1887

Abstract

Two Bifidobacterium strains, TMW 2.2057 and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (, , , , and ) demonstrated that both strains represented a member of the genus , with DSM 20096 as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by (ANIb) and DNA–DNA hybridization (isDDH) calculations of their genome sequences confirmed DSM 20096 as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057 and TMW 2.1764 from all hitherto described species of the genus with validly published names. We therefore propose a novel species with the name , for which TMW 2.2057 (=DSM 108414=LMG 31086) is the type strain.

Funding
This study was supported by the:
  • Allianz Industrie Forschung (Award AiF19180 N)
    • Principle Award Recipient: Not Applicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003936
2019-12-20
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/1562.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003936&mimeType=html&fmt=ahah

References

  1. Ventura M, van Sinderen D, Fitzgerald GF, Zink R. Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie Van Leeuwenhoek 2004; 86:205–223 [View Article]
    [Google Scholar]
  2. Biavati B, Mattarelli P. The family Bifidobacteriaceae . The prokaryotes New York: Springer; 2006 pp 322–382
    [Google Scholar]
  3. Tissier H. Recherches sur la flore intestinale des nourrissons (état normal et pathologique). Thesis Université de Paris; 1900 pp 2–253
  4. Modesto M, Michelini S, Stefanini I, Sandri C, Spiezio C et al. Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta). Int J Syst Evol Microbiol 2015; 65:1726–1734 [View Article]
    [Google Scholar]
  5. Tissier H. La reaction chromophile d'Escherich et le bacterium coli. C R Soc Biol 1899; 51:943–945
    [Google Scholar]
  6. Crociani F, Biavati B, Alessandrini A, Chiarini C, Scardovi V. Bifidobacterium inopinatum sp. nov. and Bifidobacterium denticolens sp. nov., two new species isolated from human dental caries. Int J Syst Bacteriol 1996; 46:564–571 [View Article]
    [Google Scholar]
  7. Scardovi V, Crociani F. Bifidobacterium catenulatum, Bifidobacterium dentium, and Bifidobacterium angulatum: Three new species and their deoxyribonucleic acid homology relationships. Int J Syst Bacteriol 1974; 24:6–20 [View Article]
    [Google Scholar]
  8. Beighton D, Al-Haboubi M, Mantzourani M, Gilbert SC, Clark D et al. Oral bifidobacteria: caries-associated bacteria in older adults. J Dent Res 2010; 89:970–974 [View Article]
    [Google Scholar]
  9. Mitsuoka T. Bifidobacteria and their role in human health. J Ind Microbiol 1990; 6:263–267 [View Article]
    [Google Scholar]
  10. Guyonnet D, Chassany O, Ducrotte P, Picard C, Mouret M et al. Effect of a fermented milk containing Bifidobacterium animalis DN-173 010 on the health-related quality of life and symptoms in irritable bowel syndrome in adults in primary care: a multicentre, randomized, double-blind, controlled trial. Aliment Pharmacol Ther 2007; 26:475–486 [View Article]
    [Google Scholar]
  11. Biavati B, Vescovo M, Torriani S, Bottazzi V. Bifidobacteria: history, ecology, physiology and applications. Ann Microbiol 2000; 50:117–132
    [Google Scholar]
  12. Delcenserie V, Gavini F, Beerens H, Tresse O, Franssen C et al. Description of a new species, Bifidobacterium crudilactis sp. nov., isolated from raw milk and raw milk cheeses. Syst Appl Microbiol 2007; 30:381–389 [View Article]
    [Google Scholar]
  13. Watanabe K, Makino H, Sasamoto M, Kudo Y, Fujimoto J et al. Bifidobacterium mongoliense sp. nov., from airag, a traditional fermented mare's milk product from Mongolia. Int J Syst Evol Microbiol 2009; 59:1535–1540 [View Article]
    [Google Scholar]
  14. Laureys D, Cnockaert M, De Vuyst L, Vandamme P. Bifidobacterium aquikefiri sp. nov., isolated from water kefir. Int J Syst Evol Microbiol 2016; 66:1281–1286 [View Article]
    [Google Scholar]
  15. Meile L, Ludwig W, Rueger U, Gut C, Kaufmann P et al. Bifidobacterium lactis sp. nov., a moderately oxygen tolerant species isolated from fermented milk. Syst Appl Microbiol 1997; 20:57–64 [View Article]
