Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France
Abstract
:1. Introduction
2. Material and Methods
2.1. Samples and qPCR Method
2.2. qPCR Data
2.3. Climate Data and Land Use
2.4. Statistical Analyses
3. Results
3.1. qPCR Analysis
3.2. Spatio-Temporal Distribution of Microorganisms
3.3. Climate and Biophysical Land Use for Each Individual Target
3.4. Microorganism Community
4. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Targets and Designers [Reference] | (5’–3’) Sequences | ||
---|---|---|---|
Molds | Alternaria alternata designed by EPA [41] | Forward primer | GGCGGGCTGGAACCTC |
Reverse primer | GCAATTACAAAAGGTTTATGTTTGTCGTA | ||
Probe | TTACAGCCTTGCTGAATTATTCACCCTTGTCTTT | ||
Aspergillus fumigatus designed by EPA [41] | Forward primer | GCCCGCCGTTTCGAC | |
Reverse primer | CCGTTGTTGAAAGTTTTAACTGATTAC | ||
Probe | CCCGCCGAAGACCCCAACATG | ||
Aspergillus versicolor designed by EPA [41] | Forward primer | CGGCGGGGAGCCCT | |
Reverse primer | CCATTGTTGAAAGTTTTGAcTGATCTTA | ||
Probe | AGACTGCATCACTCTCAGGCATGAAGTTCAG | ||
Cladosporium sphaerospermum designed by EPA [41] | Forward primer | ACCGGCTGGGTCTTTCG | |
Reverse primer | GGGGTTGTTTTACGGCGTG | ||
Probe | CCCGCGGCACCCTTTAGCGA | ||
Epicoccum nigrum designed by EPA [41] # | Forward primer | TTGTAGACTTCGGTCTGCTACCTCTT | |
Reverse primer | TGCAACTGCAAAGGGTTTGAAT | ||
Probe | CATGTCTTTTGAGTACCTTCGTTTCCTCGGC | ||
Penicillium chrysogenum Modified from EPA [40] | Forward primer | TGCCTGTCCGAGCGTCATT | |
Reverse primer | CCCCCGGGATCGGAG | ||
Probe | CCAACACACAAGCCGTGCTTGAGG | ||
Stachybotrys chartarum designed by EPA [41] | Forward primer | TCCCAAACCCTTATGTGAACC | |
Reverse primer | GTTTGCCACTCAGAGAATACTGAAA | ||
Probe | CTGCGCCCGGATCCAGGC | ||
Trichoderma viride designed by EPA [41] # | Forward primer | CCCAAACCCAATGTGAACCA | |
Reverse primer | TCCGCGAGGGGACTACAG | ||
Probe | CCAAACTGTTGCCTCGGCGGG | ||
Chaetomium globosum designed by EPA [41] # | Forward primer | CCGCAGGCCCTGAAAAG | |
Reverse primer | CGCGGCGCGACCA | ||
Probe | AGATGTATGCTACTACGCTCGGTGCGACAG | ||
Yeasts | Cryptococcus spp. designed for this study # | Forward primer | CCTGCGGAAGGATCATTAATG |
Reverse primer | GCACAGGTGTTATGGATATGATGTG | ||
Probe | TTGACCGTCTGTCGAGCTTGCTCACA | ||
Mites | Acarus siro Designed by our team [34] # | Forward primer | CGCAAACTGTGGTGCGAGTA |
Reverse primer | GCTCCTTGGTCCGTGTTTCA | ||
Probe | TCGGTCTCCACCCGACCCGTC | ||
Dermatophagoïdes spp. Designed by our team [34] | Forward primer | TGTTGTGGTTAAAAAGCTCGTAGTTG | |
Reverse primer | ATGCGATAATCTGCTCAGTATGACA | ||
Probe | CAGCTCATGTATGGCGGTCCACCTG | ||
Dermatophagoïdes farinea Designed by our team [34] # | Forward primer | CACACATTCAACCAGAGTGGTACTT | |
Reverse primer | GGCTAACACTCCCCCTAGTTTAGA | ||
Probe | CGCTTACGCGATCCTACGAGCCATT | ||
Dermatophagoïdes pteronyssinus Designed by our team [34] # | Forward primer | CATCCAACCAGAGTGGTATTTCC | |
Reverse primer | GCTATTGCGCATACTCCACCTA | ||
Probe | TATGCAATCCTTCGGGCTATCCCATCA | ||
Bacteria | Enterobacteriaceae designed by Sen and Asher [42] | Forward primer | GGCGGCAGGCCTAAC |
Reverse primer | CAGGCAGTTTCCCAGACATTACT | ||
Probe | AGCAAGCTCTCTGTGCTACCGCTCGA | ||
Mycobacteria designed by Torvinen et al. [43] | Forward primer | GATGCAACGCGAAGAACCTT | |
Reverse primer | TGCACCACCTGCACACAGG | ||
Probe | CCTGGGTTTGACATGCACAGGACG | ||
Streptomyces spp. designed by Rintala and Nevalainen [44] | Forward primer | GCCGATTGTGGTGAAGTGGA | |
Reverse primer | GTACGGGCCGCCATGAAA | ||
Probe | ATCCTATGCTGTCGAGAAAAGCCTCTAGCG |
qPCR Targets | Number of Positive EDCs | Median Value (copy/µL) | Max Value (copy/µL) | |
---|---|---|---|---|
Fungi (molds and yeasts) | E. nigrum | 2763 | 76 | 39106 |
A. alternata | 2752 | 66 | 32634 | |
P. chrysogenum | 2660 | 9 | 19169 | |
C. sphaerospermum | 2195 | 8 | 12162 | |
A. versicolor | 2307 | 2 | 5671 | |
A. fumigatus | 1468 | 0 | 5138 | |
T. viride | 1390 | 0 | 1536 | |
