Table 2_Advancing periodontitis microbiome research: integrating design, analysis, and technology.xlsx

Periodontitis, a chronic inflammatory disease affecting 20%-50% of adults worldwide, is driven by polymicrobial synergy and dysbiosis. Despite numerous studies on the oral microbiota in periodontitis, significant heterogeneity exists between findings, posing challenges for treatment strategies. To understand the sources of this variability and establish standardized protocols, we reviewed the literature to identify potential factors contributing to these discrepancies. We found most studies focus on microbial communities in periodontal pockets, with fewer investigating microbial composition within gingival tissue. Research indicates that bacterial communities in gingival tissue exist as biofilms, potentially serving as reservoirs for persistent infection. Therefore, further exploration of the microbiome within periodontal tissues is needed, which may offer new insights for treatment strategies. Metatranscriptomics provides valuable insights into gene expression patterns of the oral microbiota, enabling the exploration of microbial activity at a functional level. Previous studies revealed that most upregulated virulence factors in periodontitis originate from species not traditionally considered major periodontal pathogens. However, current studies have not fully identified or revealed the functional changes in key symbiotic microbes in periodontitis. We reviewed the analytical paradigms of metatranscriptomics and found that current analysis is largely limited to assessing functional changes in known periodontal pathogens, highlighting the need for a functional-driven approach. Beyond the limitations of current analytical paradigms, the metatranscriptomics also has inherent constraints. We suggested integrating emerging high-throughput microbial sequencing technologies with functional-driven analytical strategies to provide a more comprehensive and higher-resolution insight for microbiome reconstruction in periodontitis.

牙周炎（Periodontitis）是一种累及全球20%~50%成人的慢性炎症性疾病，其发病由多微生物协同与菌群失调驱动。尽管目前针对牙周炎患者的口腔微生物群已开展大量研究，但不同研究结果间存在显著异质性，这为治疗策略的制定带来了挑战。为明确该差异的来源并建立标准化研究流程，我们对现有文献进行了综述，以梳理导致这些研究结果不一致的潜在因素。我们发现，多数研究聚焦于牙周袋内的微生物群落，而针对牙龈组织内微生物组成的探索相对较少。已有研究表明，牙龈组织内的细菌群落以生物膜形式存在，或可作为持续性感染的储存库。因此，进一步探索牙周组织内的微生物组具有重要意义，或可为治疗策略提供全新视角。宏转录组学（metatranscriptomics）可为口腔微生物群的基因表达模式提供宝贵见解，助力从功能层面探究微生物活性。既往研究显示，牙周炎中多数上调的毒力因子（virulence factors）来自传统意义上并非主要牙周致病菌的菌种。然而，当前研究尚未完全阐明或揭示牙周炎中关键共生微生物的功能变化。我们对宏转录组学的分析范式（analytical paradigms）进行了综述，发现当前分析大多局限于评估已知牙周致病菌的功能变化，这凸显了采用功能导向型分析方法的必要性。除现有分析范式的局限外，宏转录组学本身也存在固有局限性。我们建议将新兴的高通量微生物测序（high-throughput microbial sequencing）技术与功能导向型分析策略相结合，以期为牙周炎相关微生物组重构提供更全面、更高分辨率的认知。