Greengenes2 unifies microbial data in a single reference tree
University of California San Diego · Arizona State University · +15 more institutions
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Abstract
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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25Topics & keywords
Topics
Keywords
- Tree (set theory)
- Biology
- Computational biology
- Computer science
- Mathematics
- Combinatorics
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Funding
- NSNational Science FoundationAwards: U19AG063744, 2137603, and 2138296, 2138259, 2138296, 2138307, 2138286, RAPID 20385.09, XSEDE BIO210103
- DDanone
- EFEmerald Foundation
- DNDanone Nutricia Research
- NINational Institutes of HealthAwards: 1R35GM142725, 2138307, 2138286, 2138296, U19AG063744, U24DK131617, 2137603, DP1-AT010885, 2138259
- UOUniversity of California, San Diego
- NINational Institute of Child Health and Human Development
- OOOffice of Advanced CyberinfrastructureAwards: 2138286, 2138259, 2137603, 2138307, 2138296
- EKEunice Kennedy Shriver National Institute of Child Health and Human Development