Clostridia dominate 16S rRNA gene libraries prepared from the hindgut of temperate marine herbivorous fishes

Marine Biology

Volumn 150, Issue 6, 2007, Pages 1431-1440

  Clements, Kendall D ^a   Pasch, Isabel B Y ^a   Moran, Damian ^a   Turner, Susan J ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; CLADISTICS; DNA FINGERPRINTING; ENDOSYMBIONT; GENETIC ANALYSIS; HERBIVORE; MICROBIAL COMMUNITY; PERCIFORM; SPECIES DIVERSITY; STOMACH CONTENT;

AUSTRALASIA; HAURAKI GULF; NEW ZEALAND; NORTH ISLAND;

APLODACTYLIDAE; APLODACTYLUS ARCTIDENS; BACTERIA (MICROORGANISMS); CLOSTRIDIA; EUBACTERIUM DESMOLANS; FIRMICUTES; KYPHOSIDAE; KYPHOSUS SYDNEYANUS; LABRIDAE; ODAX PULLUS; PAPILLIBACTER CINNAMIVORANS; PISCES; VERTEBRATA;

EID: 33847284121     PISSN: 00253162     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00227-006-0443-9     Document Type: Article

References (61)

1. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
2. Andreesen JR, Bahl H, Gottschalk G (1989) Introducing the physiology and biochemistry of the genus Clostridium. In: Minton NP, Clarke DJ (eds) Biotechnology Handbook "Clostridia". Plenum Press, New York, pp 27-62
3. Angert ER, Clements KD, Pace NR (1993) The largest bacterium. Nature 362:239-241
4. Angert ER, Brooks AE, Pace NR (1996) Phylogenetic analysis of Metabacterium polyspora: clues to the evolutionary origin of daughter cell production in Epulopiscium species, the largest bacteria. J Bact 178:1451-1456
5. Bjorndal KA (1997) Fermentation in reptiles and amphibians. In: Mackie RI, White BA (eds) Gastrointestinal Microbiology, Vol. 1 Gastrointestinal ecosystems and fermentations. Chapman and Hall, New York, pp 199-230
6. Brosius J, Dull TJ, Sleeter DD, Noller HF (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107-127
7. Caldwell DR, Keeney M, van Soest PJ (1969) Effects of carbon dioxide on growth and maltose fermentation by Bacteroides. J Bacteriol 98:668-676
8. Choat JH, Clements KD (1992) Diet in odacid and aplodactylid fishes from Australia and New Zealand. Aust J Mar Freshwat Res 43:1451-1459
9. Choat JH, Clements KD (1998) Vertebrate herbivores in marine and terrestrial environments: a nutritional ecology perspective. Ann Rev Ecol Syst 29:375-403
10. Clements KD (1991) Endosymbiotic communities of two herbivorous labroid fishes, the temperate Odax pullus and the tropical Scarus rubroviolaceus. Mar Biol 109:223-229
11. Clements KD (1997) Fermentation and gastrointestinal microorganisms in fishes. In: Mackie RI, White BA (eds) Gastrointestinal Microbiology, Vol. 1 Gastrointestinal ecosystems and fermentations. Chapman and Hall, New York, pp 156-198
12. Clements KD, Choat JH (1993) Influence of season, ontogeny and tide on the diet of the temperate marine herbivorous fish Odax pullus (Odacidae). Mar Biol 117:213-220
13. Clements KD, Choat JH (1995) Fermentation in tropical marine herbivorous fishes. Physiol Zool 68:355-378
14. Clements KD, Choat JH (1997) Comparison of herbivory in the closely-related marine fish genera Girella and Kyphosus. Mar Biol 127:579-586
15. Clements KD, Gleeson VP, Slaytor M (1994) Short-chain fatty acid metabolism in temperate marine herbivorous fish. J Comp Physiol B 164:372-377
16. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P, Cai J, Hippie H, Farrow JAE (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44:812-826
17. Defnoun S, Labat M, Ambrosio M, Gacia J-L, Patel BKC (2000) Papillibacter cinnamivorans gen. nov., sp. nov.,a cinnamate-transforming bacterium from ashea cake digester. Int J Syst and Evol Microbiol 50:1221-1228
18. Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nuc Acid Res 12:387-395
19. Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ (2002) Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol 52:2141-2146
20. Fidopiastis PM, Bezdek DJ, Horn MH, Kandel JS (2006) Characterizing the resident, fermentative microbial consortium in the hindgut of the temperate-zone herbivorous fish, Hermosilla azurea (Teleostei: Kyphosidae). Mar Biol 148:631-642 DOI 10.1007/s00227-005-0106-2
21. Forney LJ, Zhou X, Brown CJ (2004) Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 7:210-220
22. Franks AH, Harmsen HJM, Raangs GC, Jansen GJ, Schut F, Welling GW (1998) Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 64:3336-3345
23. Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrica 40:237-264
24. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95-98
25. Heilig HGHJ, Zoetendal EG, Vaughan EE, Marteau P, Akkermans ADL, De Vos WM (2002) Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl Environ Microbiol 68:114-123
26. Hespell RB, Akin DE, Dehority BA (1997) Bacteria, fungi, and protozoa of the rumen. In:Mackie RI, White BA, Isaacson RE (eds) Gastrointestinal Microbiology, vol. 2, Gastrointestinal microbiology and host interactions. Chapman and Hall, New York, pp 59-141
27. Holt JG, Krieg NR, Sneath PHA, Staley JT, Williams ST (eds) (1994) Bergey's Manual of Determinative Bacteriology, Ninth Edition. Williams and Wilkins, Baltimore
28. Hongoh Y, Ohkuma M, Kudo T (2003) Molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidae). FEMS Microbiol Ecol 44:231-242
29. Horn MH (1989) Biology of marine herbivorous fishes. Oceanogr Mar Biol Annu Rev 27:167-272
