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 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 revealedmore »
- Authors:
-
- Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy, and Management; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
- City Univ. of Hong Kong (China)
- Univ. of California, Berkeley, CA (United States). Dept. of Environmental Science, Policy, and Management; Univ. of California, San Francisco, CA (United States). Dept. of Physical Therapy and Rehabilitation Science
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology Division
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF)
- OSTI Identifier:
- 1559142
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Microbiome
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2049-2618
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; DNA; RNA; Indoor microbiome; Surface; Air; Sample storage; RNAStable; Extraction kit
Citation Formats
Gomez-Silvan, Cinta, Leung, Marcus H. Y., Grue, Katherine A., Kaur, Randeep, Tong, Xinzhao, Lee, Patrick K. H., and Andersen, Gary L. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. United States: N. p., 2018.
Web. doi:10.1186/s40168-018-0453-0.
Gomez-Silvan, Cinta, Leung, Marcus H. Y., Grue, Katherine A., Kaur, Randeep, Tong, Xinzhao, Lee, Patrick K. H., & Andersen, Gary L. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. United States. https://doi.org/10.1186/s40168-018-0453-0
Gomez-Silvan, Cinta, Leung, Marcus H. Y., Grue, Katherine A., Kaur, Randeep, Tong, Xinzhao, Lee, Patrick K. H., and Andersen, Gary L. Mon .
"A comparison of methods used to unveil the genetic and metabolic pool in the built environment". United States. https://doi.org/10.1186/s40168-018-0453-0. https://www.osti.gov/servlets/purl/1559142.
@article{osti_1559142,
title = {A comparison of methods used to unveil the genetic and metabolic pool in the built environment},
author = {Gomez-Silvan, Cinta and Leung, Marcus H. Y. and Grue, Katherine A. and Kaur, Randeep and Tong, Xinzhao and Lee, Patrick K. H. and Andersen, Gary L.},
abstractNote = {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.},
doi = {10.1186/s40168-018-0453-0},
journal = {Microbiome},
number = 1,
volume = 6,
place = {United States},
year = {Mon Apr 16 00:00:00 EDT 2018},
month = {Mon Apr 16 00:00:00 EDT 2018}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 15 works
Citation information provided by
Web of Science
Web of Science
Figures / Tables:
Fig. 1: Schematic chart of in vitro workflow organized by sequence of tasks involved in sampling and extraction. Multiple stages of the in vitro sampling and extraction processes (types of swabs, and surfaces, sample storage prior to extraction, extraction method, and nucleic acid preservation) were tested for the optimal methodsmore »
All figures and tables
(6 total)
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Biofilm Formation Enhances Fomite Survival of Streptococcus pneumoniae and Streptococcus pyogenes
journal, December 2013
- Marks, Laura R.; Reddinger, Ryan M.; Hakansson, Anders P.
- Infection and Immunity, Vol. 82, Issue 3
Molecular identification of potential pathogens in water and air of a hospital therapy pool
journal, March 2005
- Angenent, L. T.; Kelley, S. T.; Amand, A. St.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 13
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
journal, June 2012
- Ye, Jian; Coulouris, George; Zaretskaya, Irena
- BMC Bioinformatics, Vol. 13, Issue 1
Origin, dynamics, and implications of extracellular DNA pools in marine sediments
journal, December 2015
- Torti, Andrea; Lever, Mark Alexander; Jørgensen, Bo Barker
- Marine Genomics, Vol. 24
UCHIME2: improved chimera prediction for amplicon sequencing
posted_content, January 2016
- Edgar, Robert C.
Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes
journal, August 2015
- Mahnert, Alexander; Vaishampayan, Parag; Probst, Alexander J.
- PLOS ONE, Vol. 10, Issue 8
Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities
journal, October 2015
- Checinska, Aleksandra; Probst, Alexander J.; Vaishampayan, Parag
- Microbiome, Vol. 3, Issue 1
Passive dust collectors for assessing airborne microbial material
journal, October 2015
- Adams, Rachel I.; Tian, Yilin; Taylor, John W.
