Abstract
People spend a lot of time indoors and the indoor microbiome is a major part of the environment that we are exposed to. However, awareness of the exposure to the indoor microbiome and its health effects remains poor. Outdoor environment (soil and air), indoor sources (ventilation, dampness and building materials), human occupants, and pets compose the indoor microbial community. It has been estimated that up to 500–1000 different species can be present in house dust. House dust is a major source and reservoir of indoor microbiome, which influences human microbiome and determines health and disease. Herein, we review the origins and the components of the fungal and bacterial communities in house dust and their possible effect on human health, in particular on allergic disorders, intestinal microbiome, and immune responses. We expect to lay a solid foundation for the further study on the mechanisms of how the house dust microbes interact with the host microbiome and the human immune system.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Adams RI, Miletto M, Taylor JW, Bruns TD (2013) Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 7:1262–1273. https://doi.org/10.1038/ismej.2013.28
Adams RI, Miletto M, Lindow SE, Taylor JW, Bruns TD (2014) Airborne bacterial communities in residences: similarities and differences with fungi. PLoS One 9:e91283. https://doi.org/10.1371/journal.pone.0091283
Adhikari A, Kettleson EM, Vesper S, Kumar S, Popham DL, Schaffer C, Indugula R, Chatterjee K, Allam KK, Grinshpun SA, Reponen T (2014) Dustborne and airborne Gram-positive and Gram-negative bacteria in high versus low ERMI homes. Sci Total Environ 482-483:92–99. https://doi.org/10.1016/j.scitotenv.2014.02.110
Alenius H, Pakarinen J, Saris O, Andersson MA, Leino M, Sirola K, Majuri ML, Niemelä J, Matikainen S, Wolff H, von Hertzen L, Mäkelä M, Haahtela T, Salkinoja-Salonen M (2009) Contrasting immunological effects of two disparate dusts - preliminary observations. Int Arch Allergy Immunol 149:81–90
Amend AS, Seifert KA, Samson R, Bruns TD (2010) Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci U S A 107:13748–13753. https://doi.org/10.1073/pnas.1000454107
Andersen B, Frisvad JC, Sondergaard I, Rasmussen IS, Larsen LS (2011) Associations between fungal species and water-damaged building materials. Appl Environ Microbiol 77:4180–4188. https://doi.org/10.1128/Aem.02513-10
Andersson AM, Weiss N, Rainey F, Salkinoja-Salonen MS (1999) Dust-borne bacteria in animal sheds, schools and children’s day care centres. J Appl Microbiol 86:622–634. https://doi.org/10.1046/j.1365-2672.1999.00706.x
Ayerst G (1969) The effects of moisture and temperature on growth and spore germination in some fungi. J Stored Prod Res 5:127–141. https://doi.org/10.1016/0022-474X(69)90055-1
Barberan A et al (2015a) The ecology of microscopic life in household dust. Proc Biol Sci 282:20151139. https://doi.org/10.1098/rspb.2015.1139
Barberan A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N (2015b) Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A 112:5756–5761. https://doi.org/10.1073/pnas.1420815112
Beguin H (1995) Mould biodiversity in homes II. Analysis of mattress dust. Aerobiologia 11:3–10. https://doi.org/10.1007/bf02136138
Beguin H, Nolard N (1996) Prevalence of fungi in carpeted floor environment: analysis of dust samples from living-rooms, bedrooms, offices and school classrooms. Aerobiologia 12:113–120. https://doi.org/10.1007/bf02446603
Bouillard L, Michel O, Dramaix M, Devleeschouwer M (2005) Bacterial contamination of indoor air, surfaces, and settled dust, and related dust endotoxin concentrations in healthy office buildings. Ann Agric Environ Med 12:187–192
