Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.
Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.
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DOI：
10.1186/s40168-015-0136-z
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发表时间：
2015-12-19
期刊：
影响因子：
15.5
通讯作者：
Griffin TJ
中科院分区：
文献类型：
--
作者：
Rudney JD;Jagtap PD;Reilly CS;Chen R;Markowski TW;Higgins L;Johnson JE;Griffin TJ
龋齿的病因是多因素的，但频繁食用游离糖，尤其是蔗糖，似乎是导致龈上微生物群失调的一个主要因素。最近基于 16S rRNA 的研究表明，龋齿相关群落的多样性不如健康的龈上菌斑，但个体之间仍表现出相当大的分类多样性。宏基因组研究同样发现，不同人的健康口腔部位在基因功能方面大致相似，尽管其分类谱存在广泛的个体差异。这种模式也可能延伸到生态失调的社区。在这种情况下，群落范围内蛋白质相对丰度的变化可能会提供更好的生态失调生物标志物，而这可以仅通过分类学来实现。在这项研究中，我们使用配对的龋齿口腔微观生物膜模型来研究存在和不存在蔗糖时群落组成和蛋白质相对丰度的差异。这种方法提供了大量的蛋白质，有利于深入的宏蛋白质组分析。使用 16S rRNA 测序和宏蛋白质组学方法评估群落组成。尽管蔗糖脉冲降低了分类多样性，但群落组成仍然存在相当大的个体间差异。相比之下，使用 SEED 本体论的功能分析发现，蔗糖诱导了涉及糖酵解、乳酸产生、酸尿度和氨/谷氨酸代谢途径的蛋白质相对丰度模式的变化，这些途径在分类学上多样化的失调口腔微观生物膜群落中是保守的。我们的研究结果支持使用基于功能的蛋白质相对丰度变化作为生态失调指标的概念。我们的微观模型无法复制口腔环境的所有方面，但它允许进行深层次的宏蛋白质组分析，使其适合发现哪些蛋白质在菌群失调期间最丰富。这样就有可能定义生物标志物，用于在出现明显的龋齿病变之前检测有风险的牙齿表面。本文的在线版本 (doi:10.1186/s40168-015-0136-z) 包含补充材料，可供授权用户使用。
The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone. In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities. Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are most consistently abundant during dysbiosis. It then may be possible to define biomarkers that could be used to detect at-risk tooth surfaces before the development of overt carious lesions. The online version of this article (doi:10.1186/s40168-015-0136-z) contains supplementary material, which is available to authorized users.