Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis | Alaa Muayad Altaie et al. | ResearchPod

Transcript: Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis

[[RP_SECTION:unculturable-bacterial-diversity|Unculturable bacterial diversity]]

Sam: [steady, grounded, matter-of-fact] Approximately 13% of the microbial diversity within periapical abscesses consists of bacteria that cannot be cultured using standard laboratory techniques. That figure comes from a systematic review in PLOS ONE by Alaa Muayad Altaie.

Alex: [leaning in, curious] That's a meaningful slice. If these organisms aren't showing up on culture plates, does that mean our current diagnostic approach is systematically missing a large part of the pathology?

Sam: [measured, teaching mode] That is the central implication. For decades, endodontic diagnostics have relied on what we can grow in a petri dish, which biases our picture toward the most robust, easily cultured species. By aggregating data from 13 studies, this review reveals that unculturable phylotypes are a consistent presence that standard diagnostics simply fail to detect.

Alex: [thoughtful, processing] So if a patient has a persistent abscess that isn't responding to antibiotics, these unculturable organisms could be part of the reason treatment is failing?

Sam: [precise, nodding in voice] That's the clinical implication the authors are pointing toward. Think of it like a census where 13% of the population are invisible to the official registry—they don't show up on culture plates, but molecular methods like 16S rRNA sequencing confirm they're there. The meta-analysis frames them as likely overlooked pathogens, though that causal link still needs functional evidence. [[RP_SECTION:methodological-limitations-and-bias|Methodological limitations and bias]]

Alex: [deliberate] So the methodology is doing a lot of work here. They're not just counting bacteria—they're using molecular tools to detect organisms that refuse to grow. How did they make sure the pooled estimate was reliable?

Sam: [calm, expansive] They ran a meta-regression to account for moderators like study location and sequencing platform. One finding worth noting is that hybridization techniques showed up as particularly sensitive for capturing low-abundance phylotypes—more so than some high-throughput sequencing approaches. That matters because it means the 13% diversity estimate isn't platform-agnostic. It's partly a function of which molecular toolkit was used. [[RP_SECTION:statistical-stability-and-heterogeneity|Statistical stability and heterogeneity]]

Alex: [analytical, probing] Which raises the heterogeneity question. Thirteen studies across different labs, different methods—how stable is that pooled figure?

Sam: [direct, acknowledging the weight of the point] It's not especially stable, and the authors are transparent about that. I-squared values exceeding 75% tell you the pooled effect sizes are sensitive to which studies you include. They used a random-effects model to handle that, and they checked for publication bias via funnel plots and Egger's regression—and found statistically significant bias. So the 13% figure is better read as a signal of consistent presence than as a precise constant. The load-bearing claim is that unculturable phylotypes appear across studies, not that they appear at exactly this frequency.

Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis

Alaa Muayad Altaie, Basema Saddik, Mohammed Amjed Alsaegh, Sameh S. M. Soliman, Rifat Hamoudi, Lakshman P. Samaranayake

Aug 5, 2021·4:17·user_upload·Original Paper

Unculturable bacteriaPeriapical abscessSystematic review and meta-analysisPrincipal component analysis (PCA)16S rRNA sequencingNext-generation sequencing (NGS)

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4 min

Briefing

Research Question and Approach

Periapical abscesses are common infections of the alveolar bone, typically originating from root canal infections. While traditional culture-based methods have identified common pathogens, next-generation sequencing has revealed that a large portion of the oral microbiome remains unculturable. This study aimed to systematically review and perform a meta-analysis on the prevalence, diversity, and abundance of these unculturable bacteria in periapical abscesses, radicular cysts, and periapical granulomas using culture-independent molecular techniques.

The researchers searched four major databases for cross-sectional studies published between 1990 and 2020. Out of 14,780 records, 13 studies met the criteria for the final quantitative meta-analysis. The authors assessed the risk of bias using the Joanna Briggs Institute checklist and utilized meta-regression to account for moderators such as lesion type, country of origin, and the specific molecular technique employed.

Main Findings

The meta-analysis revealed that approximately 13% of the cumulative bacterial population in periapical abscesses is unculturable. The pooled frequency of these bacteria was estimated at 8%, while their pooled abundance was 5%. The study identified that the country of origin significantly influenced both the diversity and abundance of these unculturable species, suggesting potential geographic variations in the oral microbiome.

Among the 62 identified unculturable bacteria, Peptostreptococcus sp. oral clone CK035 was found to be the most abundant species in periapical abscesses. Furthermore, the researchers found that hybridization-based molecular techniques were generally more reliable than standard sequencing methods for detecting the abundance and frequency of these elusive bacterial taxa.

Why It Matters

Understanding the composition of the unculturable microbiome is crucial for advancing our knowledge of dental infections. Because these bacteria cannot be grown in standard laboratory conditions, they have historically been overlooked in clinical diagnostics. This study highlights that they are not merely incidental bystanders but are likely active contributors to the virulence and progression of periapical disease. These findings underscore the need for more advanced, culture-independent diagnostic strategies to better characterize the full spectrum of pathogens involved in oral infections, which could eventually lead to more effective, targeted therapeutic interventions.

Key Terms and Definitions

Unculturable Bacteria — Bacterial species that cannot be grown or isolated using standard laboratory culture media and techniques.
Periapical Abscess — A localized collection of pus within the alveolar bone at the root apex of a tooth, typically resulting from a pulp infection.
16S rRNA Sequencing — A molecular technique used to identify and classify bacteria based on the highly conserved 16S ribosomal RNA gene.
Hybridization Techniques — Molecular methods, such as DNA-DNA hybridization or T-RFLP, that detect specific bacterial DNA sequences by binding them to complementary probes.
Principal Component Analysis (PCA) — A statistical procedure used to simplify complex datasets by reducing the number of variables while retaining the most important patterns of variation.

Abstract

OBJECTIVE: To assess the prevalence of unculturable bacteria in periapical abscess, radicular cyst, and periapical granuloma. METHODS: PubMed, Scopus, Science Direct, and Ovid databases were systematically searched from January 1990 to May 2020. All the included studies were cross-sectional design. The risk of bias was assessed using Joanna Briggs Institute check-list. Heterogeneity was described using meta-regression and mixed-effects model for lesion, country, and sequence technique moderators. Funnel plot and unweighted Egger's regression test were used to estimate the publication bias. Microbiome data on diversity, abundance, and frequency of unculturable bacteria in the periapical lesions were reviewed, analysed, and the principal component analysis (PCA) was performed. RESULTS: A total of 13 studies out of 14,780, were selected for the final analysis. These studies focused on the prevalence of unculturable bacteria in periapical abscesses and related lesions. Approximately 13% (95% CI: 7-23%) of the cumulative number of bacteria derived from periapical abscesses was unculturable. Country moderator significantly (P = 0.05) affects the diversity summary proportion. While the pooled frequency of unculturable bacteria was 8%; 95% CI: 5, 14%, the estimate of the pooled abundance of unculturable bacteria was 5%; 95% CI: 2, 12% with a significant (P = 0.05) country moderator that affects the abundance summary proportion. Of the 62 unculturable bacteria, 35 were subjected to PCA and Peptostreptococcus sp. oral clone CK035 was the most abundant species in periapical abscesses. Hybridization techniques were found to be the most reliable molecular methods in detecting the abundance and frequency of unculturable bacteria. CONCLUSION: The significant prevalence of unculturable bacteria in the periapical abscess, suggests that they are likely to play, a yet unknown, critical role in the pathogenesis and progression of the disease. Further research remains to be done to confirm their specific contributions in the virulence and disease progression.

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