Restricted Distribution of the Butyrate Kinase Pathway among Butyrate-Producing Bacteria from the Human Colon

Journal of Bacteriology

Volumn 186, Issue 7, 2004, Pages 2099-2106

  Louis, Petra ^a   Duncan, Sylvia H ^a   McCrae, Sheila I ^a   Millar, Jacqueline ^a   Jackson, Michelle S ^a,b   Flint, Harry J ^a  

^a ROWETT RESEARCH INSTITUTE   (United Kingdom)

^b CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; BACTERIAL ENZYME; BUTYRATE KINASE; BUTYRIC ACID; BUTYRYL COENZYME A:ACETATE COENZYME A TRANSFERASE; COENZYME A; PHOSPHOTRANSBUTYRYLASE; PROTEIN KINASE; TRANSFERASE; UNCLASSIFIED DRUG;

ANAEROBIC BACTERIUM; ARTICLE; BACTERIUM ISOLATE; CLOSTRIDIUM; COLON FLORA; DNA FLANKING REGION; ENZYME ACTIVITY; ENZYME LOCALIZATION; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

BACTERIA, ANAEROBIC; BUTYRATES; COENZYME A-TRANSFERASES; COLON; DNA, RIBOSOMAL; ECOSYSTEM; HUMANS; MOLECULAR SEQUENCE DATA; PHOSPHATE ACETYLTRANSFERASE; PHOSPHOTRANSFERASES (CARBOXYL GROUP ACCEPTOR); POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); CLOSTRIDIA; CLOSTRIDIUM; POSIBACTERIA;

EID: 1642277665     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.7.2099-2106.2004     Document Type: Article

