Sources of microbial reference materials

Pereira, Rui P. A.1; Bagnoli, John2; Karstens, Lisa3; Locken, Kris4; Maki, Katherine A.5; Ramay, Hena6; Rivers, Adam7; Servetas, Stephanie8; Valyi, Kezia9; Wang, Yan10; Carpenter, Meredith L.11 ; O'Sullivan, Denise M.1 ; Whiteson, Katrine L.12 ; Willis, Amy D.13

Published Oct 20, 2023 on Dryad. https://doi.org/10.5061/dryad.m63xsj45z

Data files

Oct 20, 2023 version files 91.26 KB

Abstract

Despite the importance of the microbiome in a wide array of human and environmental health settings, challenges remain in taking accurate and precise measurements of microbial communities. Challenges in measuring microbial communities can be partially addressed through the use of "reference materials," which we interpret as any physical material that can be used for quality control, validation, diagnostics, and standardization in metagenomic, microbiome, or multi-omics workflows. As members of the International Microbiome and Multi'Omics Standards Alliance (IMMSA) Reference Materials Working Group, we collated a list of available sources of microbial reference material standards. Each entry in our list includes a description, type of material, availability, storage requirements, biosafety level, species richness, and more. Due to the geographical composition of the working group, the list of materials may be biased towards materials that are available in regions of North America and Western Europe. This list is a living document, and we welcome revisions and contributions from the global microbiome community.

README: Sources of microbial reference materials

https://doi.org/10.5061/dryad.m63xsj45z

This datasheet lists sources and descriptions of microbial reference material standards, which we interpret as any physical material that can be used for quality control, validation, diagnostics, and standardization in metagenomic, microbiome, or multi-omics workflows. Each entry in our list includes a description, type of material, availability, storage requirements, biosafety level, species richness, and more.

Description of the data and file structure

Our submission is a single datasheet. Each row in the datasheet corresponds to a microbial reference material standard, and each column corresponds to a specific descriptor for that standard. Cells list "unknown" (or are left blank) when it was not possible to find the needed information from publicly available provider descriptions. Information for spreadsheet v1.1 was collated in August 2022, and can be considered "current" at that time. Columns include

Name (short)
Name (extended)
Description
Host Site Association -- e.g., Stool, Oral, Vaginal, None.
Type -- e.g., Purified DNA, Whole Cell, etc.
Availability -- Availability of the material.
Source -- The name of the material's provider.
Format -- e.g., Frozen, Freeze-Dried, etc. May include information on the material's buffer.
Biosafety Level -- BSL levels, ranging from 1 (lowest) to 4 (highest).
Storage requirements
Richness, strain-level, bacteria only (number of distinct bacterial populations present)
Richness, strain-level, archaea only (number of distinct archaeal populations present)
Richness, strain-level, fungi only (number of distinct fungi present)
Richness, strain-level, virus only (number of distinct virus present)
Richness, genome-level, human only (number of distinct human genomes present)
Names of genomes present -- Includes target percentages (DNA copies or concentration) where available.
Scope: genomes -- Yes or No. Is the material a genome reference material?
Scope: proteins -- Yes or No. Is the material a proteome reference material?
Scope: metabolomics -- Yes or No. Is the material a metabolome reference material?
Other information -- may include specification range (if available), additional availability information, additional development information, etc.
Links -- sources used to populate the row.

References used to compile the spreadsheet

The column "Links" lists the source information for each reference material.

Additions and corrections

This list is a living document, and we welcome revisions and contributions from the global microbiome community. To contribute an addition or a correction, please reach out to Dr. Amy Willis adwillis@uw.edu and/or the co-leaders of the International Microbiome and Multi'Omics Standards Alliance (IMMSA) Reference Materials Working Group.