- Microbiome, Vol. 3, Issue 1
The Diversity and Distribution of Fungi on Residential Surfaces
journal, November 2013
- Adams, Rachel I.; Miletto, Marzia; Taylor, John W.
- PLoS ONE, Vol. 8, Issue 11
Evaluation of DNAstable™ for DNA storage at ambient temperature
journal, January 2014
- Howlett, Susanne E.; Castillo, Hilda S.; Gioeni, Lora J.
- Forensic Science International: Genetics, Vol. 8, Issue 1
Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants
journal, April 2016
- Weikl, Fabian; Tischer, Christina; Probst, Alexander J.
- PLOS ONE, Vol. 11, Issue 4
Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea
journal, April 2014
- Zhang, Yao; Zhao, Zihao; Dai, Minhan
- Molecular Ecology, Vol. 23, Issue 9
Comparison of surface sampling methods and cleanability assessment of stainless steel surfaces subjected or not to shot peening
journal, December 2003
- Foschino, Roberto; Picozzi, Claudia; Civardi, Alessandro
- Journal of Food Engineering, Vol. 60, Issue 4
Evaluation of the Biological Sampling Kit (BiSKit) for Large-Area Surface Sampling
journal, December 2004
- Buttner, M. P.; Cruz, P.; Stetzenbach, L. D.
- Applied and Environmental Microbiology, Vol. 70, Issue 12
Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant
journal, March 2017
- Steven, Blaire; Hesse, Cedar; Soghigian, John
- Applied and Environmental Microbiology, Vol. 83, Issue 11
Optimizing methods and dodging pitfalls in microbiome research
journal, May 2017
- Kim, Dorothy; Hofstaedter, Casey E.; Zhao, Chunyu
- Microbiome, Vol. 5, Issue 1
Molecular Evidence for Metabolically Active Bacteria in the Atmosphere
journal, May 2016
- Klein, Ann M.; Bohannan, Brendan J. M.; Jaffe, Daniel A.
- Frontiers in Microbiology, Vol. 7
RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition
journal, March 2015
- McCarthy, Ann; Chiang, Edna; Schmidt, Marian L.
- PLOS ONE, Vol. 10, Issue 3
Characteristic and Concentration Distribution of Culturable Airborne Bacteria in Residential Environments in Beijing, China
journal, January 2014
- Fang, Zhiguo; Gong, Chanjuan; Ouyang, Zhiyun
- Aerosol and Air Quality Research, Vol. 14, Issue 3
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
journal, July 2013
- Blazewicz, Steven J.; Barnard, Romain L.; Daly, Rebecca A.
- The ISME Journal, Vol. 7, Issue 11
Protocols for dry DNA storage and shipment at room temperature
journal, June 2013
- Ivanova, Natalia V.; Kuzmina, Masha L.
- Molecular Ecology Resources, Vol. 13, Issue 5
The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review
journal, May 2016
- Leung, Marcus H. Y.; Lee, Patrick K. H.
- Microbiome, Vol. 4, Issue 1
Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes: Household air bacteria differ from occupant skin
journal, June 2015
- Wilkins, David; Leung, Marcus HY; Lee, Patrick KH
- Environmental Microbiology, Vol. 18, Issue 6
Microbiota fingerprints lose individually identifying features over time
journal, January 2017
- Wilkins, David; Leung, Marcus H. Y.; Lee, Patrick K. H.
- Microbiome, Vol. 5, Issue 1
Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children's classrooms
journal, December 2014
- Hospodsky, D.; Yamamoto, N.; Nazaroff, W. W.
- Indoor Air, Vol. 25, Issue 6
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
journal, May 2015
- Kurtz, Zachary D.; Müller, Christian L.; Miraldi, Emily R.
