1887

Abstract

Two strains of a Gram-staining-positive species were isolated from German bulk tank milk. On the basis of their 16S rRNA sequences they were affiliated to the genus but could not be assigned to any species with a validly published name. ATCC BAA-466 (97.3 % 16S rRNA sequence similarity), CCUG 37842 (96.9 %), and CCUG 36813 (96.6 %) are the closest relatives. In the 16S rRNA phylogeny and in the core-genome phylogeny strains WS 5301 and WS 5302 form a well-supported, separate lineage. Pairwise average nucleotide identity calculated using MUMmer (ANIm) between WS 5301 and type strains of other species is well below the species cut-off (95 %) and ranges from 83.4 to 87.7 %. The DNA G+C content of the type strain is 36.4 mol% and the assembly size of the genome is 2.2 Mb. Cells of WS 5301 are non-motile, non-endospore-forming, oxidase-negative, catalase-negative and facultatively anaerobic cocci. The fastidious species grows at 10–40 °C and with up to 7.0 % (w/v) NaCl in BHI supplemented with 5 g l yeast extract. Major polar lipids are phosphatidylglycerol, diphosphatidylglycerol and two glycolipids. Predominant fatty acids are Cω9 and Cω9. On the basis of their genomic, physiological and chemotaxonomic characteristics the strains examined in this study represent the same, hitherto unknown species. We propose the name sp. nov. for which WS 5301 (=DSM 111018=LMG 31861) is the type strain and WS 5302 (=DSM 111019=LMG 31862) is an additional strain of this novel species.

Funding
This study was supported by the:
  • Bundesministerium für Ernährung und Landwirtschaft (Award 281A105616)
    • Principle Award Recipient: NotApplicable
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2021-07-12
2021-08-02
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References