    [Google Scholar]
  16. Gulitz A, Stadie J, Ehrmann MA, Ludwig W, Vogel RF. Comparative phylobiomic analysis of the bacterial community of water kefir by 16S rRNA gene amplicon sequencing and ARDRA analysis. J Appl Microbiol 2013; 114:1082–1091 [View Article]
    [Google Scholar]
  17. Laureys D, De Vuyst L, diversity Mspecies. Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation. Appl Environ Microbiol 2014; 80:2564–2572 [View Article]
    [Google Scholar]
  18. Ward HM. V. the ginger-beer plant, and the organisms composing it: a contribution to the study of fermentation-yeasts and bacteria. Philos Trans R Soc London, Ser B 1892125–197
    [Google Scholar]
  19. Lutz L. Recherches biologiques sur la constitution du tibi. Bul Trim Soc Myc Fr 1899; 15:68
    [Google Scholar]
  20. Kebler LF. California bees. J Am Pharm Assoc Am Pharm Assoc 1921; 10:939–943
    [Google Scholar]
  21. Marsh AJ, O'Sullivan O, Hill C, Ross RP, Cotter PD. Sequence-based analysis of the microbial composition of water kefir from multiple sources. FEMS Microbiol Lett 2013; 348:79–85 [View Article]
    [Google Scholar]
  22. Laureys D, Aerts M, Vandamme P, De Vuyst L. Oxygen and diverse nutrients influence the water kefir fermentation process. Food Microbiol 2018; 73:351–361 [View Article]
    [Google Scholar]
  23. Xu D, Bechtner J, Behr J, Eisenbach L, Geißler AJ et al. Lifestyle of Lactobacillus hordei isolated from water kefir based on genomic, proteomic and physiological characterization. Int J Food Microbiol 2019; 290:141–149 [View Article]
    [Google Scholar]
  24. Bechtner J, Xu D, Behr J, Vogel RF. Comparative proteomic analysis of Lactobacillus nagelii and Lactobacillus hordei in the presence of Saccharomyces cerevisiae isolated from water kefir. Front Microbiol 2019; 10:325
    [Google Scholar]
  25. Xu D, Behr J, Geißler AJ, Bechtner J, Ludwig C et al. Label-free quantitative proteomic analysis reveals the lifestyle of Lactobacillus hordei in the presence of Sacchromyces cerevisiae . Int J Food Microbiol 2019; 294:18–26 [View Article]
    [Google Scholar]
  26. Miranda RO, Carvalho AF de, Nero LA. Development of a selective culture medium for bifidobacteria, raffinose-propionate lithium mupirocin (RP-MUP) and assessment of its usage with Petrifilm™ aerobic count plates. Food Microbiol 2014; 39:96–102 [View Article]
    [Google Scholar]
  27. Kern CC, Vogel RF, Behr J. Differentiation of Lactobacillus brevis strains using matrix-assisted-laser-desorption-ionization-time-of-flight mass spectrometry with respect to their beer spoilage potential. Food Microbiol 2014; 40:18–24 [View Article]
    [Google Scholar]
  28. Ehrmann MA, Müller MRA, Vogel RF. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov. Int J Syst Evol Microbiol 2003; 53:7–13 [View Article]
    [Google Scholar]
  29. Jarocki P, Podleśny M, Komoń-Janczara E, Kucharska J, Glibowska A et al. Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level. BMC Microbiol 2016; 16:159–170
    [Google Scholar]
  30. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  31. Madden T. The BLAST sequence analysis tool.. The NCBI Handbook, 2nd edition ed. Bethesda (MD): National Center for Biotechnology Information; 2013
    [Google Scholar]
  32. NCBI Resource Coordinators Database resources of the National center for biotechnology information. Nucleic Acids Res 2013; 41:D8–D20 [View Article]
    [Google Scholar]
  33. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article]
    [Google Scholar]
  34. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
    [Google Scholar]
  35. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095
    [Google Scholar]
  36. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526
    [Google Scholar]
  37. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  38. Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M et al. Tracking the taxonomy of the genus Bifidobacterium based on a phylogenomic approach. Appl Environ Microbiol 2018; 84:e02249–17