Braun-Fahrlander C et al (2002) Environmental exposure to endotoxin and its relation to asthma in school-age children. N Engl J Med 347:869–877. https://doi.org/10.1056/Nejmoa020057
Chen YS, Jan RL, Lin YL, Chen HH, Wang JY (2010) Randomized placebo-controlled trial of lactobacillus on asthmatic children with allergic rhinitis. Pediatr Pulmonol 45:1111–1120. https://doi.org/10.1002/ppul.21296
Dannemiller KC, Mendell MJ, Macher JM, Kumagai K, Bradman A, Holland N, Harley K, Eskenazi B, Peccia J (2014) Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. Indoor Air 24:236–247. https://doi.org/10.1111/ina.12072
Dannemiller KC, Gent JF, Leaderer BP, Peccia J (2016) Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children. Indoor Air 26:179–192. https://doi.org/10.1111/ina.12205
Dannemiller KC, Weschler CJ, Peccia J (2017) Fungal and bacterial growth in floor dust at elevated relative humidity levels. Indoor Air 27:354–363. https://doi.org/10.1111/ina.12313
Debarry J, Hanuszkiewicz A, Stein K, Holst O, Heine H (2010) The allergy-protective properties of Acinetobacter lwoffii F78 are imparted by its lipopolysaccharide. Allergy 65:690–697. https://doi.org/10.1111/j.1398-9995.2009.02253.x
Douwes J, Zuidhof A, Doekes G, van der Zee S, Wouters I, Boezen HM, Brunekreef B (2000) (1 -> 3)-beta-D-glucan and endotoxin in house dust and peak flow variability in children. Am J Respir Crit Care Med 162:1348–1354. https://doi.org/10.1164/ajrccm.162.4.9909118
Eder W, von Mutius E (2004) Hygiene hypothesis and endotoxin: what is the evidence? Curr Opin Allergy Clin Immunol 4:113–117
Ege MJ, Mayer M, Normand AC, Genuneit J, Cookson WOCM, Braun-Fahrländer C, Heederik D, Piarroux R, von Mutius E (2011) Exposure to environmental microorganisms and childhood asthma. N Engl J Med 364:701–709. https://doi.org/10.1056/NEJMoa1007302
Ege MJ, Mayer M, Schwaiger K, Mattes J, Pershagen G, van Hage M, Scheynius A, Bauer J, von Mutius E (2012) Environmental bacteria and childhood asthma. Allergy 67:1565–1571. https://doi.org/10.1111/all.12028
Fujimura KE et al (2010) Man’s best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol 126:410–412, 412 e411-413. https://doi.org/10.1016/j.jaci.2010.05.042
Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, Zoratti E, Ownby D, Lukacs NW, Lynch SV (2014) House dust exposure mediates gut microbiome lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A 111:805–810. https://doi.org/10.1073/pnas.1310750111
Gliniewicz A et al (2003) German cockroaches (Blattella Germanica L.) as a potential source of pathogens causing nosocomial infections. Indoor Built Environ. https://doi.org/10.1177/1420326x03012001009
Goyert SM, Ferrero E, Rettig WJ, Yenamandra AK, Obata F, Le Beau MM (1988) The CD14 monocyte differentiation antigen maps to a region encoding growth factors and receptors. Science 239:497–500
Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, Laatikainen T, Karisola P, Auvinen P, Paulin L, Makela MJ, Vartiainen E, Kosunen TU, Alenius H, Haahtela T (2012) Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci U S A 109:8334–8339. https://doi.org/10.1073/pnas.1205624109
Hanson B, Zhou Y, Bautista EJ, Urch B, Speck M, Silverman F, Muilenberg M, Phipatanakul W, Weinstock G, Sodergren E, Gold DR, Sordillo JE (2016) Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study. Environ Sci Processes Impacts 18:713–724. https://doi.org/10.1039/c5em00639b
Heldal KK, Halstensen AS, Thorn J, Eduard W, Halstensen TS (2003) Airway inflammation in waste handlers exposed to bioaerosols assessed by induced sputum. Eur Respir J 21:641–645
