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Abstract

Six strains of anaerobic bacteria, C13EG70, C13EG118, C13EG186, C13GAMG5, C13GAMG28 and C13GAMG40, were isolated from the caecum of a healthy chicken bred in Bogor, Indonesia. Phylogenetic analysis showed the isolates were separated into two groups. Group I (C13EG70 and C13EG118) showed nearly identical 16S rRNA gene sequences (99.9 % sequence similarity). Group II (C13EG186, C13GAMG5, C13GAMG28 and C13GAMG40) showed nearly identical 16S rRNA gene sequences (>99.4 % sequence similarity). The isolates showed low 16S rRNA gene sequence similarities to recognized species of the genus . High gene sequence similarities were found between type strains (C13EG70 and C13EG186) and JCM 13657 (87.9, 91.5 %, respectively). Physiological, biochemical and genotypic characteristics demonstrated that these strains could be separated from the type strain of . It is concluded that Group I and Group II represent novel species. Two novel species of the genus are proposed as sp. nov. (type strain C13EG70 = LIPI12-4-Ck732 = JSAT12-4-Ck732 = InaCC B449 = NBRC 110958) and sp. nov. (type strain C13EG186 = LIPI12-4-Ck844 = JSAT12-4-Ck884 = InaCC B451 = NBRC 110963).

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2016-03-01
2022-01-27
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References

  1. Collins M. D., Jones D. 1981; Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354[PubMed]
    [Google Scholar]
  2. Darriba D., Taboada G. L., Doallo R., Posada D. 2012; jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772 [View Article][PubMed]
    [Google Scholar]
  3. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  4. Guindon S., Gascuel O. 2003; A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [View Article][PubMed]
    [Google Scholar]
  5. Holdeman L. V., Cato E. P., Moore W. E. C.editors 1977 Anaerobe Laboratory Manual, 4th edn. Blacksburg, VA: Virginia Polytechnic Institute and State University;
    [Google Scholar]
  6. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [View Article][PubMed]
    [Google Scholar]
  7. Kitahara M., Takamine F., Imamura T., Benno Y. 2001; Clostridium hiranonis sp. nov., a human intestinal bacterium with bile acid 7α-dehydroxylating activity. Int J Syst Evol Microbiol 51:39–44 [View Article][PubMed]
    [Google Scholar]
  8. Kitahara M., Sakamoto M., Benno Y. 2010; Lactobacillus similis sp. nov., isolated from fermented cane molasses. Int J Syst Evol Microbiol 60:187–190 [View Article][PubMed]
    [Google Scholar]
  9. Komagata K., Suzuki K. 1987; Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207 [View Article]
    [Google Scholar]
  10. Lan P. T., Hayashi H., Sakamoto M., Benno Y. 2002; Phylogenetic analysis of cecal microbiota in chicken by the use of 16S rDNA clone libraries. Microbiol Immunol 46:371–382 [View Article][PubMed]
    [Google Scholar]
  11. Lan P. T., Sakamoto M., Sakata S., Benno Y. 2006; Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum. Int J Syst Evol Microbiol 56:2853–2859 [View Article][PubMed]
    [Google Scholar]
  12. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A., other authors. 2007; Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  13. Lu J., Idris U., Harmon B., Hofacre C., Maurer J. J., Lee M. D. 2003; Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl Environ Microbiol 69:6816–6824 [View Article][PubMed]
    [Google Scholar]
  14. Mayberry W. R., Lambe D. W. Jr, Ferguson K. P. 1982; Identification of Bacteroides species by cellular fatty acid profiles. Int J Syst Bacteriol 32:21–27 [View Article]
    [Google Scholar]
  15. Miyagawa E., Azuma R., Suto T. 1979; Cellular fatty acid composition in gram-negative obligately anaerobic rods. J Gen Appl Microbiol 25:41–51 [View Article]
    [Google Scholar]
  16. Qu A., Brulc J. M., Wilson M. K., Law B. F., Theoret J. R., Joens L. A., Konkel M. E., Angly F., Dinsdale E. A., other authors. 2008; Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3:e2945 [View Article][PubMed]
    [Google Scholar]
  17. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  18. Sakamoto M., Ohkuma M. 2010; Usefulness of the hsp60 gene for the identification and classification of Gram-negative anaerobic rods. J Med Microbiol 59:1293–1302 [View Article][PubMed]
    [Google Scholar]
  19. Sakamoto M., Ohkuma M. 2011; Identification and classification of the genus Bacteroides by multilocus sequence analysis. Microbiology 157:3388–3397 [View Article][PubMed]
    [Google Scholar]
  20. Sakamoto M., Ohkuma M. 2013; Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus). Int J Syst Evol Microbiol 63:691–695 [View Article][PubMed]
    [Google Scholar]
  21. Sakamoto M., Suzuki M., Umeda M., Ishikawa I., Benno Y. 2002; Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol 52:841–849[PubMed]
    [Google Scholar]
  22. Sakamoto M., Suzuki M., Huang Y., Umeda M., Ishikawa I., Benno Y. 2004; Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 54:877–883 [View Article][PubMed]
    [Google Scholar]
  23. Sakamoto M., Huang Y., Umeda M., Ishikawa I., Benno Y. 2005; Prevotella multiformis sp. nov., isolated from human subgingival plaque. Int J Syst Evol Microbiol 55:815–819 [View Article][PubMed]
    [Google Scholar]
  24. Sakamoto M., Suzuki N., Benno Y. 2010; hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes . Int J Syst Evol Microbiol 60:2984–2990 [View Article][PubMed]
    [Google Scholar]
  25. Sakamoto M., Tanaka Y., Benno Y., Ohkuma M. 2014; Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas . Int J Syst Evol Microbiol 64:2992–2997 [View Article][PubMed]
    [Google Scholar]
  26. Shah H. N. 1992; The genus Bacteroides and related taxa. In The Prokaryotes, 2nd edn.. pp 3593–3607Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. New York: Springer; [View Article]
    [Google Scholar]
  27. Shah H. N., Collins M. D. 1983; Genus Bacteroides. A chemotaxonomical perspective. J Appl Bacteriol 55:403–416 [View Article][PubMed]
    [Google Scholar]
  28. Song Y., Liu C., Finegold S. M. 2011; Genus I. Bacteroides Castellani and Chalmers 1919, 959AL emend. Shah and Collins 1989, 85. In Bergey's Manual of Systematic Bacteriology, 2nd edn.. vol. 4 pp 27–41Edited by Krieg N. R., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N. L., Brown D. R., Parte A. New York: Springer;
    [Google Scholar]
  29. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
    [Google Scholar]
  30. Thomas D. H., Skadhauge E. 1988; Transport function and control in bird caeca. Comp Biochem Physiol A 90:591–596 [View Article][PubMed]
    [Google Scholar]
  31. Zhu X. Y., Zhong T., Pandya Y., Joerger R. D. 2002; 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl Environ Microbiol 68:124–137 [View Article][PubMed]
    [Google Scholar]
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