title: 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.
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Anirikh
authors.initials: A
authors.lastname: Chakrabarti
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Jay
authors.initials: J
authors.lastname: Siddharth
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Christian L
authors.initials: CL
authors.lastname: Lauber
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Membrez
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Betrisey
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Carole
authors.initials: C
authors.lastname: Loyer
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Chieh Jason
authors.initials: CJ
authors.lastname: Chou
authors.affiliation: Service of Therapeutic Education for Chronic Diseases, WHO Collaborating Centre, University Hospitals of Geneva and University of Geneva, Geneva, Switzerland.
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Pataky
authors.affiliation: Service of Therapeutic Education for Chronic Diseases, WHO Collaborating Centre, University Hospitals of Geneva and University of Geneva, Geneva, Switzerland.
authors.forename: Alain
authors.initials: A
authors.lastname: Golay
authors.affiliation: Nestlé Institute of Health Sciences, Lausanne, Switzerland.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Parkinson
mesh_terms: D000465:Algorithms; D000818:Animals; D005856:Germ-Free Life; D006801:Humans; D051379:Mice; D064307:Microbiota