Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Moissl Eichinger, Christine ^a,b,c   Auerbach, Anna K ^a   Probst, Alexander J ^a,i   Mahnert, Alexander ^d   Tom, Lauren ^e   Piceno, Yvette ^e   Andersen, Gary L ^e   Venkateswaran, Kasthuri ^f   Rettberg, Petra ^g   Barczyk, Simon ^g   Pukall, Rüdiger ^h   Berg, Gabriele ^d  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b MEDICAL UNIVERSITY OF GRAZ   (Austria)

^c BIOTECHMED GRAZ   (Austria)

^d GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^g GERMAN AEROSPACE CENTER DLR   (Germany)

^h LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARCHAEON; BACTERIUM; BIODIVERSITY; CLASSIFICATION; CLUSTER ANALYSIS; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INDOOR AIR POLLUTION; METAGENOME; METAGENOMICS; MICROBIOLOGY; MICROCLIMATE; PROCEDURES;

AIR MICROBIOLOGY; AIR POLLUTION, INDOOR; ARCHAEA; BACTERIA; BIODIVERSITY; CLUSTER ANALYSIS; ENVIRONMENT, CONTROLLED; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; METAGENOMICS; RNA, RIBOSOMAL, 16S;

EID: 84925002963     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep09156     Document Type: Article

References (54)

