The mycobiomes and bacteriomes of sputum, saliva, and home dust.
childhood exposure
home dust
indoor microbiome
induced sputum
respiratory microbiome
traffic-related air pollution
Journal
Indoor air
ISSN: 1600-0668
Titre abrégé: Indoor Air
Pays: England
ID NLM: 9423515
Informations de publication
Date de publication:
03 2021
03 2021
Historique:
received:
13
04
2020
revised:
11
09
2020
accepted:
15
09
2020
pubmed:
25
9
2020
medline:
25
2
2023
entrez:
24
9
2020
Statut:
ppublish
Résumé
Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet, we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.
Substances chimiques
DNA, Bacterial
0
DNA, Fungal
0
Dust
0
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
357-368Subventions
Organisme : NIOSH CDC HHS
ID : T42OH008432
Pays : United States
Organisme : NIEHS NIH HHS
ID : R21ES024807
Pays : United States
Informations de copyright
© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Références
Dickson RP, Huffnagle GB. The lung microbiome: new principles for respiratory bacteriology in health and disease. PLoS Pathog. 2015;11(7):e1004923.
Navarro J, Rainisio M, Harms HK, et al. Factors associated with poor pulmonary function: cross-sectional analysis of data from the ERCF. European epidemiologic registry of cystic fibrosis. Eur Respir J. 2001;18(2):298-305.
Carpagnano GE, Malerba M, Lacedonia D, et al. Analysis of the fungal microbiome in exhaled breath condensate of patients with asthma. Paper presented at: Allergy Asthma Proc2016.
Bassis CM, Erb-Downward JR, Dickson RP, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio. 2015;6(2):e00037-15.
Stressmann FA, Rogers GB, Klem ER, et al. Analysis of the bacterial communities present in lungs of patients with cystic fibrosis from American and British centers. J Clin Microbiol. 2011;49(1):281-291.
Niemeier-Walsh C, Ryan PH, Meller J, Ollberding NJ, Adhikari A, Reponen T. Exposure to traffic-related air pollution is associated with greater bacterial community diversity in the lower respiratory tract of children. Sci Total Environ. 2020 (Submitted).
White A, Watts G, Lu Z, et al. Environmental arsenic exposure and microbiota in induced sputum. Int J Environ Res Public Health. 2014;11(2):2299-2313.
Vangay P, Johnson AJ, Ward TL, et al. US immigration westernizes the human gut microbiome. Cell. 2018;175(4):962-972.e910.
Kaplan RC, Wang Z, Usyk M, et al. Gut microbiome composition in the hispanic community health study/study of latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol. 2019;20(1):219.
Grice EA, Segre JA. The skin microbiome. Nat Rev Microbiol. 2011;9(4):244-253.
Lax S, Smith DP, Hampton-Marcell J, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014;345(6200):1048-1052.
Richard ML, Lamas B, Liguori G, Hoffmann TW, Sokol H. Gut fungal microbiota: the Yin and Yang of inflammatory bowel disease. Inflamm Bowel Dis. 2015;21(3):656-665.
Wall R, Ross R, Ryan C, et al. Role of gut microbiota in early infant development. Clin Med Pediatr. 2009;3:45-54.
Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336(6086):1268-1273.
Dannemiller KC, Mendell MJ, Macher JM, et al. Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. Indoor Air. 2014;24(3):236-247.
Fu X, Norbäck D, Yuan Q, et al. Indoor microbiome, environmental characteristics and asthma among junior high school students in Johor Bahru, Malaysia. Environ Int. 2020;138:105664.
Ryan PH, LeMasters G, Biagini J, et al. Is it traffic type, volume, or distance? Wheezing in infants living near truck and bus traffic. J Allergy Clin Immunol. 2005;116(2):279-284.
Ryan PH, LeMasters GK, Biswas P, et al. A comparison of proximity and land use regression traffic exposure models and wheezing in infants. Environ Health Perspect. 2007:115;278-284.
Ryan PH, LeMasters GK, Levin L, et al. A land-use regression model for estimating microenvironmental diesel exposure given multiple addresses from birth through childhood. Sci Total Environ. 2008;404(1):139-147.
