Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes

International Journal of Systematic and Evolutionary Microbiology

Volumn 64, Issue PART 6, 2014, Pages 2137-2145

  Qiu, Yan Ling ^a,b   Hanada, Satoshi ^b   Kamagata, Yoichi ^c   Guo, Rong Bo ^a   Sekiguchi, Yuji ^b  

^a QINGDAO INSTITUTE OF BIOENERGY AND BIOPROCESS TECHNOLOGY   (China)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOGLUTARIC ACID; ACETIC ACID; ALANINE; ALCOHOL; ARGININE; ASPARAGINE; ASPARTIC ACID; BUTANOL; CASAMINO ACID; CYSTEINE; FUMARIC ACID; GLUCOSE; GLUTAMIC ACID; GLUTAMINE; GLYCEROL; HISTIDINE; HYDROGEN; ISOLEUCINE; LACTIC ACID; LEUCINE; LYSINE; MALIC ACID; METHIONINE; PROPANOL; PYRUVIC ACID; RIBOSE; SERINE; THREONINE; VALINE; XYLOSE;

AMINIVIBRIO PYRUVATIPHILUS; AMINOBACTERIUM COLOMBIENSE; ARTICLE; BACTERIAL CELL; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM ISOLATION; CELL MOTILITY; COCULTURE; DNA BASE COMPOSITION; FERMENTATION; GENE SEQUENCE; GENETIC SIMILARITY; GRAM NEGATIVE ANAEROBIC BACTERIA; INCUBATION TEMPERATURE; LACTIVIBRIO ALCOHOLICUS; MESOPHILIC BACTERIUM; METHANOSPIRILLUM HUNGATEI; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UPFLOW REACTOR; WASTE WATER MANAGEMENT; YEAST;

ALCOHOLS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CARBOHYDRATE METABOLISM; DNA, BACTERIAL; FATTY ACIDS; FERMENTATION; GRAM-NEGATIVE ANAEROBIC STRAIGHT, CURVED, AND HELICAL RODS; LACTIC ACID; MOLECULAR SEQUENCE DATA; PHOSPHOLIPIDS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEWAGE; WASTE DISPOSAL, FLUID;

EID: 84902684940     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.060681-0     Document Type: Article

References (44)

