MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (GigaScience)
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, 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.
Article activity feed
-
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 …
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.Competing Interest StatementThe authors have declared no competing interest.
Reviewer 3. Xiaoxu Sun
The paper titled "MISIP: A Data Standard for the Reuse and Reproducibility of Stable Isotope Probing Derived Nucleic Acid Sequence and Experiment" presents a compelling argument for establishing a minimum information standard for stable isotope probing (SIP) experiments. The proposed MISIP standard aims to facilitate data reuse and ensure the reproducibility of results within the scientific community. The authors have meticulously considered the essential information required for MISIP, resulting in a well-articulated manuscript. However, I have a few suggestions that could further refine the proposed standard.
To me, one critical aspect of MISIP is to ensure it provides necessary details of the SIP incubations. Although the authors have integrated some of this information, which can overlap with other existing standards like MIMS/MIMARKS (e.g., sample origin), there are additional elements that should be included in MISIP, either as mandatory or recommended information.
Suggestion 1: Inclusion of Additional Substrates in Incubations
The paper rightly identifies the isotopologue as a requisite detail for MISIP. However, I recommend expanding this requirement to include a mention of other substrates added during incubations, at least as a recommended piece of information. While specifying the primary substrate (e.g., 13C-labeled glucose) is often sufficient for studies targeting heterotrophic processes, the identification of autotrophic populations using substrates like 13C-bicarbonate necessitates the disclosure of electron donors/acceptors to clarify the targeted metabolic processes.
Suggestion 2: Detailed Reporting of Incubation Progress
Although incubation time is suggested as a recommended field, I propose that details regarding the progress of the specified reactions should also be documented, such as the incorporated dose. This is particularly relevant when different substrate doses are used, as these can yield varied outcomes. For instance, the rate of substrate utilization can significantly differ across inoculums at identical time points; coastal sediment might consume 1 mM of glucose in a day, whereas deep-sea samples might take longer. Therefore, merely reporting incubation time without context may not provide sufficient insight for readers to gauge the dynamics of potential cross-feeding or other relevant processes.
In conclusion, integrating these suggestions into the MISIP standard could enhance its comprehensiveness and utility. By providing a more detailed framework, researchers can better interpret experimental setups and results, fostering a more robust foundation for data reuse and reproducibility in the field of stable isotope probing.
Re-review: Nice work on addressing all the comments. All my concerns have been addressed.
-
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 …
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.
Reviewer 2. Jibing Li
In this study, the authors meticulously delineated the Minimum Information about Stable Isotope Probing (MISIP) data standard within the broader framework of the Minimum Information about any (x) Sequence (MIxS) data standard. By extending the scope of MIxS to incorporate SIP-specific metadata, the authors have provided invaluable guidance to SIP practitioners regarding the collection and reporting of essential metadata for SIP experiments. Adoption of the proposed MISIP data standards is poised to significantly augment the reusability of sequence data derived from SIP experiments, thereby fostering a deeper understanding of in situ biogeochemical processes and microbial ecology. While the manuscript presents novel insights, further refinement is necessary to optimize its impact.
The MISIP data standard holds paramount importance in the realm of stable isotope probe (SIP) technology as it standardizes the collection and reporting of metadata essential for SIP experiments. This significance will be elucidated in the introduction to underscore the necessity and relevance of the MISIP framework.
The "Excess Atom Fraction" (EAF) serves as a pivotal metric for evaluating the isotopic enrichment of specific taxa, genomes, or genes in SIP experiments. It plays a crucial role in quantifying the incorporation of isotopically labeled substrates into microbial biomass, thereby providing valuable insights into microbial community dynamics and functional gene expression.
The introduction section will be expanded to provide a comprehensive background on DNA/RNA-stable isotope probing (SIP) technology, emphasizing the need for standardized data reporting through the MISIP framework. This contextualization will elucidate the motivation behind the development of MISIP and underscore its significance in promoting data reuse and reproducibility in SIP research.
To enhance transparency and credibility, a detailed account of the development process of the MISIP data standard, including the methodologies employed and potential challenges encountered, will be incorporated. This supplementary information will provide readers with insights into the rigor and practicality of the standard.
Specific application cases showcasing the efficacy of the MISIP data standard in actual research scenarios will be integrated into the manuscript. These case studies will serve to illustrate the practical utility of MISIP and bolster the persuasiveness of the article.
A comparative analysis of the MISIP data standard with existing similar standards will be conducted to highlight its advantages and uniqueness. This comparative approach will furnish readers with a comprehensive understanding of the distinctive features and benefits of MISIP.
The article will delve into the limitations of the MISIP data standard, explore potential avenues for future improvement, and delineate its application prospects in fields such as microbial ecology. This discussion will offer critical insights into the current state and future trajectory of MISIP.
The manuscript will be supplemented with a thorough examination of the limitations of MISIP data standards, potential avenues for future enhancement, and its implications for microbial ecology and other relevant fields. This holistic approach will ensure that the article comprehensively addresses all facets of the MISIP framework.
Re-review: Overall, the author addressed the questions I raised; however, the existing SIP research overlooked some representative authors I consider important, such as Thomas, F. (SME J. 2019;13:1814-30) and Luo, CL (Environ Int. 2023;180:108215). The author should include a more thorough review of the relevant literature to provide a well-rounded context for the study. Additionally, I identified several formatting errors in the manuscript, such as the incorrect citation in reference 15. These errors should be rectified to meet the journal's standards.
-
This work has been published in GigaScience Journal under a CC-BY 4.0 license (https://doi.org/10.1093/gigascience/giae071). These reviews are as follows.
Reviewer 1. Dayi Zhang The topic is quite interesting and important for microbiologists who are doing SIP work. However, there are some concerns about its quality and novelty.
- 15N is widely used in SIP but the authors did not mention them in this work. As an important labelling isotope, it is not acceptable to exclude 15N work.
- The authors have well designed and explained the catalog of MISIP, but how to standardize data from different sources are is not mentioned. In other words, there is only a method to put information together but no protocol to compare data from different studies or extract useful information from others' work. I think this is the most important expectation of …
This work has been published in GigaScience Journal under a CC-BY 4.0 license (https://doi.org/10.1093/gigascience/giae071). These reviews are as follows.
Reviewer 1. Dayi Zhang The topic is quite interesting and important for microbiologists who are doing SIP work. However, there are some concerns about its quality and novelty.
- 15N is widely used in SIP but the authors did not mention them in this work. As an important labelling isotope, it is not acceptable to exclude 15N work.
- The authors have well designed and explained the catalog of MISIP, but how to standardize data from different sources are is not mentioned. In other words, there is only a method to put information together but no protocol to compare data from different studies or extract useful information from others' work. I think this is the most important expectation of this work.
- As different protocols were used by different researchers to achieve SIP results, the authors should give criteria for their quality and the way to improve the quality for comparison. However, I cannot find such information.
- For the reason above, I think this is only a very preliminary concept, and the datasets and methods should be further developed for practical purposes.
---Editors Comments--- This work was then rejected to allow more work and revision. and then resubmitted.
-
-
