Amplicon Sequencing of Single-Copy Protein-Coding Genes Reveals Accurate Diversity for Sequence-Discrete Microbiome Populations.
Amplicon Sequencing of Single-Copy Protein-Coding Genes Reveals Accurate Diversity for Sequence-Discrete Microbiome Populations.
复制标题
单拷贝蛋白质编码基因的扩增子测序揭示了序列离散微生物组群体的准确多样性。
DOI：
10.1128/spectrum.02105-21
复制
发表时间：
2022-04-27
影响因子：
3.7
通讯作者：
Zhou, Xin
中科院分区：
文献类型：
--
作者：
Yang, Chengfeng;Su, Qinzhi;Tang, Min;Luo, Shiqi;Zheng, Hao;Zhang, Xue;Zhou, Xin
要深入了解微生物的功能和生态位的划分，就需要在精细的分类学分辨率下对微生物进行准确的描绘和鉴定。微生物种型通常使用97%小亚单位（16S） rRNA阈值来定义。然而，越来越多的证据表明，在种型中普遍存在不同功能的分类单位。这些所谓的序列离散种群（sdp）过去主要是通过全基因组水平上的分离序列相似性来描述的。然而，在微生物群落研究中缺乏能够准确识别和量化sdp的基因标记。在这里，我们开发了一个管道来筛选单拷贝蛋白质编码基因，可以通过微生物群落的扩增子测序准确地表征SDP多样性。采用三个标准（序列差异程度、系统发育准确性和引物区域的保守性）对15个候选标记基因进行了评估，并对所选基因进行了测试，以区分Gilliamella（蜜蜂肠道微生物的核心种型）中sps的效率，作为概念验证。结果表明，16S V4区由于分类学分辨率低、拷贝数变化等原因，未能准确报道SDP多样性。相比之下，我们推荐的单拷贝基因能够成功地量化模拟样本和蜜蜂内脏的吉利亚菌sps，结果与宏基因组学的结果高度一致。本研究开发的管道有望鉴定能够在SDP水平上准确定量不同细菌群落的单拷贝蛋白质编码基因。微生物群落可以通过离散的遗传和生态特征来区分。这些序列离散种群是高分辨率研究微生物群落组成和功能结构的基础。在这项研究中，我们筛选了可靠的单拷贝蛋白质编码标记基因，通过我们的管道来识别序列离散的群体。利用标记基因扩增子测序，可以准确、高效地描述微生物群落的种群多样性。这些结果表明，单拷贝蛋白质编码基因可以作为一种准确、定量和经济的替代方法来表征群体多样性。此外，通过本文提出的管道，可以快速评估基因作为任何细菌群体鉴定标记的可行性。
An in-depth understanding of microbial function and the division of ecological niches requires accurate delineation and identification of microbes at a fine taxonomic resolution. Microbial phylotypes are typically defined using a 97% small subunit (16S) rRNA threshold. However, increasing evidence has demonstrated the ubiquitous presence of taxonomic units of distinct functions within phylotypes. These so-called sequence-discrete populations (SDPs) have used to be mainly delineated by disjunct sequence similarity at the whole-genome level. However, gene markers that could accurately identify and quantify SDPs are lacking in microbial community studies. Here, we developed a pipeline to screen single-copy protein-coding genes that could accurately characterize SDP diversity via amplicon sequencing of microbial communities. Fifteen candidate marker genes were evaluated using three criteria (extent of sequence divergence, phylogenetic accuracy, and conservation of primer regions) and the selected genes were subject to test the efficiency in differentiating SDPs within Gilliamella, a core honeybee gut microbial phylotype, as a proof-of-concept. The results showed that the 16S V4 region failed to report accurate SDP diversities due to low taxonomic resolution and changing copy numbers. In contrast, the single-copy genes recommended by our pipeline were able to successfully quantify Gilliamella SDPs for both mock samples and honeybee guts, with results highly consistent with those of metagenomics. The pipeline developed in this study is expected to identify single-copy protein coding genes capable of accurately quantifying diverse bacterial communities at the SDP level. IMPORTANCE Microbial communities can be distinguished by discrete genetic and ecological characteristics. These sequence-discrete populations are foundational for investigating the composition and functional structures of microbial communities at high resolution. In this study, we screened for reliable single-copy protein-coding marker genes to identify sequence-discrete populations through our pipeline. Using marker gene amplicon sequencing, we could accurately and efficiently delineate the population diversity in microbial communities. These results suggest that single copy protein-coding genes can be an accurate, quantitative, and economical alternative for characterizing population diversity. Moreover, the feasibility of a gene as marker for any bacterial population identification can be quickly evaluated by the pipeline proposed here.
登录
查看更多内容
影响因子：
3.7
作者：
Calderone NW
通讯作者：
Calderone NW
影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP
DOI：
10.1073/pnas.0409727102
发表时间：
2005-02-15
影响因子：
11.1
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM
影响因子：
5.8
作者：
Edgar, Robert C.
通讯作者：
Edgar, Robert C.
影响因子：
3.2
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM