Phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout (Oncorhynchus mykiss, Walbaum)

Journal of Applied Microbiology

Volumn 96, Issue 1, 2004, Pages 117-132

  Huber, I ^a,d   Spanggaard, B ^b,e   Appel, K F ^a   Rossen, L ^a   Nielsen, T ^c,f   Gram, L ^b  

^a Biotechnological Institute Denmark   (Denmark)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c BioMar Group   (Denmark)

^d Eurofins Medinet Inc   (Germany)

^e NOVOZYMES A S   (Denmark)

^f c/o Technical University of Denmark ^*  (Denmark)

Author keywords

16S rDNA sequence analysis; Fish microbiota; Fluorescence in situ hybridization; Microbial diversity

Indexed keywords

AEROBIC BACTERIA; ELECTROPHORESIS; FLUORESCENCE; FLUORESCENCE MICROSCOPY; GENES; OLIGONUCLEOTIDES; PROBES; RNA;

16S RDNA SEQUENCE; 16S RDNA SEQUENCE ANALYSE; FISH MICROBIOTA; FLUORESCENCE IN SITU HYBRIDIZATION; MICROBIAL DIVERSITY; MICROBIOTAS; PROTEOBACTERIA; RAINBOW TROUT; SEQUENCE ANALYSIS; TRYPTONE;

FISH;

4',6 DIAMIDINO 2 PHENYLINDOLE; AGAR; BACTERIAL DNA;

DIGESTIVE SYSTEM; MICROBIAL COMMUNITY; PHYLOGENETICS; SALMONID;

ACINETOBACTER; AEROMONAS; ANIMAL TISSUE; BACTERIAL COUNT; BACTERIAL FLORA; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CONFERENCE PAPER; CONTROLLED STUDY; CULTURE MEDIUM; DNA DETERMINATION; ENTEROBACTERIACEAE; FLUORESCENCE IN SITU HYBRIDIZATION; GEL ELECTROPHORESIS; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; INTESTINE FLORA; MICROSCOPY; MOLECULAR PROBE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLESIOMONAS; POPULATION DENSITY; PROTEUS; PSEUDOMONAS; RAINBOW TROUT; SEQUENCE ANALYSIS; SHEWANELLA;

ACINETOBACTER; AEROMONAS; ANAEROFILUM PENTOSOVORANS; ANIMALIA; BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE; MICROBIOTA; MYKISS; NEGIBACTERIA; ONCORHYNCHUS MYKISS; PLESIOMONAS; POSIBACTERIA; PROKARYOTA; PROTEOBACTERIA; PROTEUS; PSEUDOMONAS; SALMONIDAE; SHEWANELLA; UNCULTURED BACTERIUM;

EID: 0842308827     PISSN: 13645072     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2672.2003.02109.x     Document Type: Conference Paper

References (60)

