Elucidating the Beta-Diversity of the Microbiome: from Global Alignment to Local Alignment

Quantitative comparison among microbiomes can link microbial beta-diversity to environmental features, thus enabling prediction of ecosystem properties or dissection of host-microbiome interaction. However, to compute beta-diversity, current methods mainly employ the entire community profiles of tax...

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Bibliographic Details
Published in:mSystems 2021-08, Vol.6 (4), p.e0036321-e0036321
Main Author: Su, Xiaoquan
Format: Article
Language:English
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Commentary
Computational Biology
Sponsored by Floré: Early-Career Special Series
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Summary:Quantitative comparison among microbiomes can link microbial beta-diversity to environmental features, thus enabling prediction of ecosystem properties or dissection of host-microbiome interaction. However, to compute beta-diversity, current methods mainly employ the entire community profiles of taxa or functions, which can miss the subtle differences caused by low-abundance community members that may play crucial roles in the properties of interest. In this work, I review the distance metrics and search engines that we developed to match microbiomes at a large scale based on whole-community-level similarities, as well as their limitations in tackling the microbiome changes caused by less abundant community features. Then I propose the concept of microbiome “local alignment,” including an algorithm to measure microbiome similarity on specific fractions of biodiversity and an indexing strategy for rapidly fetching microbiome local-alignment matches from the data repository.
ISSN:2379-5077
2379-5077
DOI:10.1128/mSystems.00363-21