    [Google Scholar]
  39. Jian W, Zhu L, Dong X. New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 2001; 51:1633–1638 [View Article]
    [Google Scholar]
  40. Kim BJ, Kim H-Y, Yun Y-J, Kim B-J, Kook Y-H. Differentiation of Bifidobacterium species using partial RNA polymerase β-subunit (rpoB) gene sequences. Int J Syst Evol Microbiol 2010; 60:2697–2704 [View Article]
    [Google Scholar]
  41. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
    [Google Scholar]
  42. Huptas C, Scherer S, Wenning M. Optimized illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly. BMC Res Notes 2016; 9:269 [View Article]
    [Google Scholar]
  43. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
    [Google Scholar]
  44. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. Refseq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article]
    [Google Scholar]
  45. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
    [Google Scholar]
  46. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
    [Google Scholar]
  47. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  48. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
    [Google Scholar]
  49. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article]
    [Google Scholar]
  50. Liu S, Ren F, Zhao L, Jiang L, Hao Y et al. Starch and starch hydrolysates are favorable carbon sources for bifidobacteria in the human gut. BMC Microbiol 2015; 15:54 [View Article]
    [Google Scholar]
  51. Ávila-Fernández Á, Cuevas-Juárez E, Rodríguez-Alegría ME, Olvera C, López-Munguía A. Functional characterization of a novel β-fructofuranosidase from Bifidobacterium longum subsp. infantis ATCC 15697 on structurally diverse fructans. J Appl Microbiol 2016; 121:263–276 [View Article]
    [Google Scholar]
  52. Kim JK, Shin S-Y, Moon JS, Li L, Cho SK et al. Isolation of dextran-hydrolyzing intestinal bacteria and characterization of their dextranolytic activities. Biopolymers 2015; 103:321–327 [View Article]
    [Google Scholar]
  53. De Man JC, Rogosa M, Sharpe ME. A medium for the cultivation of lactobacilli. J Appl Bacteriol 1960; 23:130–135 [View Article]
    [Google Scholar]
  54. Scardovi V. Genus Bifidobacterium . Bergey's Manual of Systematic Bacteriology Baltimore: Williams & Wilkins; 1986 pp 1418–1434
    [Google Scholar]
  55. Schumann P. Peptidoglycan structure. Methods in Microbiology 2011; 38:101–129
    [Google Scholar]
  56. Mattarelli P, Biavati B, Holzapfel WH, Wood BJ. The Bifidobacteria and Related Organisms: Biology, Taxonomy, Applications London, UK: Academic Press; 2017
    [Google Scholar]
  57. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477
    [Google Scholar]
  58. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. Journal of Clinical Microbiology 1982; 16:584–586
    [Google Scholar]
  59. Kuykendall LD, Roy MA, O'NEILL JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  60. Gram HCJ. Ueber die isolirte Färbung Der Schizomyceten: in Schnitt-und Trockenpräparaten. Fortschritte der Medicin 1884; 2:185–189
    [Google Scholar]
  61. Smibert RM, Krieg NR. Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp 409–443
    [Google Scholar]
  62. Gaby W, Hadley C. Practical laboratory test for the identification of Pseudomonas aeruginosa . J Bacteriol 1957; 74:356
    [Google Scholar]
  63. Orban JI, Patterson JA. Modification of the phosphoketolase assay for rapid identification of bifidobacteria. J Microbiol Methods 2000; 40:221–224 [View Article]
    [Google Scholar]
  64. Mattarelli P, Holzapfel W, Franz CMAP, Endo A, Felis GE et al. Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434–1451 [View Article]
    [Google Scholar]
  65. Simpson PJ, Ross RP, Fitzgerald GF, Stanton C. Bifidobacterium psychraerophilum sp. nov. and Aeriscardovia aeriphila gen. nov., sp. nov., isolated from a porcine caecum. Int J Syst Evol Microbiol 2004; 54:401–406 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003936
Loading
/content/journal/ijsem/10.1099/ijsem.0.003936
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error