1. Amann, R.I., Krumholz, L. and Stahl, D.A. (1990) Fluorescent- oligonucleotide probing of whole cells for determinative phylogenetic and environmental studies in microbiology. Journal of Bacteriology 172, 762-770.
2. Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59, 143-169.
3. Austin, B. and Al-Zahrani, A.M.J. (1988) The effect of antimicrobial compounds on the gastrointestinal microflora of rainbow trout, Salmo gairdneri Richardson. Journal of Fish Biology 33, 1-14.
4. Austin, B., Stuckey, L.F., Robertson, P.A.W., Effendi, I. and Griffith, D.R.W. (1995) A probiotic strain of Vibrio alginolyticus effective in reducing diseases caused by Aeromonas salmonicida, Vibrio anguillarum and Vibrio ordalii. Journal of Fish Diseases 18, 93-96.
5. Berg, R.D. (1996) The indigenous gastrointestinal microflora. Trends in Microbiology 4, 430-435.
6. Bernadsky, G. and Rosenberg, E. (1992) Drag-reducing properties of bacteria from the skin mucus of the cornetfish (Fistularia commersonii). Microbial Ecology 24, 63-74.
7. Bly, J.E., Quiniou, S.M.A., Lawson, L.A. and Clem, L.W. (1997) Inhibition of Saprolegnia pathogenic for fish by Pseudomonas fluorescens. Journal of Fish Diseases 20, 35-40.
8. Brosius, J., Dull, T.J., Sleeter, D.D. and Noller, H.F. (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. Journal of Molecular Biology 148, 107-127.
9. Cahill, M.M. (1990) Bacterial flora of fishes: a review. Microbial Ecology 19, 21-41.
10. Casamayor, E., Schäfer, H., Bañeras, L., Pedrós- Alió, C. and Muyzer, G. (2000) Identification of spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 66, 499-508.
11. Daims, H., Bruhl, A., Amann, R.I., Schleifer, K.H. and Wagner, M. (1999). The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Systematic and Applied Microbiology 22, 434-444.
12. Franks, A.H., Harmsen, H.J.M., Raangs, G.C., Jansen, G.J., Schut, F. and Welling, G.W. (1998) Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Applied and Environmental Microbiology 64, 3336-3345.
13. Giovannoni, S., Britschgi, T.B., Moyer, C.L. and Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63.
14. Gram, L., Wedell-Neergaard, C. and Huss, H. (1990) The bacteriology of fresh and spoiling Lake Victorian Nile perch (Lates niloticus). International Journal of Food Microbiology 10, 303-316.
15. Gram, L., Melchiorsen, J., Spanggaard, B., Huber, I. and Nielsen, T.F. (1999) Inhibition of Vibrio anguillarum by Pseudomonas fluorescens AH2, a possible probiotic treatment of fish. Applied and Environmental Microbiology 65, 969-973.
16. Griffith, S., Melville, K., Cook, M., Vincent, S., St. Pierre, M. and Lanteigne, C. (2001) Profiling of bacterial species associated with haddock larviculture by PCR amplification of 16S rDNA and denaturing gradient gel electrophoresis. Journal of Aquatic Animal Health 13, 355-363.
17. Holben, W.E., Williams, P., Saarinen, M., Särkilahti, L.K. and Apajalahti, J.H.A. (2002) Phylogenetic analysis of intestinal microflora indicates a novel mycoplasma phylotype in farmed and wild salmon. Microbial Ecology 44, 175-185.
18. Horsley, R.W. (1977) A review of the bacterial flora of teleosts and elasmobranchs, including methods for its analysis. Journal of Fish Biology 10, 529-553.
19. Kämpfer, P., Erhart, R., Beimfohr, C., Böhringer, M., Wagner, R. and Amann, R.I. (1996) Characterization of bacterial communities from activated sludge: culture-dependent numerical identification versus in situ identification using group-and genus-specific rRNA-targeted oligonucleotide probes. Microbial Ecology 32, 101-121.
20. Langendijk, P.S., Schut, F., Jansen, G.J., Raangs, G.C., Kamphuis, G.R., Wilkinson, M.H.F. and Welling, G.W. (1995) Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Applied and Environmental Microbiology 61, 3069-3075.