Hospodsky D, Qian J, Nazaroff WW, Yamamoto N, Bibby K, Rismani-Yazdi H, Peccia J (2012) Human occupancy as a source of indoor airborne bacteria. PLoS One 7:e34867. https://doi.org/10.1371/journal.pone.0034867
Hospodsky D, Yamamoto N, Nazaroff WW, Miller D, Gorthala S, Peccia J (2015) Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children’s classrooms. Indoor Air 25:641–652. https://doi.org/10.1111/ina.12172
Iossifova YY, Reponen T, Bernstein DI, Levin L, Kalra H, Campo P, Villareal M, Lockey J, Hershey GKK, LeMasters G (2007) House dust (1-3)-beta-D-glucan and wheezing in infants. Allergy 62:504–513. https://doi.org/10.1111/j.1398-9995.2007.01340.x
Jaakkola JJK, Hwang BF, Jaakkola MS (2010) Home dampness and molds as determinants of allergic rhinitis in childhood: a 6-year, population-based cohort study. Am J Epidemiol 172:451–459. https://doi.org/10.1093/aje/kwq110
Kaarakainen P, Rintala H, Vepsalainen A, Hyvarinen A, Nevalainen A, Meklin T (2009) Microbial content of house dust samples determined with qPCR. Sci Total Environ 407:4673–4680. https://doi.org/10.1016/j.scitotenv.2009.04.046
Kabesch M (2006) A glitch in the switch? Of endotoxin, CD14, and allergy. Am J Respir Crit Care Med 174:365–366. https://doi.org/10.1164/rccm.2604006
Karvala K, Toskala E, Luukkonen R, Lappalainen S, Uitti J, Nordman H (2010) New-onset adult asthma in relation to damp and moldy workplaces. Int Arch Occup Environ Health 83:855–865. https://doi.org/10.1007/s00420-010-0507-5
Kembel SW, Jones E, Kline J, Northcutt D, Stenson J, Womack AM, Bohannan BJM, Brown GZ, Green JL (2012) Architectural design influences the diversity and structure of the built environment microbiome. ISME J 6:1469–1479. https://doi.org/10.1038/ismej.2011.211
Khoo SK, Mäkelä M, Chandler D, Schultz EN, Jamieson SE, Goldblatt J, Haahtela T, LeSouëf P, Zhang G (2016) No simple answers for the Finnish and Russian Karelia allergy contrast: methylation of CD14 gene. Pediatr Allergy Immunol 27:721–727. https://doi.org/10.1111/pai.12612
Korpi A, Pasanen AL, Pasanen P, Kalliokoski P (1997) Microbial growth and metabolism in house dust. Int Biodeterior Biodegrad 40:19–27
Korthals M, Ege M, Lick S, von Mutius E, Bauer J (2008) Occurrence of Listeria spp. in mattress dust of farm children in Bavaria. Environ Res 107:299–304. https://doi.org/10.1016/j.envres.2008.02.007
Laubach CA (1916) Spore-bearing bacteria in dust. J Bacteriol 1:493
Macher JM (2001) Review of methods to collect settled dust and isolate culturable microorganisms. Indoor Air 11:99–110
Marsh DG, Neely J, Breazeale D, Ghosh B, Freidhoff L, Ehrlich-Kautzky E, Schou C, Krishnaswamy G, Beaty T (1994) Linkage analysis of IL4 and other chromosome 5q31.1 markers and total serum immunoglobulin E concentrations. Science 264:1152–1156
Martinez FD (1999) Maturation of immune responses at the beginning of asthma. J Allergy Clin Immunol 103:355–361. https://doi.org/10.1016/S0091-6749(99)70456-2
Mckinney ML (2006) Urbanization as a major cause of biotic homogenization. Biol Conserv 127:247–260
Meadow JF, Altrichter AE, Kembel SW, Kline J, Mhuireach G, Moriyama M, Northcutt D, O'Connor TK, Womack AM, Brown GZ, Green JL, Bohannan BJM (2014) Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source. Indoor Air 24:41–48. https://doi.org/10.1111/ina.12047
Moschandreas DJ, Pagilla KR, Storino LV (2003) Time and space uniformity of indoor bacteria concentrations in Chicago area residences. Aerosol Sci Technol 37:899–906. https://doi.org/10.1080/02786820300935
