A Metataxonomic Tool to Investigate the Diversity of Treponema
A Metataxonomic Tool to Investigate the Diversity of Treponema
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DOI：
10.3389/fmicb.2019.02094
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发表时间：
2019-09-10
影响因子：
5.2
通讯作者：
Knauf, Sascha
中科院分区：
文献类型：
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作者：
Hallmaier-Wacker, Luisa K.;Lueert, Simone;Knauf, Sascha
密螺旋体属包含许多人类和动物病原体以及共生细菌，这些细菌在非常不同的解剖学和环境栖息地中发现。我们对这些重要细菌的物种范围、进化和生物学的了解仍然有限。为了探索密螺旋体的多样性，我们建立，验证和测试了一种新的metataxonomic方法。由于16S rRNA基因的高变区的信息性质不同，我们首先独立地分析了每个可变区。考虑到获得的计算机模拟结果，我们使用已知的密螺旋体属物种混合物以及选定数量的临床样本建立并验证了16S rRNA基因V4区的测序。元分类方法能够在近种属水平上识别密螺旋体。我们证明，使用螺旋体特异性富集，我们的方法适用于复杂的微生物群落和各种各样的生物样品。所描述的元分类学方法提供了一种有用的方法来揭示密螺旋体在各种生态系统中的全部多样性和范围。
The genus Treponema contains a number of human and animal pathogenic as well as symbiotic bacteria that are found in vastly different anatomical and environmental habitats. Our understanding of the species range, evolution, and biology of these important bacteria is still limited. To explore the diversity of treponemes, we established, validated, and tested a novel metataxonomic approach. As the informative nature of the hypervariable regions of the 16S rRNA gene differ, we first analyzed each variable region independently. Considering the in silico results obtained, we established and validated the sequencing of the V4-region of the 16S rRNA gene using known mixtures of Treponema species as well as a selected number of clinical samples. The metataxonomic approach was able to identify Treponema to a near-species level. We demonstrate that using a spirochete-specific enrichment, our method is applicable to complex microbial communities and large variety of biological samples. The metataxonomic approach described provides a useful method to unravel the full diversity and range of Treponema in various ecosystems.