Culture-independent characterization of bacteria and fungi in a poultry bioaerosol using pyrosequencing: A new approach

Journal of Occupational and Environmental Hygiene

Volumn 7, Issue 12, 2010, Pages 693-699

  Nonnenmann, M W ^a   Bextine, B ^b   Dowd, S E ^c   Gilmore, K ^a   Levin, J L ^a  

^a UNIVERSITY OF TEXAS HEALTH CENTER   (United States)

^b UNIVERSITY OF TEXAS AT TYLER   (United States)

^c Pathogen Research Laboratory   (United States)

Author keywords

Aspergillus ochraceus; Bioaerosol; Organic dust; Poultry; Pyrosequencing

Indexed keywords

AEROSOL; AIR POLLUTANT; ANIMAL; ARTICLE; BACTERIUM; CHICKEN; DNA SEQUENCE; DUST; ENVIRONMENTAL MONITORING; EXPOSURE; FUNGUS; HUMAN; INDOOR AIR POLLUTION; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; OCCUPATIONAL EXPOSURE; POLYMERASE CHAIN REACTION; POULTRY; UNITED STATES;

AEROSOLS; AIR MICROBIOLOGY; AIR POLLUTANTS, OCCUPATIONAL; AIR POLLUTION, INDOOR; ANIMALS; BACTERIA; CHICKENS; DUST; ENVIRONMENTAL MONITORING; FUNGI; HUMANS; INHALATION EXPOSURE; OCCUPATIONAL EXPOSURE; POLYMERASE CHAIN REACTION; POULTRY; SEQUENCE ANALYSIS, DNA; TEXAS;

EID: 79952198950     PISSN: 15459624     EISSN: 15459632     Source Type: Journal    
DOI: 10.1080/15459624.2010.526893     Document Type: Article

References (39)