Mutius V et al (2010) Exposure to endotoxin or other bacterial components might protect against the development of atopy. Clin Exp Allergy 30:1230–1234
Nevalainen A, Taubel M, Hyvarinen A (2015) Indoor fungi: companions and contaminants. Indoor Air 25:125–156. https://doi.org/10.1111/ina.12182
Noris F, Siegel JA, Kinney KA (2011) Evaluation of HVAC filters as a sampling mechanism for indoor microbial communities. Atmos Environ 45:338–346. https://doi.org/10.1016/j.atmosenv.2010.10.017
Pakarinen J, Hyvärinen A, Salkinoja-Salonen M, Laitinen S, Nevalainen A, Mäkelä MJ, Haahtela T, von Hertzen L (2008) Predominance of Gram-positive bacteria in house dust in the low-allergy risk Russian Karelia. Environ Microbiol 10:3317–3325. https://doi.org/10.1111/j.1462-2920.2008.01723.x
Pitkaranta M, Meklin T, Hyvarinen A, Paulin L, Auvinen P, Nevalainen A, Rintala H (2008) Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture. Appl Environ Microbiol 74:233–244. https://doi.org/10.1128/AEM.00692-07
Pitkaranta M et al (2011) Molecular profiling of fungal communities in moisture damaged buildings before and after remediation--a comparison of culture-dependent and culture-independent methods. BMC Microbiol 11:235. https://doi.org/10.1186/1471-2180-11-235
Pugin J et al (1994) Cd14 is a pattern-recognition receptor. Immunity 1:509–516. https://doi.org/10.1016/1074-7613(94)90093-0
Raison CL, Lowry CA, Rook GA (2010) Inflammation, sanitation, and consternation: loss of contact with coevolved, tolerogenic microorganisms and the pathophysiology and treatment of major depression. Arch Gen Psychiatry 67:1211–1224. https://doi.org/10.1001/archgenpsychiatry.2010.161
Riedler J, Eder W, Oberfeld G, Schreuer M (2000) Austrian children living on a farm have less hay fever, asthma and allergic sensitization. Clin Exp Allergy 30:194–200
Riedler J, Braun-Fahrländer C, Eder W, Schreuer M, Waser M, Maisch S, Carr D, Schierl R, Nowak D, von Mutius E (2001) Exposure to farming in early life and development of asthma and allergy: a cross-sectional survey. Lancet 358:1129–1133. https://doi.org/10.1016/S0140-6736(01)06252-3
Rintala H, Pitkaranta M, Toivola M, Paulin L, Nevalainen A (2008) Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol 8:56. https://doi.org/10.1186/1471-2180-8-56
Rintala H, Pitkaranta M, Taubel M (2012) Microbial communities associated with house dust. Adv Appl Microbiol 78:75–120. https://doi.org/10.1016/B978-0-12-394805-2.00004-X
Rook GA, Martinelli R, Brunet LR (2003) Innate immune responses to mycobacteria and the downregulation of atopic responses. Curr Opin Allergy Clin Immunol 3:337–342. https://doi.org/10.1097/01.all.0000092602.76804.ad
Round JL, Lee SM, Li J, Tran G, Jabri B, Chatila TA, Mazmanian SK (2011) The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science 332:974–977. https://doi.org/10.1126/science.1206095
Rylander R, Holt PG (1998) (1-->3)-beta-D-glucan and endotoxin modulate immune response to inhaled allergen. Mediat Inflamm 7:105–110. https://doi.org/10.1080/09629359891252
Sharpe RA, Bearman N, Thornton CR, Husk K, Osborne NJ (2015) Indoor fungal diversity and asthma: a meta-analysis and systematic review of risk factors. J Allergy Clin Immunol 135:110–122. https://doi.org/10.1016/j.jaci.2014.07.002
Simpson A, John SL, Jury F, Niven R, Woodcock A, Ollier WER, Custovic A (2006) Endotoxin exposure, CD14, and allergic disease - an interaction between genes and the environment. Am J Respir Crit Care Med 174:386–392. https://doi.org/10.1164/rccm.200509-1380OC
Sing D, Sing CF (2010) Impact of direct soil exposures from airborne dust and geophagy on human health. Int J Environ Res Public Health 7:1205–1223. https://doi.org/10.3390/ijerph7031205
