Standardized naming of microbiome samples in Genomes OnLine Database

Mukherjee, Supratim; Ovchinnikova, Galina; Stamatis, Dimitri; Li, Cindy Tianqing; Chen, I-Min A.; Kyrpides, Nikos C.; Reddy, T. B. K.

doi:10.1093/database/baad001

DOE OSTI · 2234138

Standardized naming of microbiome samples in Genomes OnLine Database

Mukherjee, Supratim·Ovchinnikova, Galina·Stamatis, Dimitri·Li, Cindy Tianqing·Chen, I-Min A.·Kyrpides, Nikos C.·Reddy, T. B. K.

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Abstract

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

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Mukherjee, Supratim, Ovchinnikova, Galina, Stamatis, Dimitri, Li, Cindy Tianqing, Chen, I-Min A., Kyrpides, Nikos C., Reddy, T. B. K.. 2023-02-16. Standardized naming of microbiome samples in Genomes OnLine Database. https://doi.org/10.1093/database%2Fbaad001

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