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Abstract

A new species of , a Gram-positive, spore-forming anaerobic group, proposed name sp. nov., was isolated in Northern Ireland from bovine faeces collected in 2016. Designated as MCA3, cells of sp. nov. are rod shaped and motile. Cells tolerate NaCl from 0.5 to 5.5 % (w/v), with a pH tolerance between pH 6 and 9. The optimal temperature for growth is 35–40 °C, and temperatures from 20 to 30 °C are tolerated. The polar lipid profile displays diphosphatidylglycerol, phosphatidylglycerol, two aminoglycolipids, one glycophospholipid, one aminolipid, three glycolipids, five phospholipids and one lipid. No respiratory quinones are detected. The predominant fatty acid profile includes C at 22.8 %. Strain MCA3 is positive for glucose and maltose acidification, as well as glycerol and sorbitol. The biochemical results from a VITEK2 assay of strain MCA3, LAM0A37 and DSM 6539 are also included for the first time. The closed and complete genome of strain MCA3 from a hybrid Oxford Nanopore Technology MinION/Illumina assembly reveals no evidence for known virulence genes. Draft genome sequencing of DSM 6539 and LAM0A37, as performed by Illumina MiSeq, provides reference genomes for these respective species of for the first time. DNA–DNA hybridization values (d) of MCA3 to ATCC 14880, LAM0A37 and DSM 6539 are 48.8, 67.4 and 46.3 %, with cutoff value at 70 %. The type strain for sp. nov. is MCA3 (=NCTC 14625=LMG 32430).

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-01-10
2024-04-28
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References

  1. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994; 44:812–826 [View Article]
    [Google Scholar]
  2. Gerritsen J, Fuentes S, Grievink W, van Niftrik L, Tindall BJ et al. Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat, and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov. Int J Syst Evol Microbiol 2014; 64:1600–1616 [View Article]
    [Google Scholar]
  3. Gaston LW, Stadtman ER. Fermentation of ethylene glycol by Clostridium glycolicum, sp. n. J Bacteriol 1963; 85:356–362 [View Article]
    [Google Scholar]
  4. Kane MD, Brauman A, Breznak JA. Clostridium mayombei sp. nov., an H2/CO2 acetogenic bacterium from the gut of the African soil-feeding termite, Cubitermes speciosus. Arch Microbiol 1991; 156:99–104 [View Article]
    [Google Scholar]
  5. Elsayed S, Zhang K. Clostridium glycolicum bacteremia in a bone marrow transplant patient. J Clin Microbiol 2007; 45:1652–1654 [View Article] [PubMed]
    [Google Scholar]
  6. Chamkha M, Labat M, Patel BK, Garcia JL. Isolation of a cinnamic acid-metabolizing Clostridium glycolicum strain from oil mill wastewaters and emendation of the species description. Int J Syst Evol Microbiol 2001; 51:2049–2054 [View Article]
    [Google Scholar]
  7. Jiang W, Abrar S, Romagnoli M, Carroll KC. Clostridium glycolicum wound infections: case reports and review of the literature. J Clin Microbiol 2009; 47:1599–1601 [View Article] [PubMed]
    [Google Scholar]
  8. Deng Y, Guo X, Wang Y, He M, Ma K et al. Terrisporobacter petrolearius sp. nov., isolated from an oilfield petroleum reservoir. Int J Syst Evol Microbiol 2015; 65:3522–3526 [View Article]
    [Google Scholar]
  9. Lund LC, Sydenham TV, Høgh SV, Skov M, Kemp M et al. Draft genome sequence of “Terrisporobacter othiniensis” isolated from a blood culture from a human patient. Genome Announc 2015; 3:e00042-15 [View Article]
    [Google Scholar]
  10. Cai D, Sorokin V, Lutwick L, Liu W, Dalal S et al. C. glycolicum as the sole cause of bacteremia in a patient with acute cholecystitis. Ann Clin Lab Sci 2012; 42:162–164
    [Google Scholar]
  11. Cheng MP, Domingo M-C, Lévesque S, Yansouni CP. A case report of a deep surgical site infection with Terrisporobacter glycolicus/T. Mayombei and review of the literature. BMC Infect Dis 2016; 16:529 [View Article]
    [Google Scholar]
  12. Andrews S. FastQC: a quality control tool for high throughput sequence data; 2010 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  13. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [View Article] [PubMed]
    [Google Scholar]
  14. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom 2017; 3:e000132 [View Article] [PubMed]
    [Google Scholar]
  17. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
  18. Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G et al. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol 2021; 22:266 [View Article]
    [Google Scholar]
  19. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
    [Google Scholar]
  20. Stewart RD, Auffret MD, Warr A, Walker AW, Roehe R et al. Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. Nat Biotechnol 2019; 37:953–961 [View Article]
    [Google Scholar]
  21. 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]
    [Google Scholar]
  22. 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]
  23. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article]
    [Google Scholar]
  24. Gardner SN, Slezak T, Hall BG. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 2015; 31:2877–2878 [View Article] [PubMed]
    [Google Scholar]
  25. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article]
    [Google Scholar]
  26. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article]
    [Google Scholar]
  27. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
    [Google Scholar]
  28. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014; 58:212–220 [View Article] [PubMed]
    [Google Scholar]
  29. Chen L, Zheng D, Liu B, Yang J, Jin Q. VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. Nucleic Acids Res 2016; 44:D694–7 [View Article]
    [Google Scholar]
  30. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article] [PubMed]
    [Google Scholar]
  31. Doster E, Lakin SM, Dean CJ, Wolfe C, Young JG et al. MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. Nucleic Acids Res 2020; 48:D561–D569 [View Article]
    [Google Scholar]
  32. Seemann T. Github. Abricate 2020
    [Google Scholar]
  33. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347–52 [View Article] [PubMed]
    [Google Scholar]
  34. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
    [Google Scholar]
  35. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
    [Google Scholar]
  36. Galata V, Fehlmann T, Backes C, Keller A. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res 2019; 47:D195–D202 [View Article] [PubMed]
    [Google Scholar]
  37. ATCC Terrisporobacter glycolicus Gerritsen et al. (ATCC 14880): Culture Method; 2020 https://www.lgcstandards-atcc.org/products/all/14880.aspx#history
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