible pulpitis, Firmicutes prevalence increased compared with cases of normal pulp and reversible pulpitis, while the prevalence of Actinobacteria, Proteobacteria and Bacteroidetes decreased. Lactobacillus was the most abundant genus in all cases, with its abundance in cases of symptomatic irreversible pulpitis increasing substantially.

CONCLUSIONS: The NGS studies evaluated in this review create a preliminary, but comprehensive map of the microbiome of deep caries associated with a range of pulpal diagnoses. Α shift in microbiome as the asymptomatic cases become progressively symptomatic seems to occur, which may be relevant to management of deep caries in terms of complete or selective caries removal.