S. chartarum | 848 | 0 | 333 | |
Cryptococcus spp. | 2314 | <1 | 7 | |
Bacteria | Enterobacteriaceae | 3086 | 134 | 78163 |
Mycobacteria | 3053 | 235 | 12511 | |
Streptomyces | 2879 | 51 | 5887 | |
Dust mites | Dermatophagoïdes spp. | 1505 | <1 | 97673 |
D. pteronyssinus | 1908 | 0 | 9657 | |
D. farinae | 2192 | <1 | 1330 | |
A. siro | 2300 | <1 | 348 |
qPCR Targets | p | edf | F | adjR2 | |
---|---|---|---|---|---|
Molds | A. alternata | <0.001 * | 2.954 | 162.6 | 0.12 |
A. fumigatus | <0.001 * | 2.7 | 10.54 | 0.00909 | |
E. nigrum | <0.001 * | 2.345 | 10.85 | 0.0069 | |
C. sphaerospermum | <0.001 * | 2 | 59.59 | 0.0418 | |
P. chrysogenum | 0.028 * | 2.738 | 4.472 | 0.00212 | |
S. chartarum | 0.122 | 2.853 | 1.808 | 0.00119 | |
A. versicolor | 0.126 | 2 | 2.071 | 0.000853 | |
T. viride | 0.794 | 2 | 0.231 | −0.000452 | |
Yeasts | Cryptococcus spp. | <0.001 * | 2.852 | 42.88 | 0.0391 |
Dust mites | Dermatophagoïdes spp. | <0.001 * | 2.122 | 39.51 | 0.0286 |
D. pteronyssinus | <0.001 * | 2 | 15.77 | 0.00918 | |
D. farinea | 0.672 | 2.248 | 0.44 | −0.000307 | |
A. siro | 0.779 | 2 | 0.249 | −0.000525 | |
Bacteria | Enterobacteriaceae | 0.12 | 2.25 | 1.823 | 0.00139 |
Mycobacteria | 0.009 * | 2.694 | 3.544 | 0.00456 | |
Streptomyces | <0.001 * | 2 | 11.71 | 0.00851 |
C. sphaerospermum | Dermatophagoïdes spp. | Streptomyces | E. nigrum | Mycobacteria | A. fumigatus | P. chrysogenum | Cryptococcus spp. | A. alternata | |
---|---|---|---|---|---|---|---|---|---|
Annual average temperature | + | − | + | − | + | ||||
Number of days temperature < −5 °C | − | − | − | + | + | ||||
Number of days temperature >30 °C | + | + | + | ||||||
Annual temperature range * | − | − | + | + | |||||
Total annual precipitation | + | − | − | ||||||
Number of precipitation days in January | + | + | + | + | + | − | − | ||
Number of precipitation days in July | − | ||||||||
Ratio between autumn ** and July precipitations | − | − | − | − | − | ||||
Urbanized areas | − | − | − | − | + | − | − | ||
Industrial or commercial areas | + | − | − | ||||||
Mines, landfills, and construction sites | + | ||||||||
Artificial, non-agricultural green spaces | + | − | |||||||
Arable land | + | − | − | − | − | − | − | ||
Permanent crops | + | − | − | − | − | − | − | ||
Prairies | + | − | − | − | − | + | − | − | − |
Heterogeneous agricultural areas | − | − | − | + | − | − | − | ||
Forests | + | − | − | − | + | − | − | ||
Scrub and/or herbaceous vegetation associations | + | − | − | + | |||||
Open spaces, with little or no vegetation | − | − | + | − | − | ||||
Inland wetlands | + | − | |||||||
Inland waters | + | − | − | − | − | − | |||
Maritime waters | − |
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Rocchi, S.; Reboux, G.; Scherer, E.; Laboissière, A.; Zaros, C.; Rouzet, A.; Valot, B.; Khan, S.; Dufourg, M.-N.; Leynaert, B.; et al. Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France. Microorganisms 2020, 8, 341. https://doi.org/10.3390/microorganisms8030341
Rocchi S, Reboux G, Scherer E, Laboissière A, Zaros C, Rouzet A, Valot B, Khan S, Dufourg M-N, Leynaert B, et al. Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France. Microorganisms. 2020; 8(3):341. https://doi.org/10.3390/microorganisms8030341
Chicago/Turabian StyleRocchi, Steffi, Gabriel Reboux, Emeline Scherer, Audrey Laboissière, Cécile Zaros, Adeline Rouzet, Benoit Valot, Sadia Khan, Marie-Noëlle Dufourg, Bénédicte Leynaert, and et al. 2020. "Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France" Microorganisms 8, no. 3: 341. https://doi.org/10.3390/microorganisms8030341
APA StyleRocchi, S., Reboux, G., Scherer, E., Laboissière, A., Zaros, C., Rouzet, A., Valot, B., Khan, S., Dufourg, M.-N., Leynaert, B., Raherison, C., & Millon, L. (2020). Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France. Microorganisms, 8(3), 341. https://doi.org/10.3390/microorganisms8030341