References (55)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Atlas, R. M. 1997. In L. C. Parks (ed.), Handbook of microbiological media, p. 1245. CRC Press, Cleveland, Ohio.
3. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1998. Current protocols in molecular biology. John Wiley & Sons Inc., New York, N.Y.
4. Barcenilla, A. 1999. Ph.D. thesis. Robert Gordon University, Aberdeen, United Kingdom.
5. Barcenilla, A., S. E. Pryde, J. C. Martin, S. H. Duncan, C. S. Stewart, C. Henderson, and H. J. Flint. 2000. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl. Environ. Microbiol. 66:1654-1661.
6. Barker, H. A., E. R. Stadtman, and A. Kronberg. 1955. Coenzyme A transferase from Clostridium kluyveri. Methods Enzymol. 1:599-600.
7. Bennett, G. N., and F. B. Rudolph. 1995. The central metabolic pathway from acetyl-CoA to butyryl-CoA in Clostridium acetobutylicum. FEMS Microbiol. Rev. 17:241-249.
8. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler. 2003. GenBank. Nucleic Acids Res. 31:23-27.
9. Blaut, M., M. D. Collins, G. W. Welling, J. Doré, J. van Loo, and W. de Vos. 2002. Molecular biological methods for studying the gut microbiota: the EU human gut flora project. Br. J. Nutr. 87:S203-S211.
10. Bown, R. L., J. A. Gibson, G. E. Sladen, B. Hicks, and A. M. Dawson. 1974. Effects of lactulose and other laxatives on ileal and colonic pH as measured by a radiotelemetry device. Gut 15:999-1004.
11. Boynton, Z. L., G. N. Bennett, and F. B. Rudolph. 1996. Cloning, sequencing, and expression of clustered genes encoding β -hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 178:3015-3024.
12. Brosius, J., M. L. Palmer, P. J. Kennedy, and H. F. Noller. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801-4805.
13. Bruggemann, H., S. Baumer, W. F. Fricke, A. Wiezer, H. Liesegang, I. Decker, C. Herzberg, R. Martinez-Arias, R. Merkl, A. Henne, and G. Gottschalk. 2003. The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc. Natl. Acad. Sci. USA 100:1316-1321.
14. Collins, M. D., P. A. Lawson, A. Willems, J. J. Cordoba, J. Fernandez-Garayzabal, P. Garcia, J. Cai, H. Hippe, and J. A. E. Farrow. 1994. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44:812-826.
15. Cummings, J. H., E. W. Pomare, W. J. Branch, C. P. E. Naylor, and G. T. Macfarlane. 1987. Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut 28:1221-1227.
16. Debarbouille, M., R. Gardan, M. Arnaud, and G. Rapoport. 1999. Role of BkdR, a transcriptional activator of the SigL-dependent isoleucine and valine degradation pathway in Bacillus subtilis. J. Bacteriol. 181:2059-2066.
17. Diez-Gonzalez, F., D. R. Bond, E. Jennings, and J. B. Russell. 1999. Alternative schemes of butyrate production in Butyrivibrio fibrisolvens and their relationship to acetate utilization, lactate production, and phylogeny. Arch. Microbiol. 171:324-330.
18. Duncan, S. H., A. Barcenilia, C. S. Stewart, S. E. Pryde, and H. J. Flint. 2002. Acetate utilization and butyryl coenzyme A (CoA): acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl. Environ. Microbiol. 68:5186-5190.
19. Duncan, S. H., G. L. Hold, A. Barcenilla, C. S. Stewart, and H. J. Flint. 2002. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int. J. Syst. Evol. Microbiol. 52:1615-1620.
20. Duncan, S. H., G. L. Hold, H. J. M. Harmsen, C. S. Stewart, and H. J. Flint. 2002. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 52:2141-2146.
21. Frank, D. N., and N. R. Pace. 2001. Molecular-phylogenetic analyses of human gastrointestinal microbiota. Curr. Opin. Gastroenterol. 17:52-57.
22. Franks, A. H., H. J. M. Harmsen, G. C. Raangs, G. J. Jansen, F. Schut, and G. W. Welling. 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. Guarner, F., and J. R. Malagelada. 2003. Gut flora in health and disease. Lancet 361:512-519.
24. Hobson, P. N. 1969. Rumen bacteria. Methods Microbiol. 3B:133-149.
25. Hold, G. L., S. E. Pryde, V. J. Russell, E. Furrie, and H. J. Flint. 2002. Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol. Ecol. 39:33-39.
26. Huang, K.-X., S. Huang, F. B. Rudolph, and G. N. Bennett. 2000. Identification and characterization of a second butyrate kinase from Clostridium acetobutylicum ATCC 824. J. Mol. Biotechnol. 2:33-38.
27. Macfarlane, G. T., and G. R. Gibson. 1997. Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine, p. 269-318. In R. I. Mackie and B. A. White (ed.), Gastrointestinal microbiology, vol. 1. Chapman & Hall, New York, N.Y.
28. Miller, T. L., and S. E. Jenesel. 1979. Enzymology of butyrate formation by Butyrivibrio fibrisolvens. J. Bacteriol. 138:99-104.
29. Miller, T. L., and M. J. Wolin. 1979. Fermentations by saccharolytic intestinal bacteria. Am. J. Clin. Nutr. 32:164-172.
