RESEARCH Open AccessA comparison of methods used to unveilthe genetic and metabolic pool in the builtenvironmentCinta Gomez-Silvan 1,2 , Marcus H. Y. Leung 3 , Katherine A. Grue 1,4 , Randeep Kaur 2 , Xinzhao Tong 3 ,Patrick K. H. Lee 3* and Gary L. Andersen 1,2*AbstractBackground: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are notadapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methodsare either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of thesample is more likely to represent either viable or metabolically active cells. We examined methodological variations insample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs.biological-based differences in both ribosomal transcript (rRNA) and gene (DNA) sequence community analysis. Based onin vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surfacemicrobiomes within a residential setting.Results: We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, agreater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at − 80°Cexperienced a rapid decline in nucleic acid recovery starting within the first week, although post-extractionrRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples beprocessed as quickly as possible after collection. The in vivo analysis revealed significant differences in thetwo components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbialassociation networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNAratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of theSphingomonadales order, were present in lower relative abundances in the viable community.Conclusions: Although methodological variations in sample preparations are high, large differences betweenthe DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNAisolated from a residential BE microbiome has the potential to identify the more likely viable or active portionof the microbial community. In an environment that has primarily dead and metabolically inactive cells, wesuggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight intothe factors that drive indoor microbial community dynamics.Keywords: DNA, RNA, Indoor microbiome, Surface, Air, Sample storage, RNAStable, Extraction kit* Correspondence: patrick.kh.lee@cityu.edu.hk; glandersen@lbl.gov3 School of Energy and Environment, City University of Hong Kong, Tat CheeAvenue, Kowloon, Hong Kong1 Department of Environmental Science, Policy, and Management, Universityof California, Berkeley, CA, USAFull list of author information is available at the end of the article© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, andreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link tothe Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Gomez-Silvan et al. Microbiome (2018) 6:71 https://doi.org/10.1186/s40168-018-0453-0
