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Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT?).

ABSTRACT: 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.

SUBMITTER: Chakrabarti A 

PROVIDER: S-EPMC4987704 | biostudies-other | 2016

REPOSITORIES: biostudies-other

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Resolving microbial membership using Abundance and Variability In Taxonomy ('AVIT ).

Chakrabarti Anirikh A   Siddharth Jay J   Lauber Christian L CL   Membrez Mathieu M   Betrisey Bertrand B   Loyer Carole C   Chou Chieh Jason CJ   Pataky Zoltan Z   Golay Alain A   Parkinson Scott J SJ  

Scientific reports 20160817

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 thresho  ...[more]