Analysis of oral bacterial communities: comparison of HOMINGS with a tree-based approach implemented in QIIME.
Analysis of oral bacterial communities: comparison of HOMINGS with a tree-based approach implemented in QIIME.
复制标题
口腔细菌群落分析：HOMINGS 与 QIIME 中实施的基于树的方法的比较。
DOI：
10.1080/20002297.2019.1586413
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发表时间：
2019
影响因子：
4.5
通讯作者：
Alevizos,Ilias
中科院分区：
文献类型：
--
作者：
Palmer,RobertJ;Cotton,SeanL;Kokaras,AlexisS;Gardner,Pamela;Grisius,Margaret;Pelayo,Eileen;Warner,Blake;Paster,BruceJ;Alevizos,Ilias
背景：口腔微生物群落的分子分类学分配已使用探针匹配方法进行，但从未与更容易接受的基于树的方法获得的结果进行比较。目的：比较从探针匹配方法（HOMINGS）获得的群落组成概况与基于封闭式树的方法（使用 eHOMD 数据库的 QIIME）获得的群落组成概况。设计：HOMINGS 和 QIIME 用于对 10 个模拟样本进行并行分析 社区样本，以及来自生态独特地点的 119 个龈上菌斑样本（健康受试者的健全牙齿表面、原发性干燥综合征患者的健全牙齿表面以及干燥综合征患者的龋齿病变）。 线性判别分析有效大小 (LEfSe) 用于识别天然斑块样品中的判别类群。结果：所有样品的群落组成特征在两种分析方法之间是一致的。 天然斑块群落的α和β多样性同样相似。 pSS 患者的社区和唾液流量正常的个体的社区在 α 和 β 多样性方面存在差异。 两种分类方法对来自这些受试者队列的样本的预测组成存在差异，并且方法之间的区分分类单元相似。结论：直接比较表明 HOMINGSi 很大程度上相当于此处实施的基于树的方法。试验注册：ClinicalTrials.gov 标识符：NCT00001196。试验注册：ClinicalTrials.gov 标识符： NCT01425892。试验注册：ClinicalTrials.gov 标识符：NCT00001390。
Background:Molecular taxonomic assignments in oral microbial communities have been made using probe-matching approaches, but never compared to those obtained by more readily accepted tree-based approaches.Objective:To compare community composition profiles obtained from a probe-matching approach (HOMINGS) to those from a closed-ended tree-based approach (QIIME using the eHOMD database).Design:HOMINGSand QIIME were used for parallel analysis of ten mock community samples, and of 119 supragingival plaque samples from ecologically unique sites (sound tooth surfaces in healthy subjects, sound tooth surfaces in patients with primary Sjögren’s Syndrome, and carious lesions in Sjögren’s Syndrome patients). Linear discriminant analysis Effective Size (LEfSe) was used to identify discriminating taxa among the natural plaque samples.Results:Community composition profiles of all samples were congruent between the two analysis aproaches. Alpha and beta diversity of the natural plaque communities were likewise similar. Communities from pSS patients and those from individuals with normal salivary flow differed in alpha and beta diversity. Both classification approaches yielded differences in composition predicted for samples from these subject cohorts, and discriminating taxa were similar between approaches.Conclusions:A direct comparison demonstrates that HOMINGSis largely equivalent to the tree-based approach as implemented here.Trial registration:ClinicalTrials.gov identifier: NCT00001196.Trial registration:ClinicalTrials.gov identifier: NCT01425892.Trial registration:ClinicalTrials.gov identifier: NCT00001390.