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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 8

gen. nov., sp. nov., a novel genus of the family isolated from bulk tank milk Free

Abstract

Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937, WS4759 and WS5303) constitute an independent phylogenetic lineage within the family with CCUG 36813 (93.7–94.1 %) and M1831/95/2 (93.5 %) as most closely related type species. The unclassified strains demonstrated variable growth with 6.5 % (w/v) NaCl and tolerated pH 6.5–9.5. Growth was observed from 12 to 39 °C. Their cell-wall peptidoglycan belongs to the A1 type (-Lys-direct) consisting of alanine, glutamic acid and lysine. The predominant fatty acids were C ω9, C and C ω9 and in the polar lipids profile three glycolipids, a phospholipid, phosphatidylglycerol, phosphoglycolipid and diphosphatidylglycerol were found. The G+C content of strain WS4937 was 37.4 mol% with a genome size of ~3.0 Mb. Based on phylogenetic, phylogenomic and biochemical characterizations, the isolates can be demarcated from all other genera of the family and, therefore, the novel genus gen. nov. is proposed. The type species of the novel genus is gen. nov., sp. nov. WS4937 (=DSM 109652=LMG 31441).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Aerococcaceae , Fundicoccus ignavus and raw milk
Funding
This study was supported by the:
  • Bundesanstalt für Landwirtschaft und Ernährung (Award 281A105616)
    • Principle Award Recipient: Annemarie Siebert
© 2020 The Authors
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2020-08-03
2024-04-19
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References