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottiere HM, Dore J, Marteau P, Seksik P, Langella P (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105:16731–16736. https://doi.org/10.1073/pnas.0804812105
Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9:279–290. https://doi.org/10.1038/nrmicro2540
Strachan DP (1989) Hay fever, hygiene, and household size. BMJ 299:1259–1260
Taubel M et al (2009) The occupant as a source of house dust bacteria. J Allergy Clin Immunol 124:834–840 e847. https://doi.org/10.1016/j.jaci.2009.07.045
Thorn J (2001) Seasonal variations in exposure to microbial cell wall components among household waste collectors. Ann Occup Hyg 45:153–156. https://doi.org/10.1016/S0003-4878(00)00056-9
Torvinen E, Torkko P, Rintala AN (2010) Real-time PCR detection of environmental mycobacteria in house dust. J Microbiol Methods 82:78–84. https://doi.org/10.1016/j.mimet.2010.04.007
Trinchieri G et al (1992) Natural killer cell stimulatory factor (NKSF) or interleukin-12 is a key regulator of immune response and inflammation. Prog Growth Factor Res 4:355–368
van Oosterhout AJM, Bloksma N (2005) Regulatory T-lymphocytes in asthma. Eur Respir J 26:918–932. https://doi.org/10.1183/09031936.05.00011205
Vercelli D (2003) Learning from discrepancies: CD14 polymorphisms, atopy and the endotoxin switch. Clin Exp Allergy 33:153–155
Vo N, Tsai TC, Maxwell C, Carbonero F (2017) Early exposure to agricultural soil accelerates the maturation of the early-life pig gut microbiota. Anaerobe 45:31–39. https://doi.org/10.1016/j.anaerobe.2017.02.022
Von HL, Hyvärinen A, Laatikainen T, Mäkelä MJ, Nevalainen A, Vartiainen E, Haahtela T (2010) Risk of atopy associated with microbial components in house dust. Ann Allergy Asthma Immunol 104:269–270
Weikl F, Tischer C, Probst AJ, Heinrich J, Markevych I, Jochner S, Pritsch K (2016) Fungal and bacterial communities in indoor dust follow different environmental determinants. PLoS One 11:e0154131. https://doi.org/10.1371/journal.pone.0154131
Wickman M, Gravesen S, Nordvall SL, Pershagen G, Sundell J (1992) Indoor viable dust-bound microfungi in relation to residential characteristics, living habits, and symptoms in atopic and control children. J Allergy Clin Immunol 89:752–759. https://doi.org/10.1016/0091-6749(92)90384-E
Wouters IM, Hilhorst SKM, Kleppe P, Doekes G, Douwes J, Peretz C, Heederik D (2002) Upper airway inflammation and respiratory symptoms in domestic waste collectors. Occup Environ Med 59:106–112. https://doi.org/10.1136/Oem.59.2.106
Yamamoto N, Shendell DG, Peccia J (2011) Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR. Indoor Air 21:521–530. https://doi.org/10.1111/j.1600-0668.2011.00732.x
Zhang G, Goldblatt J, LeSouef PN (2008) Does the relationship between IgE and the CD14 gene depend on ethnicity? Allergy 63:1411–1417. https://doi.org/10.1111/j.1398-9995.2008.01804.x
Zhou D, Zhang H, Bai Z, Zhang A, Bai F, Luo X, Hou Y, Ding X, Sun B, Sun X, Ma N, Wang C, Dai X, Lu Z (2016) Exposure to soil, house dust and decaying plants increases gut microbial diversity and decreases serum immunoglobulin E levels in BALB/c mice. Environ Microbiol 18:1326–1337. https://doi.org/10.1111/1462-2920.12895
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of Interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Shan, Y., Wu, W., Fan, W. et al. House dust microbiome and human health risks. Int Microbiol 22, 297–304 (2019). https://doi.org/10.1007/s10123-019-00057-5
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10123-019-00057-5