1. Allison, M. J., Mayberry, W. R., McSweeny, C. S. & Stahl, D. A. (1992). Synergistes jonesii, gen. nov., sp. nov.: a rumen bacterium that degrades toxic pyridinediols. Syst Appl Microbiol 15, 522-529.
2. Baena, S., Fardeau, M. L., Labat, M., Ollivier, B., Thomas, P., Garcia, J. L. & Patel, B. K. (1998). Aminobacterium colombiense gen. nov. sp. nov., an amino acid-degrading anaerobe isolated from anaerobic sludge. Anaerobe 4, 241-250.
3. Baena, S., Fardeau, M. L., Ollivier, B., Labat, M., Thomas, P., Garcia, J. L. & Patel, B. K. C. (1999). Aminomonas paucivorans gen. nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium. Int J Syst Bacteriol 49, 975-982.
4. Baena, S., Fardeau, M. L., Labat, M., Ollivier, B., Garcia, J. L. & Patel, B. K. C. (2000). Aminobacterium mobile sp. nov., a new anaerobic amino-acid-degrading bacterium. Int J Syst Evol Microbiol 50, 259-264.
5. Caporaso, J. G., Bittinger, K., Bushman, F. D., DeSantis, T. Z., Andersen, G. L. & Knight, R. (2010). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267.
6. Chouari, R., Le Paslier, D., Dauga, C., Daegelen, P., Weissenbach, J. & Sghir, A. (2005). Novel major bacterial candidate division within a municipal anaerobic sludge digester. Appl Environ Microbiol 71, 2145-2153.
7. Dahle, H. & Birkeland, N. K. (2006). Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-aciddegrading bacterium isolated from a North Sea oil well. Int J Syst Evol Microbiol 56, 1539-1545.
8. Davis, C. K., Webb, R. I., Sly, L. I., Denman, S. E. & McSweeney, C. S. (2012). Isolation and survey of novel fluoroacetate-degrading bacteria belonging to the phylum Synergistetes. FEMS Microbiol Ecol 80, 671-684.
9. Delbès, C., Moletta, R. & Godon, J. (2001). Bacterial and archaeal 16S rDNA and 16S rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem. FEMS Microbiol Ecol 35, 19-26.
10. Díaz, C., Baena, S., Fardeau, M. L. & Patel, B. K. (2007). Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor. Int J Syst Evol Microbiol 57, 1914-1918.
11. Doetsch, R. N. (1981). Determinative methods of light microscopy. In Manual of Methods for General Bacteriology, pp. 21-33. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips. Washington, DC: American Society for Microbiology.
12. Downes, J., Vartoukian, S. R., Dewhirst, F. E., Izard, J., Chen, T., Yu, W.-H., Sutcliffe, I. C. & Wade, W. G. (2009). Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity. Int J Syst Evol Microbiol 59, 972-980.
13. Ganesan, A., Chaussonnerie, S., Tarrade, A., Dauga, C., Bouchez, T., Pelletier, E., Le Paslier, D. & Sghir, A. (2008). Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-aciddegrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester. Int J Syst Evol Microbiol 58, 2003-2012.
14. Godon, J. J., Zumstein, E., Dabert, P., Habouzit, F. & Moletta, R. (1997). Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 63, 2802-2813.
15. Godon, J. J., Morinière, J., Moletta, M., Gaillac, M., Bru, V. & Delgènes, J. P. (2005). Rarity associated with specific ecological niches in the bacterial world: the 'Synergistes' example. Environ Microbiol 7, 213-224.
16. Hanada, S., Takaichi, S., Matsuura, K. & Nakamura, K. (2002). Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 52, 187-193.
17. Hiraishi, A. (1992). Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 15, 210-213.
18. Honda, T., Fujita, T. & Tonouchi, A. (2013). Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field. Int J Syst Evol Microbiol 63, 3679-3686.
19. Horz, H. P., Citron, D. M., Warren, Y. A., Goldstein, E. J. & Conrads, G. (2006). Synergistes group organisms of human origin. J Clin Microbiol 44, 2914-2920.
20. Hugenholtz, P., Hooper, S. D. & Kyrpides, N. C. (2009). Focus: Synergistetes. Environ Microbiol 11, 1327-1329.
21. Ito, T., Yoshiguchi, K., Ariesyady, H. D. & Okabe, S. (2011). Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge. ISME J 5, 1844-1856.
22. Jumas-Bilak, E., Carlier, J. P., Jean-Pierre, H., Citron, D., Bernard, K., Damay, A., Gay, B., Teyssier, C., Campos, J. & Marchandin, H. (2007). Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum 'Synergistetes' isolated from man. Int J Syst Evol Microbiol 57, 2743-2748.
23. Jumas-Bilak, E., Roudière, L. & Marchandin, H. (2009). Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'. Int J Syst Evol Microbiol 59, 1028-1035.
24. Kamagata, Y. & Mikami, E. (1991). Isolation and characterization of a novel thermophilic Methanosaeta strain. Int J Syst Bacteriol 41, 191-196.
25. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors (2004). ARB: a software environment for sequence data. Nucleic Acids Res 32, 1363-1371.
26. McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., Andersen, G. L., Knight, R. & Hugenholtz, P. (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610-618.
27. Menes, R. J. & Muxí, L. (2002). Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum. Int J Syst Evol Microbiol 52, 157-164.
28. Narihiro, T., Terada, T., Kikuchi, K., Iguchi, A., Ikeda, M., Yamauchi, T., Shiraishi, K., Kamagata, Y., Nakamura, K. & Sekiguchi, Y. (2009). Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microbes Environ 24, 88-96.
29. Rees, G. N., Patel, B. K. C., Grassia, G. S. & Sheehy, A. J. (1997). Anaerobaculum thermoterrenum gen. nov., sp. nov., a novel, thermophilic bacterium which ferments citrate. Int J Syst Bacteriol 47, 150-154.
30. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
31. Salminen, E. & Rintala, J. (2002). Anaerobic digestion of organic solid poultry slaughterhouse waste-a review. Bioresour Technol 83, 13-26.
32. Schink, B. & Stams, A. J. (2006). Syntrophism among prokaryotes. In The Prokaryotes, 3rd edn, vol 2, pp. 309-335. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer & E. Stackebrandt. New York: Springer.
33. Sekiguchi, Y., Kamagata, Y., Nakamura, K., Ohashi, A. & Harada, H. (2000). Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int J Syst Evol Microbiol 50, 771-779.
34. Sekiguchi, Y., Yamada, T., Hanada, S., Ohashi, A., Harada, H. & Kamagata, Y. (2003). Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53, 1843-1851.
35. Shintani, T., Liu, W. T., Hanada, S., Kamagata, Y., Miyaoka, S., Suzuki, T. & Nakamura, K. (2000). Micropruina glycogenica gen. nov., sp. nov., a new Gram-positive glycogen-accumulating bacterium isolated from activated sludge. Int J Syst Evol Microbiol 50, 201-207.
36. Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690.
37. Surkov, A. V., Dubinina, G. A., Lysenko, A. M., Glöckner, F. O. & Kuever, J. (2001). Dethiosulfovibrio russensis sp. nov., Dethosulfovibrio marinus sp. nov. and Dethosulfovibrio acidaminovorans sp. nov., novel anaerobic, thiosulfate-and sulfur-reducing bacteria isolated from 'Thiodendron' sulfur mats in different saline environments. Int J Syst Evol Microbiol 51, 327-337.
38. Swofford, D. L. (2003). PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4., Sunderland, MA: Sinauer Associates.
39. Tindall, B. J. (1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199-202.
40. Vartoukian, S. R., Palmer, R. M. & Wade, W. G. (2007). The division "Synergistes". Anaerobe 13, 99-106.
41. Vartoukian, S. R., Downes, J., Palmer, R. M. & Wade, W. G. (2013). Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 63, 458-463.
42. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. (1991). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697-703.
43. Zavarzina, D. G., Zhilina, T. N., Tourova, T. P., Kuznetsov, B. B., Kostrikina, N. A. & Bonch-Osmolovskaya, E. A. (2000). Thermanaerovibrio velox sp. nov., a new anaerobic, thermophilic, organotrophic bacterium that reduces elemental sulfur, and emended description of the genus Thermanaerovibrio. Int J Syst Evol Microbiol 50, 1287-1295.
44. Zhang, T., Ke, S. Z., Liu, Y. & Fang, H. P. (2005). Microbial characteristics of a methanogenic phenol-degrading sludge. Water Sci Technol 52, 73-78.