1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 8

Variable regions of the glyS, infB and rplB genes usable as novel genetic markers for identification and phylogenetic purposes of genera belonging to the family Propionibacteriaceae Free

Abstract

No common, unique genetic markers applicable to classification and phylogenetics for significant genera within the Propionibacteriaceae family have been suggested yet. Therefore, the aim of the study was to propose those genes in the genera Acidipropionibacterium , Cutibacterium , Propionibacterium and Pseudopropionibacterium . These genera were recently elicited from the genus Propionibacterium through whole genomic analyses. Three housekeeping genes, glyS, infB and rplB, were selected from many others according to the requirements for appropriate classification/phylogenetic markers. Concrete fragments of the genes were amplified using specific primers in most of the type (14) and 11 wild strains (originating from dairy products, human skin and the crop of a laying hen) recently classified into the genus Propionibacterium . Sequences obtained from amplicons were used to perform gene statistics and phylogenetic analyses with respect to applicability in classification, typing and phylogeny. The 16S rRNA gene sequences, still considered relevant in spite of its proven shortcomings as a basic tool for evaluation of bacterial phylogeny, were used as a baseline for comparative analyses. The statistics of the gene sequences revealed that the variable regions of all three genes have higher resolution capabilities among strains examined compared to the 16S rRNA gene analysis. Phylogenetic analyses based on individual gene sequences and their concatenate enabled to distinguish clusters of species belonging to the genera Acidipropionibacterium , Cutibacterium and Propionibacterium , which corresponds with a recently reported genomic study. Thus, the crucial importance of this study is the economically advantageous classification and typing of propionibacterial isolates and strains through the three gene regions in contrast to the requirement for whole genomic assays.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): classification , glyS, infB and rplB genes , phylogenetics , Propionibacteriaceae and Propionibacterium
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002873
2018-06-27
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/8/2697.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002873&mimeType=html&fmt=ahah

