Exploring the microbiome of the built environment: A primer on four biological methods available to building professionals

References

• Amann , R. I. , Ludwig , W. and Schleifer , K. H. 1995 . Phylogenetic indentification and in-situ detection of individual microbial-cells without cultivation . Microbiological Reviews , 59 ( 1 ) : 143 – 69 .
   PubMedGoogle Scholar
• Amend , A. S. , Seifert , K. A. , Samson , R. and Bruns , T. D. 2010 . Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics . Proceedings of the National Academy of Sciences of the United States of America , 107 ( 31 ) : 13748 – 53 .
   PubMed Web of Science ®Google Scholar
• Angenent , L. T. , Kelley , S. T. , St Amand , A. , Pace , N. R. and Hernandez , M. T. 2005 . Molecular identification of potential pathogens in water and air of a hospital therapy pool . Proceedings of the National Academy of Sciences of the United States of America , 102 ( 13 ) : 4860 – 5 .
   PubMed Web of Science ®Google Scholar
• Berhane , Z. , Perez , H. R. and Zimmerman , N. J. 2006 . Evaluation of culturable particle load on HVAC filters before and after remediation: A pilot study . Indoor and Built Environment , 15 ( 6 ) : 525 – 33 .
   Web of Science ®Google Scholar
• Bowers , R. M. , Sullivan , A. P. , Costello , E. K. , Collett , J. L. Jr. , Knight , R. and Fierer , N. 2011 . Sources of bacteria in outdoor air across cities in the Midwestern United States . Applied and Environmental Microbiology , 77 ( 18 ) : 6350 – 6 .
   PubMed Web of Science ®Google Scholar
• Burge , S. , Hedge , A. , Wilson , S. , Bass , J. H. and Robertson , A. 1987 . Sick building syndrome—A study of 4373 office workers . Annals of Occupational Hygiene , 31 ( 4 ) : 493 – 504 .
   PubMed Web of Science ®Google Scholar
• Chang , C. W. and Chou , F. C. 2011 . Methodologies for quantifying culturable, viable, and total Legionella pneumophila in indoor air . Indoor Air , 21 ( 4 ) : 291 – 9 .
   PubMed Web of Science ®Google Scholar
• Chao , A. 1987 . Estimating the population size for capture-recapture data with unequal catchability . Biometrics , 43 ( 4 ) : 783 – 91 .
   PubMed Web of Science ®Google Scholar
• Deloge-Abarkan , M. , Ha , T. L. , Robine , E. , Zmirou-Navier , D. and Mathieu , L. 2007 . Detection of airborne Legionella while showering using liquid impingement and fluorescent in situ hybridization (FISH) . Journal of Environmental Monitoring , 9 ( 1 ) : 91 – 7 .
   PubMed Web of Science ®Google Scholar
• Farnsworth , J. E. , Goyal , S. M. , Won Kim , S. , Kuehn , T. H. , Raynor , P. C. , Ramakrishnan , M. A. , Anantharaman , S. and Tang , W. 2006 . Development of a method for bacteria and virus recovery from heating, ventilation, and air conditioning (HVAC) filters . Journal of Environmental Monitoring , 8 ( 10 ) : 1006 – 13 .
   PubMed Web of Science ®Google Scholar
• Feinstein , L. M. , Sul , W. J. and Blackwood , C. B. 2009 . Assessment of bias associated with incomplete extraction of microbial DNA from soil . Applied and Environmental Microbiology , 75 ( 16 ) : 5428 – 33 .
   PubMed Web of Science ®Google Scholar
• Fierer , N. , Liu , Z. , Rodriguez-Hernandez , M. , Knight , R. , Henn , M. and Hernandez , M. T. 2008 . Short-term temporal variability in airborne bacterial and fungal populations . Applied and Environmental Microbiology , 74 ( 1 ) : 200 – 7 .
   PubMed Web of Science ®Google Scholar
• Gent , J. F. , Belanger , K. , Triche , E. W. , Bracken , M. B. , Beckett , W. S. and Leaderer , B. P. 2009 . Association of pediatric asthma severity with exposure to common household dust allergens . Environmental Research , 109 ( 6 ) : 768 – 74 .