30. Howlett MR, Mountfort DO, Turner KW, Roberton AM (1976) Metabolism and growth yields in Bacteroides ruminicola strain b14. Appl Environ Microbiol 32:274-283
31. Leff LG, Dana JR, McArthur JV, Shimkets LJ (1995) Comparison of methods of DNA extraction from stream sediments. Appl Envir Microbiol 61:1141-1143
32. Luczkovich JJ, Stellwag EJ (1993) Isolation of cellulolytic microbes from the intestinal tract of the pinfish, Lagodon rhomboides: size-related changes in diet and microbial abundance. Mar Biol 116:381-388
33. Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Envir Microbiol 65:4715-4724
34. Moran D, Clements KD (2002) Diet and endogenous carbohydrases in the temperate marine herbivorous fish Kyphosus sydneyanus. J Fish Biol 60:1190-1203
35. Moran D, Turner SJ, Clements KD (2004) Ontogenetic development of the gastrointestinal microbiota in the marine herbivorous fish Kyphosus sydneyanus. Microb Ecol 49:590-597
36. Mountfort DO, Rhodes LL (1991) Anaerobic growth and fermentation characteristics of Paecilomyces -lilacinus isolated from mullet gut. Appl Environ Microbiol 57:1963-1968
37. Mountfort DO, Grant WD, Morgan H, Rainey FA, Stackebrandt E (1993) Isolation and characterization of an obligately anaerobic, pectinolytic, member of the genus Eubacterium from mullet gut. Arch Microbiol 159:289-295
38. Mountfort DO, Rainey FA, Burghardt J, Stackebrandt E (1994) Clostridium grantii sp. nov., a new obligately anaerobic, alginolytic bacterium isolated from mullet gut. Arch Microbiol 162:173-179
39. Mountfort DO, Campbell J, Clements KD (2002) Hindgut fermentation in three species of marine herbivorous fish. Appl Environ Microbiol 68:1374-1380
40. Nelson KE (2003) The future of microbial genomics. Environ Microbiol 5:1223-1225
41. Nelson KE, Zinder SH, Hance I, Burr P, Odongo D, Wasawo D, Odenyo A, Bishop R (2003) Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract:insights into an unexplored niche. Environ Microbiol 5:1212-1220
42. Nölling J, Breton G, Omelchenko MV, Makarova KS, Zeng Q, Gibson R, Lee HM, Dubois J, Qiu D, Hitti J, GTC Sequencing Center Production, Finishing, Bioinformatics teams, Wolf YI, Tatusov RL, Sabathe F, Doucette-Stamm L, Soucaille P, Daly MJ, Bennett GM, Koonin EV, Smith DR (2001) Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bact 183:4823-4838
43. Ohkuma M, Kudo T (1996) Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl Environ Microbiol 62:461-468
44. Percival E, McDowell RH (1967) Chemistry and enzymology of marine algal polysaccharides. Academic Press, London
45. Ramirez RF, Dixon BA (2003) Enzyme production by obligate intestinal anaerobic bacteria isolated from oscars (Astronotus ocellatus), angelfish (Pterophyllum scalare) and southern flounder (Paralichthys lethostigma). Aquaculture 227:417-426
46. Rimmer DW, Wiebe WJ (1987) Fermentative microbial digestion in herbivorous fishes. J Fish Biol 31:229-236
47. Saul DJ, Aislabie JM, Brown CE, Harris LA, Foght J (2005) Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol Ecol 53:141-155
48. Seeto GS, Veivers PC, Clements KD, Slaytor M (1996) Carbohydrate utilization by microbial symbionts in the marine herbivorous fishes Odax cyanomelas and Crinodus lophodon. J Comp Physiol B 165:571-579
49. Sghir A, Gramet G, Suau A, Rochet V, Pochart P, Dore J (2000) Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol 66:2263-2266
50. Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba T, Ogasawara N, Hattori M, Kuhara S, Hayashi H (2002) Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci USA 99:996-1001
51. Skea GL, Mountfort DO, Clements KD (2005) A quantitative study of gut carbohydrases from the New Zealand marine herbivorous fishes Kyphosus sydneyanus (Kyphosidae), Aplodactylus arctidens (Aplodactylidae) and Odax pullus (Labridae). Comp Biochem Physiol B 140:259-269
52. Stevens C, Hume I (1995) Comparative physiology of the vertebrate system, 2nd edn. Cambridge University Press, Cambridge, Mass
53. Suau A, Bonnet R, Sutern M, Godon JJ, Gibson GR, Collins MD, Doré J (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65:4799-4807
54. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Envir Microbiol 62:625-630
55. Swofford D (1999) PAUP* Phylogenetic Analysis using Maximum Parsimony (* and other methods), 4.04 ed. Sinauer Associates, Sunderland, MA
56. Tajima K, Aminov RI, Nagamine T, Ogata K, Nakamura M, Matsui H, Benno Y (1999) Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol Ecol 29:159-169
57. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multipble sequence alignment aided by qualitiy analysis tools. Nucleic Acids Res 24:4876-4882
58. Van Soest PJ (1994) Nutritional ecology of the ruminant, 2nd edn. Cornell University Press, Ithaca, NY
59. Whitford MF, Forster RJ, Beard CE, Gong J, Teather RM (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4:153-163
60. Wilson KH (1997) Biota of the human gastrointestinal tract. In Mackie RI, Whie BA, Isaacson RE (eds) Gastrointestinal Microbiology, vol. 2, Gastrointestinal microbiology and host interactions. Chapman and Hall, New York, pp 39-58
61. Wintzingerode FV, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microb Rev 21:213-229