Tunney MM, Einarsson GG, Wei L, et al. Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation. Am J Respir Crit Care Med. 2013;187(10):1118-1126.
Adams RI, Tian Y, Taylor JW, Bruns TD, Hyvärinen A, Täubel M. Passive dust collectors for assessing airborne microbial material. Microbiome. 2015;3(1):46.
Luhung I, Wu Y, Ng CK, Miller D, Cao B, Chang VW-C. Protocol improvements for low concentration DNA-based bioaerosol sampling and analysis. PLoS One. 2015;10(11):e0141158.
Nadkarni MA, Martin FE, Jacques NA, Hunter N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology. 2002;148(1):257-266.
Haugland R, Vesper S, Inventors. Method of identifying and quantifying specific fungi and bacteria. 2002.
Liu J, Yu Y, Cai Z, Bartlam M, Wang Y. Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR-DGGE. World J Microbiol Biotechnol. 2015;31(9):1387-1395.
Mello A, Napoli C, Murat C, Morin E, Marceddu G, Bonfante P. ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. Mycologia. 2011;103(6):1184-1193.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10-12.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581.
Callahan B. Silva taxonomic training data formatted for DADA2 (Silva version 132). Zenodo (open access dataset). 2018.
Nilsson RH, Larsson K-H, Taylor AFS, et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2018;47(D1):D259-D264.
Wright ES. Using DECIPHER v2. 0 to analyze big biological sequence data in R. R Journal. 2016;8(1):1-8.
Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics. 2010;27(4):592-593.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460-2461.
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.
Jian C, Luukkonen P, Yki-Jarvinen H, Salonen A, Korpela K. Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling. bioRxiv. 2018;478685.
Dannemiller KC, Lang-Yona N, Yamamoto N, Rudich Y, Peccia J. Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations. Atmos Environ. 2014;84:113-121.
Kembel SW, Cowan PD, Helmus MR, et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics. 2010;26(11):1463-1464.
La Rosa PS, Brooks JP, Deych E, et al. Hypothesis testing and power calculations for taxonomic-based human microbiome data. PLoS One. 2012;7(12):e52078.
Sokol H, Leducq V, Aschard H, et al. Fungal microbiota dysbiosis in IBD. Gut. 2017;66(6):1039-1048.
Andersen BM. Transmission Routes and Survival Outside the Body. In: Andersen BM, ed. Prevention and Control of Infections in Hospitals: Practice and Theory. Cham: Springer International Publishing; 2019:23-28.
Köhler JR, Casadevall A, Perfect J. The spectrum of fungi that infects humans. Cold Spring Harb Perspect Med. 2014;5(1):a019273.
Hanson B, Zhou Y, Bautista EJ, et al. Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study. Environ Sci Process Impacts. 2016;18(6):713-724.
Rocchi S, Valot B, Reboux G, Millon L. DNA metabarcoding to assess indoor fungal communities: electrostatic dust collectors and Illumina sequencing. J Microbiol Methods. 2017;139:107-112.
Cui L, Morris A, Ghedin E. The human mycobiome in health and disease. Genome Med. 2013;5(7):63.
Turner R. Essentials of Microbiology. New Delhi: Scientific e-Resources. 2018.
Manolakaki D, Velmahos G, Kourkoumpetis T, et al. Candida infection and colonization among trauma patients. Virulence. 2010;1(5):367-375.
Jawhara S, Poulain D. Saccharomyces boulardii decreases inflammation and intestinal colonization by Candida albicans in a mouse model of chemically-induced colitis. Med Mycol. 2007;45(8):691-700.
Liguori G, Lamas B, Richard ML, et al. Fungal dysbiosis in mucosa-associated microbiota of Crohn's disease patients. J Crohns Colitis. 2016;10(3):296-305.
Degobbi C, Lopes FD, Carvalho-Oliveira R, Muñoz JE, Saldiva PH. Correlation of fungi and endotoxin with PM2. 5 and meteorological parameters in atmosphere of Sao Paulo, Brazil. Atmos Environ. 2011;45(13):2277-2283.
Du P, Du R, Ren W, Lu Z, Zhang Y, Fu P. Variations of bacteria and fungi in PM2. 5 in Beijing, China. Atmos Environ. 2018;172:55-64.