  1. Parte AC. LPSN–List of Prokaryotic names with Standing in Nomenclature (bacterio. net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  2. Vos P, Garrity G, Jones D, Krieg N, Ludwig W. Family II. Aerococcaceae fam. nov. In Bergey’s Manual of Systematic Bacteriology. the Firmicutes. Volume 3, Second. edn New York: Springer; 2009 p 533 [View Article]
    [Google Scholar]
  3. Collins MD, Falsen E, Lemozy J, Akervall E, Sjoden 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 Evol Microbiol 1997; 47:880–882 [View Article]
    [Google Scholar]
  4. Collins MD, Lawson PA, Monasterio R, Falsen E, Sjöden B et al. Facklamia ignava sp. nov., isolated from human clinical specimens. J Clin Microbiol 1998; 36:2146–2148 [View Article] [PubMed]
    [Google Scholar]
  5. Lawson PA, Collins MD, Falsen E, Sjöden B, Facklam RR. Facklamia languida sp. nov., isolated from human clinical specimens. J Clin Microbiol 1999; 37:1161–1164 [View Article] [PubMed]
    [Google Scholar]
  6. Hoyles L, Foster G, Falsen E, Thomson LF, Collins MD. Facklamia miroungae sp. nov., from a juvenile southern elephant seal (Mirounga leonina. Int J Syst Evol Microbiol 2001; 51:1401–1403 [View Article] [PubMed]
    [Google Scholar]
  7. Collins MD, Hutson RA, Falsen E, Sjödén B. Facklamia sourekii sp. nov., isolated from human sources. Int J Syst Evol Microbiol 1999; 49:635–638 [View Article]
    [Google Scholar]
  8. Collins MD, Hutson RA, Falsen E, Sjöden B. Facklamia tabacinasalis sp. nov., from powdered tobacco. Int J Syst Evol Microbiol 1999; 49:1247–1250 [View Article]
    [Google Scholar]
  9. Hoyles L. The genus Facklamia. Holzapfel W, Wood B. eds In Lactic Acid Bacteria: Biodiversity and Taxonomy, First. edn Chinchester: John Wiley & Sons; 2014 pp 91–98 [View Article]
    [Google Scholar]
  10. Thoendel MJ, Jeraldo PR, Greenwood-Quaintance KE, Yao JZ, Chia N et al. Identification of prosthetic joint infection pathogens using a shotgun metagenomics approach. Clin Infect Dis 2018; 67:1333–1338 [View Article] [PubMed]
    [Google Scholar]
  11. LaClaire L, Facklam R. Antimicrobial susceptibilities and clinical sources of Facklamia species. Antimicrob Agents Chemother 2000; 44:2130–2132 [View Article] [PubMed]
    [Google Scholar]
  12. Kim TY, Jo J, Kim N, Park H, Roh EY et al. Facklamia hominis isolated from a wound: A case report and review of the literature. Ann Clin Microbiol 2019; 22:50 [View Article]
    [Google Scholar]
  13. Tamlihat YA, Violette J, Labraousse J, Bregeaud D, Vincent JF. Identification of Facklamia hominis in a case of stercoral peritonitis a case report and review of the literature. Infect Dis Diag Treat 2020; 4:138 [View Article]
    [Google Scholar]
  14. Abat C, Garcia V, Rolain JM. Facklamia hominis scapula abscess, Marseille, France. New Microbes New Infect 2016; 9:13–14 [View Article] [PubMed]
    [Google Scholar]
  15. Ananthakrishna R, Shankarappa RK, Jagadeesan N, Math RS, Karur S et al. Infective endocarditis: a rare organism in an uncommon setting. Case Rep Infect Dis 2012; 2012:307852 [View Article] [PubMed]
    [Google Scholar]
  16. Rahmati E, Martin V, Wong D, Sattler F, Petterson J et al. Facklamia species as an underrecognized pathogen. Open Forum Infect Dis 2017; 4:ofw272 [View Article] [PubMed]
    [Google Scholar]
  17. McCann E, Barber M, Hunter P, Inverarity D. A very unusual organism causing stroke-like symptoms. Age Ageing 2014; 43:727–728 [View Article] [PubMed]
    [Google Scholar]
  18. Rasolofo EA, St-Gelais D, LaPointe G, Roy D. Molecular analysis of bacterial population structure and dynamics during cold storage of untreated and treated milk. Int J Food Microbiol 2010; 138:108–118 [View Article] [PubMed]
    [Google Scholar]
  19. Delbes C, Ali-Mandjee L, Montel MC. Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl Environ Microbiol 2007; 73:1882–1891 [View Article] [PubMed]
    [Google Scholar]
  20. Breitenwieser F, Doll EV, Clavel T, Scherer S, Wenning M. Complementary use of cultivation and high-throughput amplicon sequencing reveals high biodiversity within raw milk microbiota. Front Microbiol 2020; 11:1557 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. von Neubeck M, Baur C, Krewinkel M, Stoeckel M, Kranz B et al. Biodiversity of refrigerated raw milk microbiota and their enzymatic spoilage potential. Int J Food Microbiol 2015; 211:57–65 [View Article] [PubMed]
    [Google Scholar]
  23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  24. 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
    [Google Scholar]
  25. 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]
  26. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  27. 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 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  33. 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] [PubMed]
    [Google Scholar]
  34. 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]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  36. Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ. PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. GigaScience 2019; 8:giz119 [View Article] [PubMed]
    [Google Scholar]
  37. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  38. 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] [PubMed]
    [Google Scholar]
  39. Mattarelli P, Holzapfel W, Franz CM, 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] [PubMed]
    [Google Scholar]
  40. Gregersen T. Rapid method for distinction of Gram-negative from Gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  41. Wenning M, Breitenwieser F, Huptas C, Doll E, Bächler B et al. Brevilactibacter flavus gen. nov., sp. nov., a novel bacterium of the family Propionibacteriaceae isolated from raw milk and dairy products and reclassification of Propioniciclava sinopodophylli as Brevilactibacter sinopodophylli comb. nov. Int J Syst Evol Microbiol 2020; 70:2186–2193 [View Article] [PubMed]
    [Google Scholar]
  42. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T. eds In Methods for General and Molecular Microbiologymethods for General and Molecular Microbiology, 3rd. edn Washington: American Society of Microbiology; 2007 pp 330–393 [View Article]
    [Google Scholar]
  43. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
    [Google Scholar]
  44. Tindall B. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  45. Tindall B. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  46. 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]
  47. Kuykendall L, Roy M, O’Neill J, Devine T. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 1988; 38:358–361 [View Article]
    [Google Scholar]
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