  1. Williams RE, Hirch A, Cowan ST. Aerococcus, a new bacterial genus. J Gen Microbiol 1953; 8:475–480 [View Article][PubMed]
     [Google Scholar]
  2. Collins M, Aguirre M, Facklam R, Shallcross J, Williams A. Globicatella sanguis gen. nov., sp. nov., a new gram‐positive catalase‐negative bacterium from human sources. J Appl Microbiol 1992; 73:433–437
     [Google Scholar]
  3. Kawamura Y, Hou XG, Sultana F, Liu S, Yamamoto H et al. Transfer of Streptococcus adjacens and Streptococcus defectivus to Abiotrophia gen. nov. as Abiotrophia adiacens comb. nov. and Abiotrophia defectiva comb. nov., respectively. Int J Syst Bacteriol 1995; 45:798–803 [View Article][PubMed]
     [Google Scholar]
  4. Collins MD, Falsen E, Lemozy J, Åkervall E, Sjödén B et al. Phenotypic and phylogenetic characterization of some Globicatella-like organisms from human sources: description of Facklamia hominis gen. nov., sp. nov. Int J Syst Bacteriol 1997; 47:880–882 [View Article][PubMed]
     [Google Scholar]
  5. Collins MD, Lawson PA, Monasterio R, Falsen E, Sjödén B et al. Ignavigranum ruoffiae sp. nov., isolated from human clinical specimens. Int J Syst Bacteriol 1999; 49 Pt 1:97–101 [View Article][PubMed]
     [Google Scholar]
  6. Collins MD, Rodriguez Jovita M, Lawson PA, Falsen E, Foster G. Characterization of a novel Gram-positive, catalase-negative coccus from horses: description of Eremococcus coleocola gen. nov., sp. nov. Int J Syst Bacteriol 1999; 49 Pt 4:1381–1385 [View Article][PubMed]
     [Google Scholar]
  7. Collins MD, Rodriguez Jovita M, Hutson RA, Falsen E, Sjödén B et al. Dolosicoccus paucivorans gen. nov., sp. nov., isolated from human blood. Int J Syst Bacteriol 1999; 49 Pt 4:1439–1442 [View Article][PubMed]
     [Google Scholar]
  8. Li F, Zhao W, Li N, Li H, Liao D et al. Suicoccus acidiformans gen. nov., sp. nov., isolated from a sick pig. Int J Syst Evol Microbiol 2019; 69:1443–1451 [View Article][PubMed]
     [Google Scholar]
  9. von Neubeck M, Huptas C, Glück C, Krewinkel M, Stoeckel M et al. Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow’s milk. Int J Syst Evol Microbiol 2016; 66:1163–1173 [View Article][PubMed]
     [Google Scholar]
  10. Yoon S-H, Ha S-M, 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]
  11. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M et al. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 1998; 19:554–568 [View Article][PubMed]
     [Google Scholar]
  12. Tindall BJ, Rosselló-Móra R, Busse H-J, 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]
  13. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
     [Google Scholar]
  14. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  15. Hall BG. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol 2013; 30:1229–1235 [View Article][PubMed]
     [Google Scholar]
  16. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  17. 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][PubMed]
     [Google Scholar]
  18. Patel RK, Jain M. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 2012; 7:e30619 [View Article][PubMed]
     [Google Scholar]
  19. 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][PubMed]
     [Google Scholar]
  20. 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][PubMed]
     [Google Scholar]
  21. 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]
  22. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  23. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
     [Google Scholar]
  24. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
     [Google Scholar]
  25. Gregersen T. Rapid method for distinction of gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
     [Google Scholar]
  26. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  27. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H et al. Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999; 27:29–34 [View Article][PubMed]
     [Google Scholar]
  28. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
     [Google Scholar]
  29. Kanehisa M, Sato Y, Morishima K, BlastKOALA MK. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article][PubMed]
     [Google Scholar]
  30. Kanehisa M, Sato Y. Kegg Mapper for inferring cellular functions from protein sequences. Protein Sci 2020; 29:28–35 [View Article][PubMed]
     [Google Scholar]
  31. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985; 18:123–156
     [Google Scholar]
  32. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article][PubMed]
     [Google Scholar]
  33. Schumann P. Peptidoglycan Structure. Methods Microbiol 2011;Taxonomy of Prokaryotes. 38101–129
  34. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  35. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  36. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CBT, Breznak JA, Marzluf G, Schmidt TM, Synder LR. (editors) Methods for General and Molecular Microbiology DC: American Society of Microbiology; 2007 pp 330–393
     [Google Scholar]
  37. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article][PubMed]
     [Google Scholar]
  38. 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]
  39. Hoyles L. The genus Facklamia. Lactic Acid Bacteria: Biodiversity and Taxonomy . John Wiley & Sons, Ltd 2014 pp. 91–98
     [Google Scholar]
  40. Ludwig W, Schleifer K-H, Whitman WB et al. Family II. Aerococcaceae fam. nov. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) The Firmicutes. Bergey’s Manual of Systematic Bacteriology Springer; 2009 pp 533–548
     [Google Scholar]
  41. Lawson PA. The genus Aerococcus . In Holzapfel WH, Wood BJ. (editors) Lactic Acid Bacteria: Biodiversity and Taxonomy John Wiley & Sons, Ltd; 2014 pp 81–90
     [Google Scholar]
  42. Lawson PA. The genus Abiotrophia . In Holzapfel WH, Wood BJ. (editors) Lactic Acid Bacteria: Biodiversity and Taxonomy John Wiley & Sons, Ltd; 2014 pp 75–80
     [Google Scholar]
  43. Huch M, Gyu‐Sung C, Gálvez A, Franz CM. Minor genera of the Aerococcaceae (Dolosicoccus, Eremococcus, Globicatella, Ignavigranum). In Holzapfel WH, Wood BJ. (editors) Lactic Acid Bacteria: Biodiversity and Taxonomy John Wiley & Sons, Ltd; 2014 pp 99–105
     [Google Scholar]
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Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk
Int J Syst Evol Microbiol 70, 4774 (2020); https://doi.org/10.1099/ijsem.0.004344
/content/journal/ijsem/10.1099/ijsem.0.004344
/content/journal/ijsem/10.1099/ijsem.0.004344
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