- PLOS Computational Biology, Vol. 11, Issue 5
UniFrac: an effective distance metric for microbial community comparison
journal, September 2010
- Lozupone, Catherine; Lladser, Manuel E.; Knights, Dan
- The ISME Journal, Vol. 5, Issue 2
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014
- Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.
- BMC Biology, Vol. 12, Issue 1
Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest
journal, January 2015
- Womack, A. M.; Artaxo, P. E.; Ishida, F. Y.
- Biogeosciences, Vol. 12, Issue 21
Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces
journal, November 2014
- Gibbons, Sean M.; Schwartz, Tara; Fouquier, Jennifer
- Applied and Environmental Microbiology, Vol. 81, Issue 2
Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon
journal, September 2012
- Chugani, S.; Kim, B. S.; Phattarasukol, S.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 41
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
Airborne bacterial assemblage in a zero carbon building: A case study
journal, August 2017
- Leung, M. H. Y.; Tong, X.; Tong, J. C. K.
- Indoor Air, Vol. 28, Issue 1
Ten questions concerning the microbiomes of buildings
journal, November 2016
- Adams, Rachel I.; Bhangar, Seema; Dannemiller, Karen C.
- Building and Environment, Vol. 109
UPARSE: highly accurate OTU sequences from microbial amplicon reads
journal, August 2013
- Edgar, Robert C.
- Nature Methods, Vol. 10, Issue 10
New perspectives on viable microbial communities in low-biomass cleanroom environments
journal, October 2012
- Vaishampayan, Parag; Probst, Alexander J.; La Duc, Myron T.
- The ISME Journal, Vol. 7, Issue 2
Transmission of viruses via our microbiomes
journal, December 2016
- Ly, Melissa; Jones, Marcus B.; Abeles, Shira R.
- Microbiome, Vol. 4, Issue 1
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Comparisons of seasonal fungal prevalence in indoor and outdoor air and in house dusts of dwellings in one Northeast American county1
journal, December 1999
- Ren, Ping; Jankun, Thomas M.; Leaderer, Brian P.
- Journal of Exposure Science & Environmental Epidemiology, Vol. 9, Issue 6
Human Occupancy as a Source of Indoor Airborne Bacteria
journal, April 2012
- Hospodsky, Denina; Qian, Jing; Nazaroff, William W.
- PLoS ONE, Vol. 7, Issue 4
Humans differ in their personal microbial cloud
journal, January 2015
- Meadow, James F.; Altrichter, Adam E.; Bateman, Ashley C.
- PeerJ, Vol. 3
PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip
journal, July 2011
- DeAngelis, Kristen M.; Wu, Cindy H.; Beller, Harry R.
- Applied and Environmental Microbiology, Vol. 77, Issue 18
Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems
journal, August 2017
- Emerson, Joanne B.; Adams, Rachel I.; Román, Clarisse M. Betancourt
- Microbiome, Vol. 5, Issue 1
Microbiota of the indoor environment: a meta-analysis
journal, October 2015
- Adams, Rachel I.; Bateman, Ashley C.; Bik, Holly M.
- Microbiome, Vol. 3, Issue 1
Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor
journal, October 2014
- Gómez-Silván, C.; Vílchez-Vargas, R.; Arévalo, J.
- Bioresource Technology, Vol. 169
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
journal, December 2016
- Carini, Paul; Marsden, Patrick J.; Leff, Jonathan W.
- Nature Microbiology, Vol. 2, Issue 3
Bacterial diversity in the indoor air of pharmaceutical environment
journal, January 2014
- Park, H. K.; Han, J. -H.; Joung, Y.
- Journal of Applied Microbiology, Vol. 116, Issue 3
Evolution of the indoor biome
journal, April 2015
- Martin, Laura J.; Adams, Rachel I.; Bateman, Ashley
- Trends in Ecology & Evolution, Vol. 30, Issue 4
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003
- Shannon, P.
