Flow cytometry for fast microbial community fingerprinting

Water Research

Volumn 46, Issue 3, 2012, Pages 907-919

  De Roy, Karen ^a   Clement, Lieven ^a,c,d   Thas, Olivier ^a   Wang, Yingying ^a,b   Boon, Nico ^a  

^a GHENT UNIVERSITY   (Belgium)

^b NANKAI UNIVERSITY   (China)

^c KU LEUVEN   (Belgium)

^d HASSELT UNIVERSITY   (Belgium)

Author keywords

Flow cytometry; Microbial community fingerprinting; Statistical pipeline

Indexed keywords

AQUATIC ORGANISMS; FLOW CYTOMETRY; MICROORGANISMS; POTABLE WATER; WASTEWATER TREATMENT;

BEVERAGE PRODUCTION; CONVENTIONAL METHODS; DIFFERENT DOMAINS; FOOD PRODUCTION; HETEROTROPHIC PLATE COUNTS; MICROBIAL COMMUNITIES; MICROBIAL COMMUNITY FINGERPRINTING; PLATING TECHNIQUE; SELECTIVE PLATINGS; STATISTICAL PIPELINE;

PIPELINES;

BACTERIAL DNA; BACTERIAL RNA; DRINKING WATER;

AQUATIC ENVIRONMENT; BREWING INDUSTRY; ENVIRONMENTAL FACTOR; FLOW CYTOMETRY; FOOD PRODUCTION; HETEROTROPHY; MICROBIAL COMMUNITY; MOLECULAR ANALYSIS; PIPELINE; WASTEWATER; WATER TREATMENT;

ANALYTIC METHOD; AQUATIC ENVIRONMENT; ARTICLE; BACTERIAL CELL; DNA FINGERPRINTING; ENVIRONMENTAL FACTOR; FLOW CYTOMETRY; MICROBIAL COMMUNITY; MICROORGANISM DETECTION; NONHUMAN; PRIORITY JOURNAL; RNA FINGERPRINTING; WATER ANALYSIS;

EID: 84855306674     PISSN: 00431354     EISSN: 18792448     Source Type: Journal    
DOI: 10.1016/j.watres.2011.11.076     Document Type: Article

References (45)

