Commentary

The ISME Journal (2014) 8, 1–3; doi:10.1038/ismej.2013.176; published online 24 October 2013

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment
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Elizabeth M Glass1,1, Yekaterina Dribinsky1, Pelin Yilmaz2, Hal Levin3, Robert Van Pelt4, Doug Wendel4, Andreas Wilke1, Jonathan A Eisen5, Sue Huse6, Anna Shipanova6, Mitch Sogin6, Jason Stajich7, Rob Knight4,8, Folker Meyer1,9 and Lynn M Schriml10,1

  1. 1Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
  2. 2Max Planck Institute for Marine Microbiology, Bremen, Germany
  3. 3Building Ecology
  4. 4Department of Computer Science, University of Colorado, Boulder, CO, USA
  5. 5Davis Genome Center, University of California, Davis, CA, USA
  6. 6Marine Biological Laboratory, Woods Hole, MA, USA
  7. 7University of California, Riverside, CA, USA
  8. 8Howard Hughes Medical Institute, Chevy Chase, MD, USA
  9. 9Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
  10. 10Department of Epidemiology and Public Health, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

Correspondence: Elizabeth M Glass, E-mail: marland@mcs.anl.gov

11These authors contributed equally to this work.

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The need for metadata standards for microbe sampling in the built environment

The composition of indoor microbial communities has the potential to profoundly affect human health. A number of factors within a building or room can alter the microbial abundance and diversity, such as occupancy, temperature and humidity, which in turn impacts indoor air quality. Researchers Hospodsky et al. (2012); Kembel et al. (2012) and Dunn et al. (2013) are exploring the intersection of microbial ecology, building materials and architectural design to understand microbial diversity and abundance within a building. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection and reliability. As the impact and prevalence of large-scale metagenomic surveys grow, so does the need for more complete and standards compliant metadata (Gilbert et al., 2012). While marine, soil and the human microbiome environments have representation in the standards being developed the built environment (BE) represents a unique context in need of standards development for the use in the study of microbial sequences. Metadata collection and interpretation have become vital to the genomics and metagenomics community to share information and integrate data across resources and within data repositories. The Genomic Standards Consortium (GSC, http://gensc.org; Field et al. (2011)) has developed widely accepted metadata MIxS (MIGS, MIMS, MIMARKS; Yilmaz et al. (2011)) standards for genomic, metagenomic and amplicon (for example, 16S rRNA) sequence data sets. These standards have been developed within a framework that is both modular and extensible. The MIxS-BE, as a minimal metadata standard, represents a unique extension to the GSC’s MIxS standard as a rigorous and structured tool for the analysis of microbial sequences and ecosystems of the indoor environment. The MIxS-BE package provides the BE community with a suggested list of parameters to record and report for each sequenced sample and to compare data across studies. The MIxS-BE standard incorporates the core set of required MIxS fields for a bacterial sequence along with a Built Environment (BE) package (http://gensc.org/index.php?title=MIxS_extensions) comprised of a BE core, MIxS air environmental package terms, BE building properties and BE sample properties. The MIxS-BE package has been incorporated into the MIxS checklist and integrated into the QIIME (Caporaso et al., 2010), MoBeDAC and MG-RAST (Meyer et al., 2008) databases to foster metadata submission compliance across BE projects. Updates to the MIxS specification will be included in BioSample (Barrett et al., 2012) as part of the annual MIxS release. Requests for additions or changes to the MIxS checklists can be directed to the GSC Developers mailing list: developers@gensc.org or by contacting Lynn Schriml or Elizabeth Glass.

Development of the MIxS-BE package has been an open and iterative process engaging the GSC community, the GSC’s MIxS developers, stakeholders across the BE community including microbial ecologists, microbiologists, architects and engineers. The Microbiology of the Built Environment Alfred P. Sloan funded initiative established a metadata working group as part of the MoBeDAC, bringing together Sloan-funded researchers, architects, civil engineers, bioinformaticists and computational biologists to discuss the need and context for standards to describe the most relevant metadata to be collected for BE samples. Led by Elizabeth Glass and Lynn Schriml, the working group proposed the development of the BE-MIxS package to the GSC and gained the GSC’s board approval to develop the standard. The working group initially identified a comprehensive list of metadata terms reported in BE literature. Based on feedback solicited from industry experts and microbial ecologists, the working group established a minimal set of metadata terms for the BE package environment samples with a subset of the MIxS-BE terms classified as M (Mandatory), which indicates that the term has to be reported for the metadata to be considered compliant to the MIxS checklist. The MIxS-BE minimal set will be complemented by a MIxS-BE-Building package (under development) describing the larger set of building and room metadata pertinent to describing a BE sample (Table 1).


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References

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Acknowledgements

We would like to thank the Alfred P Sloan Foundation grant FP047325-01-PR for support for this project. We also thank the members of the BE community and the GSC for their comments on this minimal standard, especially Jessica Green, Jordan Peccia, Ju-Hyeong Park, Janet Macher and Renzo Kottmann.

This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/.