Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT)
Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT)
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DOI：
10.1038/srep31655
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发表时间：
2016-08-17
影响因子：
4.6
通讯作者：
Parkinson, Scott J.
中科院分区：
文献类型：
--
作者：
Chakrabarti, Anirikh;Siddharth, Jay;Parkinson, Scott J.
NGS的发展使微生物生态学的分析发生了革命性的变化，有助于我们更深入地了解微生物区系在健康和疾病中的作用。然而，由于样本依赖和独立的影响，总结的分类丰度的质量、数量和可信度需要进一步审查。在这篇文章中，我们介绍了AVIT(丰度和可变性)，这是一种无偏见的方法来丰富指定的微生物群落成员。与使用先验阈值不同，AVIT使用数据集中分类群的固有丰度和可变性来确定是否包含或拒绝每个分类群用于进一步的下游分析。通过使用体外和体内研究，我们对性能和参数化的AVIT进行了基准测试，以建立一个框架，用于研究临床相关场景中微生物群落成员的动态范围。
Development of NGS has revolutionized the analysis in microbial ecology contributing to our deeper understanding of microbiota in health and disease. However, the quality, quantity and confidence of summarized taxonomic abundances are in need of further scrutiny due to sample dependent and independent effects. In this article we introduce 'AVIT (Abundance and Variability In Taxonomy), an unbiased method to enrich for assigned members of microbial communities. As opposed to using a priori thresholds, 'AVIT uses inherent abundance and variability of taxa in a dataset to determine the inclusion or rejection of each taxa for further downstream analysis. Using in-vitro and in-vivo studies, we benchmarked performance and parameterized 'AVIT to establish a framework for investigating the dynamic range of microbial community membership in clinically relevant scenarios.