References

  1. Scholz CF, Kilian M. The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int J Syst Evol Microbiol 2016; 66:4422–4432 [View Article][PubMed]
     [Google Scholar]
  2. Downes J, Wade WG. Propionibacterium acidifaciens sp. nov., isolated from the human mouth. Int J Syst Evol Microbiol 2009; 59:2778–2781 [View Article][PubMed]
     [Google Scholar]
  3. Kusano K, Yamada H, Niwa M, Yamasato K. Propionibacterium cyclohexanicum sp. nov., a new acid-tolerant omega-cyclohexyl fatty acid-containing propionibacterium isolated from spoiled orange juice. Int J Syst Bacteriol 1997; 47:825–831 [View Article][PubMed]
     [Google Scholar]
  4. Lucena-Padrós H, González JM, Caballero-Guerrero B, Ruiz-Barba JL, Maldonado-Barragán A. Propionibacterium olivae sp. nov. and Propionibacterium damnosum sp. nov., isolated from spoiled packaged Spanish-style green olives. Int J Syst Evol Microbiol 2014; 64:2980–2985 [View Article][PubMed]
     [Google Scholar]
  5. Rabah H, Rosa do Carmo FL, Jan G. Dairy propionibacteria: versatile probiotics. Microorganisms 2017; 5:24 [View Article][PubMed]
     [Google Scholar]
  6. Goldschmidt P, Ferreira CC, Degorge S, Benallaoua D, Boutboul S et al. Rapid detection and quantification of Propionibacteriaceae. Br J Ophthalmol 2009; 93:258–262 [View Article][PubMed]
     [Google Scholar]
  7. Piveteau P. Metabolism of lactate and sugars by dairy propionibacteria: a review. Lait 1999; 79:23–41 [View Article]
     [Google Scholar]
  8. Meile L, Le Blay G, Thierry A. Safety assessment of dairy microorganisms: Propionibacterium and Bifidobacterium. Int J Food Microbiol 2008; 126:316–320 [View Article][PubMed]
     [Google Scholar]
  9. Le Maréchal C, Peton V, Plé C, Vroland C, Jardin J et al. Surface proteins of Propionibacterium freudenreichii are involved in its anti-inflammatory properties. J Proteomics 2015; 113:447–461 [View Article][PubMed]
     [Google Scholar]
  10. Zárate G, Palacios JM, Villena J, Zúñiga-Hansen ME. Inhibition of enteropathogens adhesion to human enterocyte-like HT-29 cells by a dairy strain of Propionibacterium acidipropionici. Benef Microbes 2016; 7:431–441 [View Article][PubMed]
     [Google Scholar]
  11. Argañaraz-Martínez E, Babot JD, Apella MC, Perez Chaia A. Physiological and functional characteristics of Propionibacterium strains of the poultry microbiota and relevance for the development of probiotic products. Anaerobe 2013; 23:27–37 [View Article][PubMed]
     [Google Scholar]
  12. Martínez EA, Babot JD, Lorenzo-Pisarello MJ, Apella MC, Chaia AP. Feed supplementation with avian Propionibacterium acidipropionici contributes to mucosa development in early stages of rearing broiler chickens. Benef Microbes 2016; 7:687–698 [View Article][PubMed]
     [Google Scholar]
  13. Mak TN, Yu SH, De Marzo AM, Brüggemann H, Sfanos KS. Multilocus sequence typing (MLST) analysis of Propionibacterium acnes isolates from radical prostatectomy specimens. Prostate 2013; 73:770–777 [View Article][PubMed]
     [Google Scholar]
  14. Yedidya I, Goldberg E, Sharoni R, Sagie A, Vaturi M. Infective endocarditis caused by Propionibacterium granulosum. Isr Med Assoc J 2015; 17:642–643[PubMed]
     [Google Scholar]
  15. Wunderink HF, Lashley EE, van Poelgeest MI, Gaarenstroom KN, Claas EC et al. Pelvic actinomycosis-like disease due to Propionibacterium propionicum after hysteroscopic removal of an intrauterine device. J Clin Microbiol 2011; 49:466–468 [View Article][PubMed]
     [Google Scholar]
  16. Dalmasso M, Nicolas P, Falentin H, Valence F, Tanskanen J et al. Multilocus sequence typing of Propionibacterium freudenreichii. Int J Food Microbiol 2011; 145:113–120 [View Article][PubMed]
     [Google Scholar]
  17. Kilian M, Scholz CF, Lomholt HB. Multilocus sequence typing and phylogenetic analysis of Propionibacterium acnes. J Clin Microbiol 2012; 50:1158–1165 [View Article][PubMed]
     [Google Scholar]
  18. Lomholt HB, Kilian M. Population genetic analysis of Propionibacterium acnes identifies a subpopulation and epidemic clones associated with acne. PLoS One 2010; 5:e12277 [View Article][PubMed]
     [Google Scholar]
  19. McDowell A, Barnard E, Nagy I, Gao A, Tomida S et al. An expanded multilocus sequence typing scheme for Propionibacterium acnes: investigation of 'pathogenic', 'commensal' and antibiotic resistant strains. PLoS One 2012; 7:e41480 [View Article][PubMed]
     [Google Scholar]
  20. McDowell A, Nagy I, Magyari M, Barnard E, Patrick S. The opportunistic pathogen Propionibacterium acnes: insights into typing, human disease, clonal diversification and CAMP factor evolution. PLoS One 2013; 8:e70897 [View Article][PubMed]
     [Google Scholar]
  21. Patwardhan A, Ray S, Roy A. Molecular markers in phylogenetic studies – a review. J Phylogen Evol Biol 2014; 2:131
     [Google Scholar]
  22. Wu D, Jospin G, Eisen JA. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One 2013; 8:e77033 [View Article][PubMed]
     [Google Scholar]
  23. Thierry A, Madec MN. Enumeration of propionibacteria in raw milk using a new selective medium. Lait 1995; 75:315–323 [View Article]
     [Google Scholar]
  24. Loy A, Lehner A, Lee N, Adamczyk J, Meier H et al. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 2002; 68:5064–5081 [View Article][PubMed]
     [Google Scholar]
  25. Ehrmann MA, Müller MR, Vogel RF. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov. Int J Syst Evol Microbiol 2003; 53:7–13 [View Article][PubMed]
     [Google Scholar]
  26. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  27. Killer J, Mekadim C, Pechar R, Bunešová V, Mrázek J et al. Gene encoding the CTP synthetase as an appropriate molecular tool for identification and phylogenetic study of the family Bifidobacteriaceae. Microbiologyopen 2018e579 [View Article][PubMed]
     [Google Scholar]
  28. Martin DP, Lemey P, Lott M, Moulton V, Posada D et al. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010; 26:2462–2463 [View Article][PubMed]
     [Google Scholar]
  29. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  30. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article][PubMed]
     [Google Scholar]
  31. Tomasini N, Lauthier JJ, Llewellyn MS, Diosque P. MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms. Infect Genet Evol 2013; 20:188–196 [View Article][PubMed]
     [Google Scholar]
  32. Patrick S, McDowell A.  Propionibacterium. In Bergey's Manual of Systematics of Archaea and Bacteria New York: John Wiley & Sons, Inc., in association with Bergey's Manual Trust; 2015 pp. 1–29
     [Google Scholar]
  33. Nuñez H, Loyola D, Cárdenas JP, Holmes DS, Johnson DB et al. Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. Res Microbiol 2014; 165:735–742 [View Article][PubMed]
     [Google Scholar]
  34. Altieri C. Dairy propionibacteria as probiotics: recent evidences. World J Microbiol Biotechnol 2016; 32:172 [View Article][PubMed]
     [Google Scholar]
  35. Moslemi M, Mazaheri Nezhad Fard R, Hosseini SM, Homayouni-Rad A, Mortazavian AM. Incorporation of propionibacteria in fermented milks as a probiotic. Crit Rev Food Sci Nutr 2016; 56:1290–1312 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002873
Loading
Variable regions of the glyS, infB and rplB genes usable as novel genetic markers for identification and phylogenetic purposes of genera belonging to the family Propionibacteriaceae
Int J Syst Evol Microbiol 68, 2697 (2018); https://doi.org/10.1099/ijsem.0.002873
/content/journal/ijsem/10.1099/ijsem.0.002873
/content/journal/ijsem/10.1099/ijsem.0.002873
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

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