1. Gilbert, J. A. & Dupont, C. L. Microbial metagenomics: beyond the genome. Ann Rev Mar Sci 3, 347-371 (2011).
2. Nocker, A., Cheung, C.-Y.&Camper, A. K. Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J Microbiol Methods 67, 310-320 (2006).
3. Huber, T., Faulkner, G. & Hugenholtz, P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317-2319 (2004).
4. Gilbert, J. A., O'Dor, R., King, N. & Vogel, T. M. The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist. Microb Inform Exp 1, 5 (2011).
5. Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (2012).
6. Arundel, A. V., Sterling, E. M., Biggin, J.H. & Sterling, T. D. Indirect health effects of relative humidity in indoor environments. Environ Health Perspect 65, 351-361 (1986).
7. Hewitt, K. M., Gerba, C. P., Maxwell, S. L. & Kelley, S. T. Office space bacterial abundance and diversity in three metropolitan areas. PLoS One 7, e37849 (2012).
8. Kembel, S. W. et al. Architectural design influences the diversity and structure of the built environment microbiome. ISME J 6, 1469-1479 (2012).
9. Flores, G. E. et al. Microbial biogeography of public restroom surfaces. PLoS One 6, e28132 (2011).
10. Moissl-Eichinger, C. Archaea in artificial environments: their presence in global spacecraft cleanrooms and impact on planetary protection. ISME J 5, 209-219 (2011).
11. Kembel, S. W. et al. Architectural design drives the biogeography of indoor bacterial communities. PLoS One 9, e87093 (2014).
12. Qian, J., Hospodsky, D., Yamamoto, N.,Nazaroff, W. W.&Peccia, J. Size-resolved emission rates of airborne bacteria and fungi in an occupied classroom. Indoor Air 22, 339-351 (2012).
13. Berg, G.,Mahnert, A. &Moissl-Eichinger, C. Beneficial effects of plant-associated microbes on indoor microbiomes and human health? Front Microbiol 5, 15 (2014).
14. Ismail, R. et al. Methods for recovering microorganisms from solid surfaces used in the food industry: a review of the literature. Int J Environ Res Public Health 10, 6169-6183 (2013).
15. Galvin, S., Dolan, A., Cahill, O., Daniels, S. & Humphreys, H. Microbial monitoring of the hospital environment: why and how? J Hosp Infect 82, 143-151 (2012).
16. Oberauner, L. et al. The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing. Sci Rep 3, 1413 (2013).
17. Crawford, R. L. Microbial diversity and its relationship to planetary protection. Appl Environ Microbiol 71, 4163-4168 (2005).
18. Kwan, K. et al. Evaluation of procedures for the collection, processing, and analysis of biomolecules from low-biomass surfaces. Appl Environ Microbiol 77, 2943-2953 (2011).
19. Puleo, J. R. et al. Microbiological profiles of the Viking spacecraft. Appl Environ Microbiol 33, 379-384 (1977).
20. La Duc, Myron, T. et al. Isolation and characterization of bacteria capable of tolerating the extreme conditions of cleanroom environments. Appl Environ Microbiol 73, 2600-2611 (2007).
21. La Duc, Myron, T. et al. Comprehensive census of bacteria in cleanrooms by using DNA microarray and cloning methods. Appl Environ Microbiol 75, 6559-6567 (2009).
22. Moissl, C. et al. Molecular bacterial community analysis of cleanrooms where spacecraft are assembled. FEMS Microbiol Ecol 61, 509-521 (2007).
23. Moissl, C., Bruckner, J. C. & Venkateswaran, K. Archaeal diversity analysis of spacecraft assembly cleanrooms. ISME J 2, 115-119 (2008).
24. Moissl-Eichinger, C. et al. Lessons learned from the microbial analysis of the Herschel spacecraft during assembly, integration, and test operations. Astrobiology 13, 1125-1139 (2013).
25. Probst, A. J., Auerbach, A. K. & Moissl-Eichinger, C. Archaea on human skin. PLoS One 8, e65388 (2013).
26. Klappenbach, J. A., Saxman, P. R., Cole, J. R. & Schmidt, T. M. Rrndb: the ribosomalRNAoperon copy number database. Nucleic acids research 29, 181-184 (2001).
27. Anderson, M. J. A new method for non-parametric multivariate analysis of variance. Austral Ecology 26, 32-46 (2001).
28. McArdle, B. H. & Anderson,M. J. Fitting multivariate models to community data: A comment on distance-based redundancy analysis. Ecology 82, 290-297 (2001).
29. Vaishampayan, P. et al.New perspectives on viable microbial communities in lowbiomass cleanroom environments. ISME J 7, 312-324 (2013).
30. Bieber, L. & Kahlmeter, G. Staphylococcus lugdunensis in several niches of the normal skin flora. Clinical Microbiology and Infection 16, 385-388 (2010).
31. Stieglmeier, M. et al. Abundance and diversity of microbial inhabitants in European spacecraft-associated cleanrooms. Astrobiology 12, 572-585 (2012).
32. Pantosti, A., Sanchini, A. & Monaco, M. Mechanisms of antibiotic resistance in Staphylococcus aureus. Future Microbiol 2, 323-334 (2007).
33. Slade, D. & Radman, M. Oxidative stress resistance in Deinococcus radiodurans. Microbiol Mol Biol Rev 75, 133-191 (2011).
34. Watve, M. et al. The 'K' selected oligophilic bacteria: a key to uncultured diversity? Current science 78, 1535-1542 (2000).
35. Berg, G., Zachow, C., Müller, H., Philipps, J. & Tilcher, R. Next-generation bioproducts sowing the seeds of success for sustainable agriculture. Agronomy 3, 648-656 (2013).
36. Stieglmeier, M., Wirth, R., Kminek, G. & Moissl-Eichinger, C. Cultivation of anaerobic and facultatively anaerobic bacteria from spacecraft-associated cleanrooms. Appl Environ Microbiol 75, 3484-3491 (2009).
37. Flores, G. E. et al. Diversity, distribution and sources of bacteria in residential kitchens. Environ Microbiol 15, 588-596 (2013).
38. Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J. &Weightman, A. J. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71, 7724-7736 (2005).
39. Good, I. J. The population frequencies of species and the estimation of population parameters. Biometrika 40, 237-264 (1953).
40. Lane, D. J. 16S/23S rRNA sequencing. (Wiley & Sons, Chichester, United Kingdom. 1991).
41. Zachow, C., Tilcher, R. & Berg, G. Sugar beet-associated bacterial and fungal communities show a high indigenous antagonistic potential against plant pathogens. Microbial ecology 55, 119-129 (2008).
42. Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63-67 (2002).
43. Baker, G. C., Smith, J. J.&Cowan, D. A. Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods 55, 541-555 (2003).
44. Gantner, S., Andersson, A. F., Alonso-Sáez, L. & Bertilsson, S. Novel primers for 16S rRNA-based archaeal community analyses in environmental samples. Journal of Microbiological Methods 84, 12-18 (2011).
45. Raskin, L., Stromley, J.M., Rittmann, B. E.&Stahl, D. A. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Applied and Environmental Microbiology 60, 1232-1240 (1994).
46. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335-336 (2010).
47. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
48. Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267 (2010).
49. Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-2504 (2003).
50. Hazen, T. C. et al. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330, 204-208 (2010).
51. McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610-618 (2012).
52. Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75, 7537-7541 (2009).
53. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73, 5261-5267 (2007).
54. R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, Austria, 2014).