   PubMed Web of Science ®Google Scholar
• Gostinčar , C. , Grube , M. and Gunde-Cimerman , N. 2011 . Evolution of fungal pathogens in domestic environments? . Fungal Biology , 115 ( 10 ) : 1008 – 18 .
   PubMed Web of Science ®Google Scholar
• Halonen , M. , Stern , D. A. , Wright , A. L. , Taussig , L. M. and Martinez , F. D. 1997 . Alternaria as a major allergen for asthma in children raised in a desert environment . American Journal of Respiratory and Critical Care Medicine Home , 155 ( 4 ) : 1356 – 61 .
   PubMed Web of Science ®Google Scholar
• Harris , J. L. 2000 . Mycopathologia. Edited by: Hoog , G. S.d. , Guarro , J. , Gene , J. and Figueras , M. J. Atlas of clinical fungi.
   Google Scholar
• Harrison , J. , Pickering , C. A.C. , Faragher , E. B. , Austwick , P. K.C. , Little , S. A. and Lawton , L. 1992 . An investigation of the relationship between micriboal and particle indoor air-pollution and sick building syndrome . Respiratory Medicine , 86 ( 3 ) : 225 – 35 .
   PubMed Web of Science ®Google Scholar
• Hedayati , M. T. , Pasqualotto , A. C. , Warn , P. A. , Bowyer , P. and Denning , D. W. 2007 . Aspergillus flavus: Human pathogen, allergen and mycotoxin producer . Microbiology (UK) , 153 : 1677 – 92 .
   PubMed Web of Science ®Google Scholar
• Horner , W. E. , Helbling , A. , Salvaggio , J. E. and Lehrer , S. B. 1995 . Fungal allergens . Clinical Microbiology Reviews , 8 ( 2 ) : 161 – 79 .
   PubMed Web of Science ®Google Scholar
• Hospodsky , D. , Yamamoto , N. and Peccia , J. 2010 . Accuracy, precision, and method detection limits of quantitative PCR for airborne bacteria and fungi . Applied and Environmental Microbiology , 76 ( 21 ) : 7004 – 12 .
   PubMed Web of Science ®Google Scholar
• Kembel , S. W. , Jones , E. , Kline , J. , Northcutt , D. , Stenson , J. , Womack , A. M. , Bohannan , B. J.M. , Brown , G. Z. and Green , J. L. 2012 . Architectural design influences the diversity and structure of the built environment microbiome . ISME Journal , : 1 – 11 .
   Google Scholar
• Kemp , P. C. , Neumeister-Kemp , H. G. , Lysek , G. and Murray , F. 2001 . Survival and growth of micro-organisms on air filtration media during initial loading . Atmospheric Environment , 35 ( 28 ) : 4739 – 49 .
   Web of Science ®Google Scholar
• King , M. D. and McFarland , A. R. 2011 . Bioaerosol sampling with a wetted wall cyclone: cell culturability and DNA integrity of Escherichia coli bacteria. . Aerosol Science and Technology , 46 ( 1 ) : 82 – 93 .
   Web of Science ®Google Scholar
• Koch , A. , Heilemann , K. J. , Bischof , W. , Heinrich , J. and Wichmann , H. E. 2000 . Indoor viable mold spores—A comparison between two cities, Erfurt (eastern Germany) and Hamburg (western Germany) . Allergy , 55 ( 2 ) : 176 – 80 .
   PubMed Web of Science ®Google Scholar
• Lebuhn , M. , Effenberger , M. , Garces , G. , Gronauer , A. and Wilderer , P. A. 2004 . Evaluating real-time PCR for the quantification of distinct pathogens and indicator organisms in environmental samples . Water Science and Technology , 50 ( 1 ) : 263 – 70 .
   PubMed Web of Science ®Google Scholar
• Liu , K.-L. , Porras-Alfaro , A. , Kuske , C. R. , Eichorst , S. A. and Xie , G. 2012 . Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes . Applied and Environmental Microbiolog , 78 ( 5 ) : 1523 – 33 .