1. Donham, K.J., D. Cumro, S.J. Reynolds, et al.: Dose-response relationships between occupational aerosol exposures and cross-shift declines of lung function in poultry workers: Recommendations for exposure limits. J. Occup. Environ. Med. 42(3):260–269 (2000).
2. Pedersen, S., M. Nonnenmann, R. Rautiainen, et al.: Dust in pig buildings. J. Agric. Saf. Health 6(4):261–274 (2000).
3. Radon, K., C. Weber, M. Iversen, et al.: Exposure assessment and lung function in pig and poultry farmers. Occup. Environ. Med. 58:405–410 (2001).
4. Donham, K.J., D. Cumro, and S.J. Reynolds: Synergistic effects of dust and ammonia on the occupational health effects of poultry production workers. J. Agromedicine 8(2):57–76 (2002).
5. Kirychuk, S.P., J.A. Dosman, S.J. Reynolds, et al.: Total dust and endotoxin in poultry operations: Comparison between cage and floor housing and respiratory effects in workers. J. Occup. Environ. Hyg. 48:741–748 (2006).
6. Oppliger, A., N. Charrière, P.O. Droz, et al.: Exposure to bioaerosols in poultry houses at different stages of fattening; use of real-time PCR for airborne bacterial quantification. Ann. Occup. Hyg. 52(5):405–412 (2008).
7. Lee, S., A. Adhikari, S.A. Grinshpun, et al.: Personal exposure to airborne dust and microorganisms in agricultural environments. J. Occup. Environ. Hyg. 3:118–130 (2006).
8. Clark, S., R. Rylander, and L. Larsson: Airborne bacteria, endotoxin and fungi in the dust of poultry and swine confinement buildings. AIHA J. 44:537–541 (1983).
9. Torsvik, V., R. Sørheim, and J. Goksøyr: Total bacterial diversity in soil and sediment communities—A review. J. Ind. Microbiol. 17:170–178 (1996).
10. Torsvik, V., F.L. Daae, R.A. Sandaa, et al.: Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64(1):53–62 (1998).
11. DeLong, E.F., and N.R. Pace: Environmental diversity of bacteria and archaea. Syst. Biol. 50(4):470–478 (2001).
12. Nehmé, B., V. Letourneau, R.J. Forster, et al.: Culture-independent approach of the bacterial bioaerosol diversity in the standard swine confinement buildings, and assessment of the seasonal effect. Environ. Microbiol. 10(3):665–675 (2008).
13. Nehmé B., Y. Gilbert, V. Letourneau, et al.: Culture-independent characterization of archaeal biodiversity in swine confinement building bioaerosols. Appl. Environ. Microbiol. 75(17):5445–5450 (2009).
14. Woese, C.: Bacterial evolution. Microbiol. Rev. 51(2):221–271 (1987).
15. Solits, D.E., P.S. Solits, M.W. Chase, et al.: Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences. Bot. J. Linn. Soc. 133(4):381–461 (2000).
16. Stackebrandt, E., and B.M. Goebel: Taxonomic note: A place for DNADNAreassociation and 16S rRNAsequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846–849 (1994).
17. Coenye, T., and P. Vandamme: Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol. Lett. 228(1):45–49 (2003).
18. Thorne, P.S., C. Duchaine, J. Douwes, et al.: Working Group Report 4: Exposure assessment for biological agents. AJIM 46(4):419–422 (2004).
19. Margulies, M., M. Egholm, W.E. Altman, et al.: Genome sequencing in open microfabricated high density picoliter reactors. Nature 437(7057):376–380 (2005).
20. Bailey, M.T., S.E. Dowd, N.M. Parry, et al.: Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium. Infect. Immun. 78(4):1509–1519 (2010).
21. Bailey, M.T., J.C. Walton, S.E. Dowd, et al.: Photoperiod modulates gut bacteria composition in male Siberian hamsters (Phodopus sungorus). Brain Behav. Immun. 24(4):577–584 (2010).
22. Dowd, S.E., R.D. Wolcott, Y. Sun, et al.: Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS. One 3(10):e3326 (2008).
23. Dowd, S.E., Y. Sun, R.D. Wolcott, et al.: Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 5:459–472 (2008).
24. Dowd, S.E., T.R. Callaway, R.D. Wolcott, et al.: Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tagencoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 8:125 (2008).
25. Dowd, S.E., Y. Sun, P.R. Secor, et al.: Survey of bacterial diversity in chronicwounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol. 8:43 (2008).
26. Leake, J.L., S.E. Dowd, R.D. Wolcott, et al.: Identification of yeast in chronic wounds using new pathogen-detection technologies. J. Wound Care 18:103–108 (2009).
27. Pitta, D.W., W.E. Pinchak, S.E. Dowd, et al.: Rumen bacterial diversity dynamics associated with changing from Bermuda grass hay to grazed winter wheat diets. Microb. Ecol. 59(3):511–522 (2009).
28. Suchodolski, J.S., S.E. Dowd, E. Westermarck, et al.: The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNAgene sequencing. BMC Microbiol. 9:210 (2009).
29. Wolcott, R.D., V. Gontcharova, Y. Sun, et al.: Bacterial diversity in surgical site infections: Not just aerobic cocci any more. J. Wound Care 18:317–323 (2009).
30. Gontcharova, V., E. Youn, R. D. Wolcott, E. B. et al.: Black box chimera check (B2C2): AWindows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. Open Micro J. 4:47–52 (2010).
31. Dowd, S.E., J. Zaragoza, J.R. Rodriguez, et al.: Windows.NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinformatics 6:93 (2005).
32. Cole, J.R., Q. Wang, E. Cardenas, et al.: The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37(database issue):D141–D145 (2009).
33. Gustafsson, G.: Factors affecting the release and concentration of dust in pig houses. J. Agr. Eng. Res. 74(4):379–390 (1999).
34. Black, J.G.: Microbiology: Principles and Applications. Upper Saddle River, N.J.: Prentice Hall, 1993.
35. Van der Merwe, K.J., P.S. Steyn, and L. Fourie: Ochratoxin A, a toxic metabolite produced by Aspergillus ochraceus. Nature 205:1112–1113 (1965).
36. Skaug, M.A.: Levels of ochratoxin A and IgG against conidia of Penicillium verrucosum in blood samples from healthy farm workers. Ann. Agric. Environ. Med. 10:73–77 (2003).
37. Nielsen, E.M., B.H. Nielsen, and N.O. Breum: Occupational bioaerosol exposure during collection of household waste. Ann. Agric. Environ. Med. 2:53–59 (1995).
38. Macher, J.: Bioaerosols Assessment and Control. Cincinnati, Ohio: American Conference of Governmental Industrial Hygienists, 1999.
39. “BLAST with Microbial Genomes.” [Online] Available at http://www.ncbi.nlm.nih.gov/sutils/genom table.cgi (Accessed June 1, 2010).