- Genome Research, Vol. 13, Issue 11
Biodiversity and biogeography of the atmosphere
journal, November 2010
- Womack, Ann M.; Bohannan, Brendan J. M.; Green, Jessica L.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 365, Issue 1558
Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea
journal, April 2015
- Hugoni, Mylène; Agogué, Hélène; Taib, Najwa
- Microbial Ecology, Vol. 70, Issue 2
QIIME allows analysis of high-throughput community sequencing data
journal, April 2010
- Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
- Nature Methods, Vol. 7, Issue 5
Culture-Independent Analysis of Aerosol Microbiology in a Metropolitan Subway System
journal, March 2013
- Robertson, Charles E.; Baumgartner, Laura K.; Harris, J. Kirk
- Applied and Environmental Microbiology, Vol. 79, Issue 11
Factors Shaping the Human Exposome in the Built Environment: Opportunities for Engineering Control
journal, July 2017
- Dai, Dongjuan; Prussin, Aaron J.; Marr, Linsey C.
- Environmental Science & Technology, Vol. 51, Issue 14
Microbial seed banks: the ecological and evolutionary implications of dormancy
journal, January 2011
- Lennon, Jay T.; Jones, Stuart E.
- Nature Reviews Microbiology, Vol. 9, Issue 2
Activity of abundant and rare bacteria in a coastal ocean
journal, July 2011
- Campbell, B. J.; Yu, L.; Heidelberg, J. F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 31
Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics
journal, August 2014
- Leung, Marcus H. Y.; Wilkins, David; Li, Ellen K. T.
- Applied and Environmental Microbiology, Vol. 80, Issue 21
Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses
journal, April 2015
- Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.
- Frontiers in Microbiology, Vol. 6
Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes
journal, May 2015
- Adams, Rachel I.; Bhangar, Seema; Pasut, Wilmer
- PLOS ONE, Vol. 10, Issue 5
Solubilzation in formamide protects RNA from degradation
journal, January 1992
- Chomczynski, Piotr
- Nucleic Acids Research, Vol. 20, Issue 14
Sampling, extraction and measurement of bacteria, endotoxin, fungi and inflammatory potential of settling indoor dust
journal, January 2012
- Madsen, Anne Mette; Matthiesen, Christoffer B.; Frederiksen, Margit W.
- Journal of Environmental Monitoring, Vol. 14, Issue 12
Bayesian community-wide culture-independent microbial source tracking
journal, July 2011
- Knights, Dan; Kuczynski, Justin; Charlson, Emily S.
- Nature Methods, Vol. 8, Issue 9
Stenotrophomonas, Mycobacterium, and Streptomyces in home dust and air: associations with moldiness and other home/family characteristics
journal, March 2013
- Kettleson, E.; Kumar, S.; Reponen, T.
- Indoor Air, Vol. 23, Issue 5
The National Human Activity Pattern Survey (NHAPS): a resource for assessing exposure to environmental pollutants
journal, July 2001
- Klepeis, Neil E.; Nelson, William C.; Ott, Wayne R.
- Journal of Exposure Science & Environmental Epidemiology, Vol. 11, Issue 3
Thermal Injury and Recovery of Bacillus subtilis
journal, January 1972
- Miller, L. Lenkart; Ordal, Z. John
- Applied Microbiology, Vol. 24, Issue 6
Precursor Ribosomal Ribonucleic Acid and Ribosome Accumulation In Vivo During the Recovery of Salmonella typhimurium from Thermal Injury1
journal, January 1971
- Tomlins, Richard I.; Ordal, Z. John
- Journal of Bacteriology, Vol. 107, Issue 1
When stable RNA becomes unstable: the degradation of ribosomes in bacteria and beyond
journal, July 2013
- Maiväli, Ülo; Paier, Anton; Tenson, Tanel
- Biological Chemistry, Vol. 394, Issue 7
Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
journal, July 2014
- Shade, A.; Jones, S. E.; Caporaso, J. G.
- mBio, Vol. 5, Issue 4
Bacterial colonization and succession in a newly opened hospital
journal, May 2017
- Lax, Simon; Sangwan, Naseer; Smith, Daniel
- Science Translational Medicine, Vol. 9, Issue 391
Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis
journal, July 2017
- Byrd, Allyson L.; Deming, Clay; Cassidy, Sara K. B.
