MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

Journal Article · Mon Oct 14 00:00:00 EDT 2024 · GigaScience

DOI:https://doi.org/10.1093/gigascience/giae071· OSTI ID:2479287

Simpson, Abigayle ^[1]; Wood-Charlson, Elisha M. ^[2]; Smith, Montana ^[3]; Koch, Benjamin J. ^[4]; Beilsmith, Kathleen ^[5]; Kimbrel, Jeffrey A. ^[6]; Kellom, Matthew ^[2]; Hunter, Christopher I. ^[7]; Walls, Ramona L. ^[8]; Schriml, Lynn M. ^[9]; Wilhelm, Roland C. ^[1]

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1. Purdue University, West Lafayette, IN (United States)
2. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
3. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
4. Northern Arizona University, Flagstaff, AZ (United States)
5. Argonne National Laboratory (ANL), Argonne, IL (United States)
6. Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
7. GigaScience (Hong Kong)
8. Critical Path Institute, Tucson, AZ (United States)
9. University of Maryland School of Medicine, Baltimore, MD (United States)

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDA National Institute of Food and Agricultural Hatch Grant; USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science (BSS)
• Grant/Contract Number: AC02-05CH11231; AC05-76RL01830; AC52-07NA27344
• OSTI ID: 2479287
• Journal Information: GigaScience, Journal Name: GigaScience Vol. 13; ISSN 2047-217X
• Publisher: BioMed Central
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
MIMARKS
MIMS
MIxS
amplicon
metagenome
metatranscriptome
microbial ecology
minimum information standard
stable isotope probing