   PubMed Web of Science ®Google Scholar
• Liu , Z. , DeSantis , T. Z. , Andersen , G. L. and Knight , R. 2008 . Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers . Nucleic Acids Research , 36 ( 18 ) : e120
   PubMedGoogle Scholar
• Maus , R. , Goppelsröder , A. and Umhauer , H. 2001 . Survival of bacterial and mold spores in air filter media . Atmospheric Environment , 35 ( 1 ) : 105 – 13 .
   Web of Science ®Google Scholar
• Mendell , M. J. , Mirer , A. G. , Cheung , K. , Tong , M. and Douwes , J. 2011 . Respiratory and allergic health effects of dampness, mold, and dampness-related agents: A review of the epidemiologic evidence . Environmental Health Perspectives , 119 ( 6 ) : 748 – 56 .
   PubMed Web of Science ®Google Scholar
• Möritz , M. , Peters , H. , Nipko , B. and Rüden , H. 2001 . Capability of air filters to retain airborne bacteria and molds in heating, ventilating and air-conditioning (HVAC) systems . International Journal of Hygiene and Environmental Health , 203 ( 5–6 ) : 401 – 9 .
   PubMed Web of Science ®Google Scholar
• Moritz , M. , Schleibinger , H. and Ruden , H. 1998 . Investigations on the survival time of outdoor microorganisms on air filters . Zentralblatt Fur Hygiene Und Umweltmedizin , 201 ( 2 ) : 125 – 33 .
   PubMedGoogle Scholar
• Mudarri , D. and Fisk , W. J. 2007 . Public health and economic impact of dampness and mold . Indoor Air , 17 ( 3 ) : 226 – 35 .
   PubMed Web of Science ®Google Scholar
• Noris , F. , Siegel , J. A. and Kinney , K. A. 2011 . Evaluation of HVAC filters as a sampling mechanism for indoor microbial communities . Atmospheric Environment , 45 ( 2 ) : 338 – 46 .
   Web of Science ®Google Scholar
• Pakarinen , J. , Hyvarinen , A. , Salkinoja-Salonen , M. , Laitinen , S. , Nevalainen , A. , Makela , M. J. , Haahtela , T. and von Hertzen , L. 2008 . Predominance of gram-positive bacteria in house dust in the low-allergy risk Russian Karelia . Environmental Microbiology , 10 ( 12 ) : 3317 – 25 .
   PubMed Web of Science ®Google Scholar
• Peccia , J. , Hospodsky , D. and Bibby , K. 2011 . New directions: A revolution in DNA sequencing now allows for the meaningful integration of biology with aerosol science . Atmospheric Environment , 45 ( 10 ) : 1896 – 97 .
   Web of Science ®Google Scholar
• Pietarinen , V. M. , Rintala , H. , Hyvarinen , A. , Lignell , U. , Karkkainen , P. and Nevalainen , A. 2008 . Quantitative PCR analysis of fungi and bacteria in building materials and comparison to culture-based analysis . Journal of Environmental Monitoring , 10 ( 5 ) : 655 – 63 .
   PubMed Web of Science ®Google Scholar
• Pitkaranta , M. , Meklin , T. , Hyvarinen , A. , Paulin , L. , Auvinen , P. , Nevalainen , A. and Rintala , H. 2008 . Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture . Applied and Environmental Microbiology , 74 ( 1 ) : 233 – 44 .
   PubMed Web of Science ®Google Scholar
• Rintala , H. , Pitkaranta , M. , Toivola , M. , Paulin , L. and Nevalainen , A. 2008 . Diversity and seasonal dynamics of bacterial community in indoor environment . BMC Microbiology , 8 : 56
   PubMed Web of Science ®Google Scholar
• Ronaghi , M. 2001 . Pyrosequencing sheds light on DNA sequencing . Genome Research , 11 ( 1 ) : 3 – 11 .
   PubMed Web of Science ®Google Scholar
• Rudnick , S. N. and Milton , D. K. 2003 . Risk of indoor airborne infection transmission estimated from carbon dioxide concentration . Indoor Air , 13 ( 3 ) : 237 – 45 .
   PubMed Web of Science ®Google Scholar
• Salyers , A. and Whitt , D. 2002 . Bacteria pathogens, a molecular approach. , Washington , D.C. : ASM Press .
