A comparison of methods used to unveil the genetic and metabolic pool in the built environment
Abstract Background A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many excepti...
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doaj-7bc324c507044204b5e7e8335c08b6972020-11-24T22:43:58ZengBMCMicrobiome2049-26182018-04-016111610.1186/s40168-018-0453-0A comparison of methods used to unveil the genetic and metabolic pool in the built environmentCinta Gomez-Silvan0Marcus H. Y. Leung1Katherine A. Grue2Randeep Kaur3Xinzhao Tong4Patrick K. H. Lee5Gary L. Andersen6Department of Environmental Science, Policy, and Management, University of CaliforniaSchool of Energy and Environment, City University of Hong KongDepartment of Environmental Science, Policy, and Management, University of CaliforniaEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratorySchool of Energy and Environment, City University of Hong KongSchool of Energy and Environment, City University of Hong KongDepartment of Environmental Science, Policy, and Management, University of CaliforniaAbstract Background A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample 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 on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. Results We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at − 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. Conclusions Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics.http://link.springer.com/article/10.1186/s40168-018-0453-0DNARNAIndoor microbiomeSurfaceAirSample storage |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Cinta Gomez-Silvan Marcus H. Y. Leung Katherine A. Grue Randeep Kaur Xinzhao Tong Patrick K. H. Lee Gary L. Andersen |
spellingShingle |
Cinta Gomez-Silvan Marcus H. Y. Leung Katherine A. Grue Randeep Kaur Xinzhao Tong Patrick K. H. Lee Gary L. Andersen A comparison of methods used to unveil the genetic and metabolic pool in the built environment Microbiome DNA RNA Indoor microbiome Surface Air Sample storage |
author_facet |
Cinta Gomez-Silvan Marcus H. Y. Leung Katherine A. Grue Randeep Kaur Xinzhao Tong Patrick K. H. Lee Gary L. Andersen |
author_sort |
Cinta Gomez-Silvan |
title |
A comparison of methods used to unveil the genetic and metabolic pool in the built environment |
title_short |
A comparison of methods used to unveil the genetic and metabolic pool in the built environment |
title_full |
A comparison of methods used to unveil the genetic and metabolic pool in the built environment |
title_fullStr |
A comparison of methods used to unveil the genetic and metabolic pool in the built environment |
title_full_unstemmed |
A comparison of methods used to unveil the genetic and metabolic pool in the built environment |
title_sort |
comparison of methods used to unveil the genetic and metabolic pool in the built environment |
publisher |
BMC |
series |
Microbiome |
issn |
2049-2618 |
publishDate |
2018-04-01 |
description |
Abstract Background A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample 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 on in vitro tests, a protocol was adopted for the analysis of the genetic and metabolic pool (DNA vs. rRNA) of air and surface microbiomes within a residential setting. Results We observed differences in DNA/RNA co-extraction efficiency for individual microbes, but overall, a greater recovery of rRNA using FastPrep (> 50%). Samples stored with various preservation methods at − 80°C experienced a rapid decline in nucleic acid recovery starting within the first week, although post-extraction rRNA had no significant degradation when treated with RNAStable. We recommend that co-extraction samples be processed as quickly as possible after collection. The in vivo analysis revealed significant differences in the two components (genetic and metabolic pool) in terms of taxonomy, community structure, and microbial association networks. Rare taxa present in the genetic pool showed higher metabolic potential (RNA:DNA ratio), whereas commonly detected taxa of outdoor origins based on DNA sequencing, especially taxa of the Sphingomonadales order, were present in lower relative abundances in the viable community. Conclusions Although methodological variations in sample preparations are high, large differences between the DNA and RNA fractions of the total microbial community demonstrate that direct examination of rRNA isolated from a residential BE microbiome has the potential to identify the more likely viable or active portion of the microbial community. In an environment that has primarily dead and metabolically inactive cells, we suggest that the rRNA fraction of BE samples is capable of providing a more ecologically relevant insight into the factors that drive indoor microbial community dynamics. |
topic |
DNA RNA Indoor microbiome Surface Air Sample storage |
url |
http://link.springer.com/article/10.1186/s40168-018-0453-0 |
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