30. Mitsumori, M., L. Xu, H. Kajikawa, M. Kurihara, K. Tajima, J. Hai, and A. Takenaka. 2003. Possible quorum sensing in the rumen microbial community: detection of quorum-sensing signal molecules from rumen bacteria. FEMS Microbiol. Lett. 219:47-52.
31. 14. Anaerobe 3:373-381.
32. Mullany, P., C. L. Clayton, M. J. Pallen, S. Slone, and A. al-Saleh. 1994. Genes encoding homologues of three consecutive enzymes in the butyrate/butanol-producing pathway of Clostridium acetobutylicum are clustered on the Clostridium difficile chromosome. FEMS Microbiol. Lett. 124:61-68.
33. Myrick, K. V., and W. M. Gelbart. 2002. Universal fast walking for direct and versatile determination of flanking sequence. Gene 284:125-131.
34. Nolling, J., G. Breton, M. V. Omelchenko, K. S. Markarova, Q. Zeng, R. Gibson, H. M. Lee, J. Dubois, D. Qiu, J. Hitti, Y. I. Wolf, R. L. Tatusov, F. Sabathe, L. Doucette-Stamm, P. Soucaille, M. J. Daly, G. N. Bennett, E. V. Koonin, and D. R. Smith. 2001. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183:4823-4838.
35. Oultram, J. D., I. D. Burr, M. J. Elmore, and N. P. Minton. 1993. Cloning and sequence analysis of the genes encoding phosphotransbutyrylase and butyrate kinase from Clostridium acetobutylicum NCIMB 8052. Gene 131: 107-112.
36. Pryde, S. E., S. H. Duncan, G. L. Hold, C. S. Stewart, and H. J. Flint. 2002. The microbiology of butyrate formation in the human colon. FEMS Microbiol. Lett. 217:133-139.
37. Richardson, A. J., G. C. Calder, C. S. Stewart, and A. Smith. 1989. Simultaneous determination of volatile and non-volatile fermentation products of anaerobes by capillary gas chromatography. Lett. Appl. Microbiol. 9:5-8.
38. Rigottier-Gois, L, A. G. Le Bourhis, G. Gramet, V. Rochet, and J. Doré. 2003. Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes. FEMS Microbiol. Ecol. 43:237-245.
39. Roe, A. J., D. McLaggan, I. Davidson, C. O'Byrne, and I. R. Booth. 1998. Perturbation of anion balance during inhibition of growth of Escherichia coli by weak acids. J. Bacteriol. 180:767-772.
40. Rose, I. A. 1955. Acetate kinase of bacteria. Methods Enzymol. 1:591-595.
41. Rose, T. M., E. R. Schultz, J. G. Henikoff, S. Pietrokovski, C. M. McCallum, and S. Henikoff. 1998. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 26:1628-1635.
42. Rumney, C. J., S. H. Duncan, C. Henderson, and C. S. Stewart. 1995. Isolation and characteristics of a wheat bran-degrading Butyrivibrio from human faeces. Lett. Appl. Microbiol. 20:232-236.
43. Schauder, S., K. Shokat, M. G. Surette, and B. L. Bassler. 2001. The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule. Mol. Microbiol. 41:463-476.
44. Schwiertz, A., G. L. Hold, S. H. Duncan, B. Gruhl, M. D. Collins, P. A. Lawson, H. J. Flint, and M. Blaut. 2002. Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces. Syst. Appl. Microbiol. 25:46-51.
45. Setlow, P. 1995. Mechanisms for the prevention of damage to DNA in spores of Bacillus species. Annu. Rev. Microbiol. 49:29-54.
46. Sghir, A., G. Gramet, A. Suau, V. Rochet, P. Pochart, and J. Doré. 2000. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 66:2263-2266.
47. Shimizu, T., K. Ohtani, H. Hirakawa, K. Ohshima, A. Yamashita, T. Shiba, N. Ogasawara, M. Hattori, S. Kuhara, and H. Hayashi. 2002. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc. Natl. Acad. Sci. USA 99:996-1001.
48. Skantar, A. M., and L. K. Carta. 2000. Amplification of Hsp90 homologs from plant-parasitic nematodes using degenerate primers and ramped annealing PCR. BioTechniques 29:1182-1185.
49. Smith, R. F., B. A. Wiese, M. K. Wojzynski, D. B. Davison, and K. C. Worley. 1996. BCM search launcher - an integrated interface to molecular biology data base search and analysis services available on the world wide web. Genome Res. 6:454-462.
50. Suau, A., R. Bonnet, M. Sutren, J.-J. Godon, G. R. Gibson, M. D. Collins, and J. Doré. 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.
51. Wächtershäuser, A., and J. Stein. 2000. Rationale for the luminal provision of butyrate in intestinal diseases. Eur. J. Nutr. 39:164-171.
52. Walter, K. A., R. V. Nair, J. W. Cary, and G. N. Bennett. 1993. Sequence and arrangement of two genes of the butyrate-synthesis pathway of Clostridium acetobutylicum ATCC 824. Gene 134:107-111.
53. Ward, D. E., P. Ross, C. C. van der Weijden, J. L. Snoep, and A. Claiborne. 1999. Catabolism of branched-chain α-keto acids in Enterococcus faecalis: the bkd gene cluster, enzymes, and metabolic route. J. Bacteriol. 181:5433-5442.
54. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.
55. Winzer, K., K. R. Hardie, N. Burgess, N. Doherty, D. Kirke, M. T. G. Holden, R. Linforth, K. A. Cornell, A. J. Taylor, P. J. Hill, and P. Williams. 2002. LuxS: its role in central metabolism and the in vitro synthesis of 4-hydroxy-5-methyl-3(2H)-furanone. Microbiology 148:909-922.