Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries.
Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries.
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DOI：
10.1093/pnasnexus/pgac239
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发表时间：
2022-11
期刊：
影响因子：
--
通讯作者：
Dupont, Chris L.
中科院分区：
文献类型：
--
作者：
Espinoza, Josh L.;Torralba, Manolito;Leong, Pamela;Saffery, Richard;Bockmann, Michelle;Kuelbs, Claire;Singh, Suren;Hughes, Toby;Craig, Jeffrey M.;Nelson, Karen E.;Dupont, Chris L.
龋齿是一种微生物疾病，也是最常见的慢性健康疾病，全球有近35亿人受到影响。在这项研究中，我们使用多组学方法对91名澳大利亚儿童的牙龈上菌斑微生物组进行了表征，通过转录图谱和基因表达网络分析产生了658个细菌和189个病毒元基因组组装的基因组。我们开发了一条可重复的管道，用于聚集特定样本的基因组，以整合元基因组学和元转录组学分析，而不考虑生物样本的重叠。我们介绍了新的特征工程和成分感知的集成网络框架，同时展示了它们在研究与龋病失调相关的制度转变方面的效用。当差异丰度模型没有捕捉到统计上的丰富，或者这种分析的结果不足以提供对疾病的更深层次的了解时，可以应用这些方法。我们确定了哪些生物和代谢途径是共表达网络的中心，以及这些网络是如何在龋齿和无龋表型之间重新连接的。我们的发现提供了核心细菌微生物组的证据，该微生物组在所有参与者的牙龈上菌斑中转录活跃，无论表型如何，但也显示出生物相互作用方式的高度诊断性变化。具体地说，许多生物表现出与心脏细菌中心碳代谢的高度连接性，这种转变起到了表型之间的桥梁作用。我们的证据支持这一假设，即龋病是一种多因素的生态疾病。
Dental caries is a microbial disease and the most common chronic health condition, affecting nearly 3.5 billion people worldwide. In this study, we used a multiomics approach to characterize the supragingival plaque microbiome of 91 Australian children, generating 658 bacterial and 189 viral metagenome-assembled genomes with transcriptional profiling and gene-expression network analysis. We developed a reproducible pipeline for clustering sample-specific genomes to integrate metagenomics and metatranscriptomics analyses regardless of biosample overlap. We introduce novel feature engineering and compositionally-aware ensemble network frameworks while demonstrating their utility for investigating regime shifts associated with caries dysbiosis. These methods can be applied when differential abundance modeling does not capture statistical enrichments or the results from such analysis are not adequate for providing deeper insight into disease. We identified which organisms and metabolic pathways were central in a coexpression network as well as how these networks were rewired between caries and caries-free phenotypes. Our findings provide evidence of a core bacterial microbiome that was transcriptionally active in the supragingival plaque of all participants regardless of phenotype, but also show highly diagnostic changes in the ways that organisms interact. Specifically, many organisms exhibit high connectedness with central carbon metabolism to Cardiobacterium and this shift serves a bridge between phenotypes. Our evidence supports the hypothesis that caries is a multifactorial ecological disease.
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影响因子：
6.4
作者：
Espinoza JL;Harkins DM;Torralba M;Gomez A;Highlander SK;Jones MB;Leong P;Saffery R;Bockmann M;Kuelbs C;Inman JM;Hughes T;Craig JM;Nelson KE;Dupont CL
通讯作者：
Dupont CL
影响因子：
4.6
作者：
Hsu CL;Juan HF;Huang HC
通讯作者：
Huang HC
WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
影响因子：
4.6
作者：
Freire, Marcelo;Moustafa, Ahmed;Nelson, Karen E.
通讯作者：
Nelson, Karen E.
DOI：
10.1007/s12064-015-0220-8
发表时间：
2016-06
期刊：
Theory in biosciences = Theorie in den Biowissenschaften
影响因子：
--
作者：
Erb I;Notredame C
通讯作者：
Notredame C