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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 1

sp. nov., a novel caproic acid producing anaerobic bacterium isolated from pit clay No Access

Abstract

An anaerobic, Gram-positive, rod-shaped, motile and spore-forming bacterium, designated strain ZCY20-5, was isolated from pit clay of Chinese strong-aroma type (Chinese liquor). Phylogenetic analyses based on 16S rRNA gene and genome sequences showed that strain ZCY20-5 belonged to the genus , family , but it showed low similarity to the type species LBM18003 (98.00 %) and LBM19010 (95.67 %). In anaerobic yeast extract medium, growth was observed at 20–45 °C (optimum, 35–40 °C), at pH 4.0–9.0 (optimum, pH 6.5–7.0) and with 0.0–2.0 % NaCl (w/v). The predominant fatty acids were C, C, C 3-OH and C 3-OH, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, three phospholipids of unknown structure containing glucosamine and two unidentified phospholipids. Strain ZCY20-5 exhibited an 81.32 % pairwise average nucleotide identity value, a 78.98 % average amino acid identity value and a 22.30 % digital DNA–DNA hybridization value compared to its closest relative LBM18003. Based on morphological, physiological, biochemical, chemotaxonomic, genotypic and phylogenetic results, strain ZCY20-5 represents a novel species of , and the type strain is ZCY20-5 (=MCCC 1A19399=KCTC 25590).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): caproic acid , Caproicibacterium and novel species
© 2024 The Authors
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2024-01-24
2024-05-09
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References

  1. Yuan S, Jin Z, Ali A, Wang C, Liu J. Caproic acid-producing bacteria in Chinese Baijiu Brewing. Front Microbiol 2022; 13:883142 [View Article] [PubMed]
     [Google Scholar]
  2. Wang C, Chen Q, Wang Q, Li C, Leng Y et al. Long-term batch brewing accumulates adaptive microbes, which comprehensively produce more flavorful Chinese liquors. Food Res Int 2014; 62:894–901 [View Article]
     [Google Scholar]
  3. Hu XL, Du H, Xu Y. Identification and quantification of the caproic acid-producing bacterium Clostridium kluyveri in the fermentation of pit mud used for Chinese strong-aroma type liquor production. Int J Food Microbiol 2015; 214:116–122 [View Article] [PubMed]
     [Google Scholar]
  4. Gu Y, Zhu X, Lin F, Shen C, Li Y et al. Caproicibacterium amylolyticum gen. nov., sp. nov., a novel member of the family Oscillospiraceae isolated from pit clay used for making Chinese strong aroma-type liquor. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  5. Wang H, Gu Y, Zhao D, Qiao Z, Zheng J et al. Caproicibacterium lactatifermentans sp. nov., isolated from pit clay used for the production of Chinese strong aroma-type liquor. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  6. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. Besemer J, Borodovsky M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 2005; 33:W451–W454 [View Article] [PubMed]
     [Google Scholar]
  9. Chan PP, Lowe Tmj. tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods Mol Biol 2019; 1962:1–14 [View Article] [PubMed]
     [Google Scholar]
  10. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ 2016 [View Article]
     [Google Scholar]
  13. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  14. Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Zentralbl Bakteriol, Mikrobiol Hyg, Ser A 1988; 268:433–434
     [Google Scholar]
  15. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article] [PubMed]
     [Google Scholar]
  16. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  17. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007; 56:564–577 [View Article] [PubMed]
     [Google Scholar]
  18. Zhang D, Gao F, Jakovlić I, Zou H, Zhang J et al. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour 2020; 20:348–355 [View Article] [PubMed]
     [Google Scholar]
  19. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article] [PubMed]
     [Google Scholar]
  20. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  21. Ding X, Wu C, Huang J, Zhou R. Characterization of interphase volatile compounds in Chinese Luzhou-flavor liquor fermentation cellar analyzed by head space-solid phase micro extraction coupled with gas chromatography mass spectrometry (HS-SPME/GC/MS). LWT - Food Sci Technol 2016; 66:124–133 [View Article]
     [Google Scholar]
  22. Park J-W, Park K-G, Lee N-Y, Lee J-H, Lee J-W. Enhanced extraction of reducing sugars from fruit of Hovenia dulcis with treatment of cellulase and sequential production of ethanol and acetic acid containing ampelopsin from extracted reducing sugars. Industr Crops Products 2019; 139:111522 [View Article]
     [Google Scholar]
  23. Seedorf H, Fricke WF, Veith B, Brüggemann H, Liesegang H et al. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci USA 2008; 105:2128–2133 [View Article] [PubMed]
     [Google Scholar]
  24. Charrier C, Duncan GJ, Reid MD, Rucklidge GJ, Henderson D et al. A novel class of CoA-transferase involved in short-chain fatty acid metabolism in butyrate-producing human colonic bacteria. Microbiology 2006; 152:179–185 [View Article] [PubMed]
     [Google Scholar]
  25. Flaiz M, Baur T, Brahner S, Poehlein A, Daniel R et al. Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens. Int J Syst Evol Microbiol 2020; 70:4269–4279 [View Article] [PubMed]
     [Google Scholar]
  26. Kim B-C, Seung Jeon B, Kim S, Kim H, Um Y et al. Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2015; 65:4902–4908 [View Article] [PubMed]
     [Google Scholar]
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Caproicibacterium argilliputei sp. nov., a novel caproic acid producing anaerobic bacterium isolated from pit clay
Int J Syst Evol Microbiol 74, 006246 (2024); https://doi.org/10.1099/ijsem.0.006246
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