21. Liesack W. and Stackebrandt, E. (1992) Occurence of novel groups of the domain bacteria as revealed by analysis of the genetic material isolated from an Australian terrestrial environment. Journal of Bacteriology 174, 5072-5078.
22. Liesack, W., Weyland, H. and Stackebrandt, E. (1991) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microbial Ecology 21, 191-198.
23. Ludwig, W. and Strunk, O. (1997) ARB: a software environment for sequence data (http://www.mikro.biologie.tu-muenchen.de/pub/ ARB/documentation/arb.ps).
24. Manz, W., Amann, R.I., Ludwig, W., Wagner, M. and Schleifer, K.H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Systematic and Applied Microbiology 15, 593-600.
25. Manz, W., Amann, R.I., Ludwig, W., Vancanneyt, M. and Schleifer, K.H. (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter- bacteroides in the natural environment. Microbiology 142, 1097-1106.
26. Meier, H., Amann, R.I., Ludwig, W. and Schleifer, K.H. (1999) Specific oligonucleotide probes for in situ detection of a major group of Gram-positive bacteria with low DNA G + C-content. Systematic and Applied Microbiology 22, 186-196.
27. Munro, P.D., Barbour, A. and Birkbeck, T.H. (1994) Comparison of the gut bacterial flora of start-feeding larval turbot under different conditions. Journal of Applied Bacteriology 77, 560-566.
28. Muyzer G., de Waal, E.C. and Uitterlinden, A.G. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59, 695-700.
29. Muyzer, G., Teske, A., Wirsen, C.O. and Jannasch, H.W. (1995) Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples during denaturing gradient gel electrophoresis of 16S rDNA fragments. Archives of Microbiology 164, 165-172.
30. Neef, A. (1997) Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozö nosen. PhD thesis, Department of Microbiology, Technical University Munich.
31. Ohkuma, M. and Kudo, T. (1996) Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes seperatus. Applied and Environmental Microbiology 62, 461-468.
32. Onarheim, A.M. and Raa, J. (1990) Characteristics and possible biological significance of an autochthonous flora in the intestinal mucosa of sea-water fish. In Microbiology in Poecilotherms ed. Lésel, R. pp. 197-201. Amsterdam: Elsevier Science Publishers.
33. Picard, C., Ponsonnet, C., Paget, E., Nesme, X. and Simonet, P. (1992) Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717-2722.
34. Poulsen, L.K., Ballard, G. and Stahl, D. (1993) Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Applied and Environmental Microbiology 59, 1354-1360.
35. Reysenbach, A.L., Giver, L.J., Wickham, S. and Pace, N.R. (1992) Differential amplification of rRNA genes by polymerase chain reaction. Applied and Environmental Microbiology 58, 3417-3418.
36. Ringø, E., Strøm, E. and Tabachek, J.A. (1995) Intestinal microflora of salmonids. A review. Aquaculture Research 26, 773-789.
37. Ringø, E., Lødemel, J.B., Myklebust, R., Kaino, T., Mayhew, T.M. and Olsen, R.E. (2001a) Epithelium-associated bacteria in the gastrointestinal tract of Arctic charr (Salvelinus alpinus L.). An electromicroscopical study. Journal of Applied Microbiology 90, 294-300.
38. Ringø, E., Wesmajervi, M.S., Bendiksen, H.R., Berg, A., Olsen, R.E., Johnsen, T., Mikkelsen, H., Seppola, M. et al. (2001b) Identification and characterization of Carnobacteria isolated from fish intestine. Systematic and Applied Microbiology 24, 183-191.
39. Robinson, I.M., Whipp, S.C., Bucklin, J.A. and Allison, M.J. (1984) Characterization of predominant bacteria from the colons of normal and dysenteric pigs. Applied and Environmental Microbiology 48, 964-969.
40. Roller, C., Wagner, M., Amann, R.I., Ludwig, W. and Schleifer, K.H. (1994) In situ probing of Gram-positive bacteria with high DNA G + C content using 23S rRNA-targeted oligonucleotides. Microbiology 140, 2849-2858.
41. Sakata, T., Okabayashi, J. and Kakimoto, D. (1980a) Variations in the intestinal flora of tilapia reared in fresh and sea water. Bulletin of the Japanese Society of Scientific Fisheries 46, 967-975.