- Science Translational Medicine, Vol. 9, Issue 397
Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula
journal, June 2020
- Roggero, Paola; Liotto, Nadia; Pozzi, Chiara
- Nature Communications, Vol. 11, Issue 1
Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase
journal, May 2020
- Ballhausen, Max-Bernhard; Hewitt, Rebecca; Rillig, Matthias C.
- Scientific Reports, Vol. 10, Issue 1
Succession of endophytic fungi and arbuscular mycorrhizal fungi associated with the growth of plant and their correlation with secondary metabolites in the roots of plants
journal, April 2021
- Dang, Hanli; Zhang, Tao; Wang, Zhongke
- BMC Plant Biology, Vol. 21, Issue 1
An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.
text, January 2021
- O'Sullivan, Denise M.; Doyle, Ronan M.; Temisak, Sasithon
- Apollo - University of Cambridge Repository
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
text, January 2014
- Salter, Susannah; Cox, Michael J.; Turek, Elena M.
- Apollo - University of Cambridge Repository
Sparse and compositionally robust inference of microbial ecological networks
text, January 2014
- Kurtz, Zachary D.; Mueller, Christian L.; Miraldi, Emily R.
- arXiv
Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor
journal, October 2014
- Gómez-Silván, C.; Vílchez-Vargas, R.; Arévalo, J.
- Bioresource Technology, Vol. 169
Ten questions concerning the microbiomes of buildings
journal, November 2016
- Adams, Rachel I.; Bhangar, Seema; Dannemiller, Karen C.
- Building and Environment, Vol. 109
Evaluation of DNAstable™ for DNA storage at ambient temperature
journal, January 2014
- Howlett, Susanne E.; Castillo, Hilda S.; Gioeni, Lora J.
- Forensic Science International: Genetics, Vol. 8, Issue 1
Origin, dynamics, and implications of extracellular DNA pools in marine sediments
journal, December 2015
- Torti, Andrea; Lever, Mark Alexander; Jørgensen, Bo Barker
- Marine Genomics, Vol. 24
Factors Shaping the Human Exposome in the Built Environment: Opportunities for Engineering Control
journal, July 2017
- Dai, Dongjuan; Prussin, Aaron J.; Marr, Linsey C.
- Environmental Science & Technology, Vol. 51, Issue 14
Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses
journal, July 2013
- Blazewicz, Steven J.; Barnard, Romain L.; Daly, Rebecca A.
- The ISME Journal, Vol. 7, Issue 11
Bayesian community-wide culture-independent microbial source tracking
journal, July 2011
- Knights, Dan; Kuczynski, Justin; Charlson, Emily S.
- Nature Methods, Vol. 8, Issue 9
Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group
journal, February 2022
- Priest, Taylor; Heins, Anneke; Harder, Jens
- The ISME Journal, Vol. 16, Issue 6
Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants
journal, July 2021
- Julca, Irene; Ferrari, Camilla; Flores-Tornero, María
- Nature Plants, Vol. 7, Issue 8
Infant gut microbiota characteristics generally do not modify effects of lipid-based nutrient supplementation on growth or inflammation: secondary analysis of a randomized controlled trial in Malawi
journal, September 2020
- Hughes, Riley L.; Arnold, Charles D.; Young, Rebecca R.
- Scientific Reports, Vol. 10, Issue 1
Comparisons of seasonal fungal prevalence in indoor and outdoor air and in house dusts of dwellings in one Northeast American county1
journal, December 1999
- Ren, Ping; Jankun, Thomas M.; Leaderer, Brian P.
- Journal of Exposure Science & Environmental Epidemiology, Vol. 9, Issue 6
The National Human Activity Pattern Survey (NHAPS): a resource for assessing exposure to environmental pollutants
journal, July 2001
- Klepeis, Neil E.; Nelson, William C.; Ott, Wayne R.
