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Volume 71, Issue 7

sp. nov., isolated from the gut of the freshwater mussel No Access

Abstract

A novel Gram-stain-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain 2T18, was isolated from the gut of the freshwater mussel collected in the Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus . Strain 2T18 formed a monophyletic clade with KCTC 42982, KACC 11706 and KCTC 23839, with sequence similarities of 98.5, 98.4 and 95.9 %, respectively. Strain 2T18 exhibited optimal growth at 30 °C, at pH 8 and with 0.5 % (w/v) NaCl. The major isoprenoid quinone was ubiquinone-8 (Q-8). The predominant fatty acids were summed feature 3 (C 6 and/or C 7) and C. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and two unidentified aminophospholipids. The G+C content of the genomic DNA was 50.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strains 2T18 and KCTC 42982 were below the thresholds used for the delineation of a novel species. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, strain 2T18 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 2T18 (=KCTC 72821=CCUG 74764).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Chitinibacter , Chitinibacter bivalviorum , genome and gut microbiota
Funding
This study was supported by the:
  • Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (Award 918011-04-1-SB010)
    • Principle Award Recipient: Jin-WooBae
  • National Institute of Biological Resources (Award NIBR202002108)
    • Principle Award Recipient: Jin-WooBae
© 2021 The Authors
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2021-07-23
2024-05-03
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References

  1. Chern LL, Stackebrandt E, Lee SF, Lee FL, Chen JK et al. Chitinibacter tainanensis gen. nov., sp. nov., a chitin-degrading aerobe from soil in Taiwan. Int J Syst Evol Microbiol 2004; 54:1387–1391 [View Article] [PubMed]
     [Google Scholar]
  2. Yang CS, Sheu SY, Young CC, Arun AB, Cheng CY et al. Chitinibacter alvei sp. nov., isolated from stream water. Int J Syst Evol Microbiol 2010; 60:1760–1764 [View Article] [PubMed]
     [Google Scholar]
  3. Sheu S-Y, Li Y-S, Young C-C, Chen W-M. Chitinibacter fontanus sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2016; 66:4262–4268
     [Google Scholar]
  4. Atkinson CL, Vaughn CC, Forshay KJ, Cooper JT. Aggregated filter‐feeding consumers alter nutrient limitation: consequences for ecosystem and community dynamics. Ecology 2013; 94:1359–1369 [View Article] [PubMed]
     [Google Scholar]
  5. Strayer DL. Freshwater Mussel Ecology: a Multifactor Approach to Distribution and Abundance Univ of California Press; 2008
     [Google Scholar]
  6. Vaughn CC, Hoellein TJ. Bivalve impacts in freshwater and marine ecosystems. Annu Rev Ecol Evol Syst 2018; 49:183–208 [View Article]
     [Google Scholar]
  7. Murphy AE, Kolkmeyer R, Song B, Anderson IC, Bowen J. Bioreactivity and microbiome of biodeposits from filter-feeding bivalves. Microb Ecol 2019; 77:343–357 [View Article] [PubMed]
     [Google Scholar]
  8. Weingarten EA, Atkinson CL, Jackson CR. The gut microbiome of freshwater Unionidae mussels is determined by host species and is selectively retained from filtered seston. PloS one 2019; 14:e0224796 [View Article] [PubMed]
     [Google Scholar]
  9. Lane D. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics 1991 pp 115–175
     [Google Scholar]
  10. 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
     [Google Scholar]
  11. 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]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  13. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Systematic Biology 1969; 18:1–32 [View Article]
     [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  16. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575 [View Article] [PubMed]
     [Google Scholar]
  17. Kim MS, Roh SW, Bae JW. Ruminococcus faecis sp. nov., isolated from human faeces. J Microbiol 2011; 49:487–491 [View Article] [PubMed]
     [Google Scholar]
  18. Leisner JJ, Larsen MH, Jorgensen RL, Brondsted L, Thomsen LE et al. Chitin hydrolysis by Listeria spp., including L. monocytogenes. Appl Environ Microbiol 2008; 74:3823–3830 [View Article]
     [Google Scholar]
  19. Collins M, Jones D. A note on the separation of natural mixtures of bacterial ubiquinones using reverse‐phase partition thin‐layer chromatography and high performance liquid chromatography. J Appl Microbiol 1981; 51:129–134 [View Article]
     [Google Scholar]
  20. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  21. MIDI Sherlock Microbial Identification System Operating Manual, Version 3.0 Inc Newark, DE: MIDI; 1999
     [Google Scholar]
  22. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark, DE: MIDI inc; 1990
     [Google Scholar]
  23. Xin H, Itoh T, Zhou P, Suzuki K, Kamekura M et al. Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. Int J Syst Evol Microbiol 2000; 50:1297–1303 [View Article] [PubMed]
     [Google Scholar]
  24. Tindall B. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  25. Rhoads A, Au KF. Pacbio sequencing and its applications. Genomics, Proteomics Bioinformatics 2015; 13:278–289
     [Google Scholar]
  26. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. 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]
     [Google Scholar]
  29. 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; 9:1–8
     [Google Scholar]
  30. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
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Chitinibacter bivalviorum sp. nov., isolated from the gut of the freshwater mussel Anodonta arcaeformis
Int J Syst Evol Microbiol 71, 004909 (2021); https://doi.org/10.1099/ijsem.0.004909
/content/journal/ijsem/10.1099/ijsem.0.004909
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