42. Sakata, T., Sugita, H., Mitsuoka, T., Kakimoto, D. and Kadota, H. (1980b) Isolation and distribution of obligate anaerobic bacteria from the intestines of freshwater fish. Bulletin of the Japanese Society of Scientific Fisheries 46, 1249-1255.
43. Singer, S.M. and Nash, T.E. (2000) The role of normal flora in Giardia lamblia infections in mice. Journal of Infectious Diseases 181, 1510-1512.
44. Skov, M.N., Pedersen, K. and Larsen, J.L. (1995) Comparison of pulsed-field gel electrophoresis, ribotyping and plasmid profiling for typing of Vibrio anguillarum serovar O1. Applied and Environmental Microbiology 61, 1540-1545.
45. Spanggaard, B., Huber, I., Nielsen, J., Nielsen, T., Appel, K.F. and Gram, L. (2000) The microflora of rainbow trout: a comparison of traditional and molecular identification. Aquaculture 182, 1-15.
46. Spanggaard, B., Huber, I., Nielsen, J., Slierendrecht, H., Sick, E.B. and Gram, L. (2001) The probiotic potential against vibriosis of the indigenous microflora of rainbow trout. Environmental Microbiology 3, 755-767.
47. Springer, N., Ludwig, W., Drozanski, W., Amann, R.I. and Schleifer, K.H. (1992) The phylogenetic status of Sarcobium lyticum, an obligate intracellular bacterial parasite of small amoebae. FEMS Microbiology Letters 75, 199-202.
48. Stackebrandt, E. and Goebel, B.M. (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44, 846-849.
49. Stackebrandt, E. and Rainey, F.A. (1995) Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies. In Molecular Microbial Ecology Manual, Vol. 3.4.4 ed. Akkermans, A.D.L., van Elsas, J.D. and de Bruijn, F.J. pp. 1-17. Dordrecht: Kluwer Academic Publishers.
50. Stahl, D.A., Flesher, B., Mansfield, H.R. and Montgomery, L. (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Applied and Environmental Microbiology 54, 1079-1084.
51. Sugita, H., Tsunohara, M., Ohkoshi, T. and Degushi, Y. (1988) The establishment of an intestinal microflora in developing goldfish (Carassius auratus) of culture ponds. Microbial Ecology 15, 333-344.
52. Sugita, H., Tanaka, K., Yoshinami, M. and Deguchi, Y. (1995) Distribution of Aeromonas species in the intestinal tracts of river fish. Applied and Environmental Microbiology 61, 4128-4130.
53. Sugita, H., Kawasaki, J. and Deguchi, Y. (1997) Production of amylase by the intestinal microflora of cultured freshwater fish. Letters in Applied Microbiology 42, 105-108.
54. Trust, T.J. and Sparrow, R.A.H. (1974). The bacterial flora in the alimentary tract of freshwater salmonid fishes. Canadian Journal of Microbiology 20, 1219-1228.
55. Van der Waaij, D. (1989) The ecology of the human intestine and its consequences for overgrowth by pathogens such as Clostridium difficile. Annual Review of Microbiology 43, 67-87.
56. Van Elsas, J.D. and van Overbeek, L.S. (1993) Bacterial responses to soil stimuli. In Starvation in Bacteria ed. Kjelleberg, S. pp. 55-80. New York: Plenum Press.
57. Wagner, M., Amann, R.I., Lemmer, H. and Schleifer, K.-H. (1993) Probing activated sludge with oligonucleotides specific for Proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Applied and Environmental Microbiology 59, 1520-1525.
58. Wagner, M., Erhart, R., Manz, W., Amann, R.I., Lemmer, H., Wedi, A. and Schleifer K.H. (1994) Development of an rRNA-targeted oligonucleotide probe for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Applied and Environmental Microbiology 60, 792-800.
59. Westerdahl, A., Olsson, J.C. and Kjelleberg, S. (1991) Isolation and characterization of turbot (Scophthalmus maximus)-isolated associated bacteria with inhibitory effects against Vibrio anguillarum. Applied and Environmental Microbiology 57, 2223-2228.
60. Yoshimizu, M. and Kimura, T. (1976) Study of the intestinal microflora of salmonids. Fish Pathology 10, 243-259.