1. Allen M.J., Edberg S.C., Reasoner D.J. Heterotrophic plate count bacteria - what is their significance in drinking water?. International Journal of Food Microbiology 2004, 92:265-274.
2. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiological Reviews 1995, 59:143-169.
3. Bartram J., Cotruvo J., Exner M., Fricker C., Glasmacher A. Heterotrophic Plate Counts and Drinking-water Safety 2003, IWA Publishing on behalf of the World Health Organization, London.
4. Bashashati A., Brinkman R.R. A Survey of flow cytometry data analysis methods. Advances in Bioinformatics 2009.
5. Berney M., Hammes F., Bosshard F., Weilenmann H.U., Egli T. Assessment and interpretation of bacterial viability by using the LIVE/DEAD BacLight kit in combination with flow cytometry. Applied and Environmental Microbiology 2007, 73:3283-3290.
6. Berney M., Vital M., Hulshoff I., Weilenmann H.U., Egli T., Hammes F. Rapid, cultivation-independent assessment of microbial viability in drinking water. Water Research 2008, 42:4010-4018.
7. Boon N., De Windt W., Verstraete W., Top E.M. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiology Ecology 2002, 39:101-112.
8. Boon N., Top E.M., Verstraete W., Siciliano S.D. Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chloroaniline shock load. Applied and Environmental Microbiology 2003, 69:1511-1520.
9. Couto J.A., Hogg T. Evaluation of a commercial fluorochromic system for the rapid detection and estimation of wine lactic acid bacteria by DEFT. Letters in Applied Microbiology 1999, 28:23-26.
10. Dewettinck T., Hulsbosch W., Van Hege K., Top E.M., Verstraete W. Molecular fingerprinting of bacterial populations in groundwater and bottled mineral water. Applied Microbiology and Biotechnology 2001, 57:412-418.
11. Diaz M., Herrero M., Garcia L.A., Quiros C. Application of flow cytometry to industrial microbial bioprocesses. Biochemical Engineering Journal 2010, 48:385-407.
12. Ding L.L., Zhou Q.X., Wang L., Zhang Q.R. Dynamics of bacterial community structure in a full-scale wastewater treatment plant with anoxic-oxic configuration using 16S rDNA PCR-DGGE fingerprints. African Journal of Biotechnology 2011, 10:589-600.
13. Dufour A. Assessing Microbial Safety of Drinking Water: Improving Approaches and Methods 2003, Published on Behalf of the World Health Organization and the Organisation for Economic Co-operation and Development by IWA Publishing, London. first ed.
14. Forster S., Lappin-Scott H.M., Snape J.R., Porter J. Rains, drains and active strains: towards online assessment of wastewater bacterial communities. Journal of Microbiological Methods 2003, 55:859-864.
15. Good P. Permutation, Parametric and Bootstrap Tests of Hypotheses 2005, Springer.
16. Hammes F., Berger C., Koster O., Egli T. Assessing biological stability of drinking water without disinfectant residuals in a full-scale water supply system. Journal of Water Supply: Research and Technology-Aqua 2010, 59:31-40.
17. Hammes F., Berney M., Wang Y.Y., Vital M., Koster O., Egli T. Flow-cytometric total bacterial cell counts as a descriptive microbiological parameter for drinking water treatment processes. Water Research 2008, 42:269-277.
18. Hammes F., Egli T. Cytometric methods for measuring bacteria in water: advantages, pitfalls and applications. Analytical and Bioanalytical Chemistry 2010, 397:1083-1095.
19. Hoefel D., Monis P.T., Grooby W.L., Andrews S., Saint C.P. Profiling bacterial survival through a water treatment process and subsequent distribution system. Journal of Applied Microbiology 2005, 99:175-186.
20. Hunter P.R. The microbiology of bottled natural mineral waters - a review. Journal of Applied Bacteriology 1993, 74:345-352.
21. Hutter K.J. Flow cytometry - A new tool for direct control of fermentation processes. Journal of the Institute of Brewing 2002, 108:48-51.
22. Kucnerowicz F., Vandewerf R., Verstraete W. Estimation of microbial ATP in waters and soils. Antonie Van Leeuwenhoek Journal of Microbiology 1982, 48:522-523.
23. Lautenschlager K., Boon N., Wang Y.Y., Egli T., Hammes F. Overnight stagnation of drinking water in household taps induces microbial growth and changes in community composition. Water Research 2010, 44:4868-4877.
24. Li C.S., Chia W.C., Chen P.S. Fluorochrome and flow cytometry to monitor microorganisms in treated hospital wastewater. Journal of Environmental Science and Health Part a-Toxic/Hazardous Substances & Environmental Engineering 2007, 42:195-203.
25. Lo K., Hahne F., Brinkman R.R., Gottardo R. flow clust: a Bioconductor package for automated gating of flow cytometry data. BMC Bioinformatics 2009, 10.
26. Luta G. On extensions of k-means clustering for automated gating of flow cytometry data. Cytometry Part A 2011, 79A:3-5.
27. Maecker H.T., Rinfret A., D'Souza P., Darden J., Roig E., Landry C., Hayes P., Birungi J., Anzala O., Garcia M., Harari A., Frank I., Baydo R., Baker M., Holbrook J., Ottinger J., Lamoreaux L., Epling C.L., Sinclair E., Suni M.A., Punt K., Calarota S., El-Bahi S., Alter G., Maila H., Kuta E., Cox J., Gray C., Altfeld M., Nougarede N., Boyer J., Tussey L., Tobery T., Bredt B., Roederer M., Koup R., Maino V.C., Weinhold K., Pantaleo G., Gilmour J., Horton H., Sekaly R.P. Standardization of cytokine flow cytometry assays. BMC Immunology 2005, 6.
28. Morton S.C., Zhang Y., Edwards M.A. Implications of nutrient release from iron metal for microbial regrowth in water distribution systems. Water Research 2005, 39:2883-2892.
29. Muyzer G., Dewaal E.C., Uitterlinden A.G. Profiling of complex microbial-populations by denaturating gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Applied and Environmental Microbiology 1993, 59:695-700.
30. Pinder A.C., Purdy P.W., Poulter S.A.G., Clark D.C. Validation of flow cytometry for rapid enumeration of bacterial concentrations in pure cultures. Journal of Applied Bacteriology 1990, 69:92-100.
31. Reznick D., Bryant M.J., Bashey F. r- and K-selection revisited: the role of population regulation in life-history evolution. Ecology 2002, 83:1509-1520.
32. Riis S.B., Pedersen H.M., Sorensen N.K., Jakobsen M. Flow cytometry and acidification power test as rapid techniques for determination of the activity of starter cultures of Lactobacillus delbrueckii ssp. bulgaricus. Food Microbiology 1995, 12:245-250.
33. Rogers W.T., Holyst H.A. FlowFP: a bioconductor package for fingerprinting flow cytometric data. Advances in Bioinformatics 2009.
34. Rogers W.T., Moser A.R., Holyst H.A., Bantly A., Mohler E.R., Scangas G., Moore J.S. Cytometric fingerprinting: quantitative characterization of multivariate distributions. Cytometry Part A 2008, 73A:430-441.
35. Ruszczynska A., Szteyn J., Wiszniewska-Laszczych A. Flow cytometry as a method for the evaluation of raw material, product and process in the dairy industry. Polish Journal of Veterinary Sciences 2007, 10:119-121.
36. Seurinck S., Defoirdt T., Verstraete W., Siciliano S.D. Detection and quantification of the human-specific HF183 bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environmental Microbiology 2005, 7:249-259.
37. Song C., Luong T.-D., Kong T.F., Nguyen N.-T., Asundi A.K. Disposable flow cytometer with high efficiency in particle counting and sizing using an optofluidic lens. Optics Letters 2011, 36:657-659.
38. Vives-Rego J., Lebaron P., Nebe-von Caron G. Current and future applications of flow cytometry in aquatic microbiology. FEMS Microbiology Reviews 2000, 24:429-448.
39. Wang Y., Hammes F., Boon N., Chami M., Egli T. Isolation and characterization of low nucleic acid (LNA)-content bacteria. Isme Journal 2009, 3:889-902.
40. Wang Y., Hammes F., De Roy K., Verstraete W., Boon N. Past, present and future applications of flow cytometry in aquatic microbiology. Trends in Biotechnology 2010, 28:416-424.
41. WHO Guidelines for Drinking-water Quality 2011, World Health Organization, Geneva. fourth ed.
42. Wittebolle L., Boon N., Vanparys B., Heylen K., De Vos P., Verstraete W. Failure of the ammonia oxidation process in two pharmaceutical wastewater treatment plants is linked to shifts in the bacterial communities. Journal of Applied Microbiology 2005, 99:997-1006.
43. Zhang T., Fang H.H.P. Digitization of DGGE (denaturing gradient gel electrophoresis) profile and cluster analysis of microbial communities. Biotechnology Letters 2000, 22:399-405.
44. Zhang Y., Edwards M. Nutrients and metals effects on nitrification in drinking water systems. Journal of the American Water Works Association 2010, 102:56+.
45. Zhao R., Natarajan A., Srienc F. A flow injection flow cytometry system for on-line monitoring of bioreactors. Biotechnology and Bioengineering 1999, 62:609-617.