- Journal of Exposure Science & Environmental Epidemiology, Vol. 11, Issue 3
Sampling, extraction and measurement of bacteria, endotoxin, fungi and inflammatory potential of settling indoor dust
journal, January 2012
- Madsen, Anne Mette; Matthiesen, Christoffer B.; Frederiksen, Margit W.
- Journal of Environmental Monitoring, Vol. 14, Issue 12
Activity of abundant and rare bacteria in a coastal ocean
journal, July 2011
- Campbell, B. J.; Yu, L.; Heidelberg, J. F.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 31
Strain-dependent diversity in the Pseudomonas aeruginosa quorum-sensing regulon
journal, September 2012
- Chugani, S.; Kim, B. S.; Phattarasukol, S.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 41
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
Solubilzation in formamide protects RNA from degradation
journal, January 1992
- Chomczynski, Piotr
- Nucleic Acids Research, Vol. 20, Issue 14
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Indoor air bacterial communities in Hong Kong households assemble independently of occupant skin microbiomes: Household air bacteria differ from occupant skin
journal, June 2015
- Wilkins, David; Leung, Marcus HY; Lee, Patrick KH
- Environmental Microbiology, Vol. 18, Issue 6
Protocols for dry DNA storage and shipment at room temperature
journal, June 2013
- Ivanova, Natalia V.; Kuzmina, Masha L.
- Molecular Ecology Resources, Vol. 13, Issue 5
Stenotrophomonas, Mycobacterium, and Streptomyces in home dust and air: associations with moldiness and other home/family characteristics
journal, March 2013
- Kettleson, E.; Kumar, S.; Reponen, T.
- Indoor Air, Vol. 23, Issue 5
Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children's classrooms
journal, December 2014
- Hospodsky, D.; Yamamoto, N.; Nazaroff, W. W.
- Indoor Air, Vol. 25, Issue 6
Airborne bacterial assemblage in a zero carbon building: A case study
journal, August 2017
- Leung, M. H. Y.; Tong, X.; Tong, J. C. K.
- Indoor Air, Vol. 28, Issue 1
Bacterial diversity in the indoor air of pharmaceutical environment
journal, January 2014
- Park, H. K.; Han, J. -H.; Joung, Y.
- Journal of Applied Microbiology, Vol. 116, Issue 3
Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea
journal, April 2014
- Zhang, Yao; Zhao, Zihao; Dai, Minhan
- Molecular Ecology, Vol. 23, Issue 9
Magnetic Bead Capture Eliminates PCR Inhibitors in Samples Collected from the Airborne Environment, Permitting Detection of Pneumocystis carinii DNA
journal, January 2001
- Maher, N.; Dillon, H. K.; Vermund, S. H.
- Applied and Environmental Microbiology, Vol. 67, Issue 1
Molecular Analysis of Shower Curtain Biofilm Microbes
journal, July 2004
- Kelley, S. T.; Theisen, U.; Angenent, L. T.
- Applied and Environmental Microbiology, Vol. 70, Issue 7
Thermal Injury and Recovery of
Bacillus subtilis
journal, December 1972
- Miller, L. Lenkart; Ordal, Z. John
- Applied Microbiology, Vol. 24, Issue 6
Thermally Induced Intracellular Alteration of Ribosomal Ribonucleic Acid1
journal, January 1970
- Rosenthal, Leonard J.; Iandolo, John J.
- Journal of Bacteriology, Vol. 103, Issue 3
Comparison of Polyurethane Foam to Nylon Flocked Swabs for Collection of Secretions from the Anterior Nares in Performance of a Rapid Influenza Virus Antigen Test in a Pediatric Emergency Department
journal, January 2010
- Scansen, Kimberly A.; Bonsu, Bema K.; Stoner, Erin
- Journal of Clinical Microbiology, Vol. 48, Issue 3
Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities
journal, October 2015
- Checinska, Aleksandra; Probst, Alexander J.; Vaishampayan, Parag
- Microbiome, Vol. 3, Issue 1
The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review
journal, May 2016
- Leung, Marcus H. Y.; Lee, Patrick K. H.
