A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)

Abstract

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, kinetics, and population dynamics, offering novel insights according to diverse research questions. Data re-use maximizes the information available from the time and resource intensive SIP experimental approach. Yet, a review of publicly available SIP sequencing metadata reveals that critical information necessary for reproducibility and reuse is 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) data standard framework and include examples of MISIP reporting for common SIP approaches. 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 five metadata fields: isotope, isotopolog, isotopolog label and approach, and gradient position, and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (ex. 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 assure the reproducibility and reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.