   Google Scholar
• Sanger , F. , Nicklen , S. and Coulson , A. R. 1977 . DNA sequencing with chain-terminating inhibitors . Proceedings of the National Academy of Sciences of the United States of America , 74 ( 12 ) : 5463 – 7 .
   PubMed Web of Science ®Google Scholar
• Stanley , N. J. , Kuehn , T. H. , Kim , S. W. , Raynor , P. C. , Anantharaman , S. , Ramakrishnan , M. A. and Goyal , S. M. 2008 . Background culturable bacteria aerosol in two large public buildings using HVAC filters as long term, passive, high-volume air samplers . Journal of Environmental Monitoring , 10 ( 4 ) : 474 – 81 .
   PubMed Web of Science ®Google Scholar
• Sterling , T. R. and Haas , D. W. 2006 . Transmission of Mycobacterium tuberculosis from health care workers . New England Journal of Medicine , 355 ( 2 ) : 118 – 21 .
   PubMed Web of Science ®Google Scholar
• Suzuki , M. T. and Giovannoni , S. J. 1996 . Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR . Applied and Environmental Microbiology , 62 ( 2 ) : 625 – 30 .
   PubMed Web of Science ®Google Scholar
• Täubel , M. , Rintala , H. , Pitkäranta , M. , Paulin , L. , Laitinen , S. , Pekkanen , J. , Hyvärinen , A. and Nevalainen , A. 2009 . The occupant as a source of house dust bacteria . Journal of Allergy and Clinical Immunology , 124 ( 4 ) : 834 – 40 .
   PubMed Web of Science ®Google Scholar
• Tedersoo , L. , Nilsson , R. H. , Abarenkov , K. , Jairus , T. , Sadam , A. , Saar , I. , Bahram , M. , Bechem , E. , Chuyong , G. and Kõljalg , U. 2010 . 454 pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases . New Phytologist , 188 ( 1 ) : 291 – 301 .
   PubMed Web of Science ®Google Scholar
• Toivola , M. , Alm , S. , Reponen , T. , Kolari , S. and Nevalainen , A. 2002 . Personal exposures and microenvironmental concentrations of particles and bioaerosols . Journal of Environmental Monitoring , 4 ( 1 ) : 166 – 74 .
   PubMed Web of Science ®Google Scholar
• Tringe , S. G. and Hugenholtz , P. 2008 . A renaissance for the pioneering 16S rRNA gene . Current Opinion in Microbiology , 11 ( 5 ) : 442 – 6 .
   PubMed Web of Science ®Google Scholar
• Tringe , S. G. , Zhang , T. , Liu , X. G. , Yu , Y. T. , Lee , W. H. , Yap , J. , Yao , F. , Suan , S. T. , Ing , S. K. , Haynes , M. , Rohwer , F. , Wei , C. L. , Tan , P. , Bristow , J. , Rubin , E. M. and Ruan , Y. J. 2008 . The airborne metagenome in an indoor urban environment . PloS One , 3 ( 4 ) : 1 – 10 .
   Web of Science ®Google Scholar
• Verhoeff , A. P. and Burge , H. A. 1997 . Health risk assessment of fungi in home environments . Annals of Allergy, Asthma & Immunology , 78 ( 6 ) : 544 – 56 .
   PubMed Web of Science ®Google Scholar
• Vesper , S. , McKinstry , C. , Hartmann , C. , Neace , M. , Yoder , S. and Vesper , A. 2008 . Quantifying fungal viability in air and water samples using quantitative PCR after treatment with propidium monoazide (PMA) . Journal of Microbiological Methods , 72 ( 2 ) : 180 – 4 .
   PubMed Web of Science ®Google Scholar
• Vesper , S. , McKinstry , C. , Haugland , R. , Wymer , L. , Bradham , K. , Ashley , P. , Cox , D. , Dewalt , G. and Friedman , W. 2007 . Development of an environmental relative moldiness index for U.S. homes . Journal of Exposure Science and Environmental Epidemiology , 49 ( 8 ) : 829 – 33 .
   Google Scholar