- Microbiome, Vol. 4, Issue 1
Microbiota fingerprints lose individually identifying features over time
journal, January 2017
- Wilkins, David; Leung, Marcus H. Y.; Lee, Patrick K. H.
- Microbiome, Vol. 5, Issue 1
Optimizing methods and dodging pitfalls in microbiome research
journal, May 2017
- Kim, Dorothy; Hofstaedter, Casey E.; Zhao, Chunyu
- Microbiome, Vol. 5, Issue 1
Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems
journal, August 2017
- Emerson, Joanne B.; Adams, Rachel I.; Román, Clarisse M. Betancourt
- Microbiome, Vol. 5, Issue 1
Human Occupancy as a Source of Indoor Airborne Bacteria
journal, April 2012
- Hospodsky, Denina; Qian, Jing; Nazaroff, William W.
- PLoS ONE, Vol. 7, Issue 4
The Diversity and Distribution of Fungi on Residential Surfaces
journal, November 2013
- Adams, Rachel I.; Miletto, Marzia; Taylor, John W.
- PLoS ONE, Vol. 8, Issue 11
Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes
journal, May 2015
- Adams, Rachel I.; Bhangar, Seema; Pasut, Wilmer
- PLOS ONE, Vol. 10, Issue 5
Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes
journal, August 2015
- Mahnert, Alexander; Vaishampayan, Parag; Probst, Alexander J.
- PLOS ONE, Vol. 10, Issue 8
Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants
journal, April 2016
- Weikl, Fabian; Tischer, Christina; Probst, Alexander J.
- PLOS ONE, Vol. 11, Issue 4
Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses
journal, April 2015
- Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.
- Frontiers in Microbiology, Vol. 6
Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics
journal, January 2009
- Poretsky, Rachel S.; Gifford, Scott; Rinta-Kanto, Johanna
- Journal of Visualized Experiments, Issue 0
Sparse and compositionally robust inference of microbial ecological networks
text, January 2014
- Kurtz, Zachary D.; Mueller, Christian L.; Miraldi, Emily R.
- arXiv
Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest
journal, January 2015
- Womack, A. M.; Artaxo, P. E.; Ishida, F. Y.
- Biogeosciences, Vol. 12, Issue 21
Humans differ in their personal microbial cloud
journal, January 2015
- Meadow, James F.; Altrichter, Adam E.; Bateman, Ashley C.
- PeerJ, Vol. 3
Works referencing / citing this record:
Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment
journal, July 2019
- Horve, Patrick F.; Lloyd, Savanna; Mhuireach, Gwynne A.
- Journal of Exposure Science & Environmental Epidemiology, Vol. 30, Issue 2
RNA-based qPCR as a tool to quantify and to characterize dual-species biofilms
journal, September 2019
- Magalhães, Andreia Patrícia; França, Ângela; Pereira, Maria Olívia
- Scientific Reports, Vol. 9, Issue 1
Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities
journal, January 2019
- Jia, Yangyang; Leung, Marcus H. Y.; Tong, Xinzhao
- mSystems, Vol. 4, Issue 1
Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment
journal, July 2019
- Horve, Patrick F.; Lloyd, Savanna; Mhuireach, Gwynne A.
- Journal of Exposure Science & Environmental Epidemiology, Vol. 30, Issue 2
Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities
journal, January 2019
- Jia, Yangyang; Leung, Marcus H. Y.; Tong, Xinzhao
- mSystems, Vol. 4, Issue 1
The environmental risk assessment of cell-processing facilities for cell therapy in a Japanese academic institution
journal, August 2020
- Mizuno, Mitsuru; Endo, Kentaro; Katano, Hisako
- PLOS ONE, Vol. 15, Issue 8
Figures / Tables found in this record:
Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.