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Volume 73, Issue 3

sp. nov., isolated from the intestinal tract of the Pacific white shrimp No Access

Abstract

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated HL-LV01, was isolated from the intestinal tract content of the Pacific white shrimp . The 16S rRNA gene sequence of strain HL-LV01 showed that the strain was clearly a member of the genus . According to the phylogenetic analyses, strain HL-LV01 was most closely related to the species KCTC 42508 with 98.2 % sequence similarity. The average nucleotide identity and digital DNA–DNA hybridization values between strain HL-LV01 and KCTC 42508 were 80.6 % and 23.0 %, respectively, indicating different genomic species in the genus . Strain HL-LV01 showed optimal growth at 35 °C, pH 7.0, and 2.5 % (w/v) sea salts. The major cellular fatty acids were iso-C (32.5 %), iso-C 3-OH (22.3 %), and iso-C G (15.5 %). The major respiratory quinone was menaquinone-6. The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids, and seven unidentified lipids. The genomic DNA G+C content of the strain was 39.8 mol%. The comprehensive phylogenetic, genomic, phenotypic, and chemotaxonomic results indicate that strain HL-LV01 is distinct from validly published species of the genus . Hence, we propose strain HL-LV01 as a novel species belonging to the genus , for which the name sp. nov. is proposed. The type strain is HL-LV01 (= KCCM 90498 = JCM 35709).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): intestinal tract , Maribacter litopenaei , new species and Pacific white shrimp
Funding
This study was supported by the:
  • Korea Institute of Marine Science & Technology Promotion (Award KIMST-20210427)
    • Principle Award Recipient: NotApplicable
  • Korea Institute of Marine Science & Technology Promotion (Award KIMST-20210469)
    • Principle Award Recipient: NotApplicable
© 2023 The Authors
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2024-04-23
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References

  1. Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Rohde M et al. Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov. Int J Syst Evol Microbiol 2004; 54:1017–1023 [View Article]
     [Google Scholar]
  2. Nedashkovskaya OI, Kim SB. Maribacter. In Bergey’s Manual of Systematics of Archaea and Bacteria 2015 pp 1–5
     [Google Scholar]
  3. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  4. Yoon JH, Kang SJ, Lee SY, Lee CH, Oh TK. Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo. Int J Syst Evol Microbiol 2005; 55:2051–2055 [View Article] [PubMed]
     [Google Scholar]
  5. Barbeyron T, Carpentier F, L’haridon S, Schüler M, Michel G et al. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter. Int J Syst Evol Microbiol 2008; 58:790–797 [View Article] [PubMed]
     [Google Scholar]
  6. Park S, Jung YT, Park JM, Won SM, Yoon JH. Maribacter confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2015; 65:3079–3085 [View Article] [PubMed]
     [Google Scholar]
  7. Jin M, Kim M, Kim JY, Song HS, Cha I-T et al. Maribacter pelagius sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:3834–3839 [View Article] [PubMed]
     [Google Scholar]
  8. Kang H, Cha I, Kim H, Joh K. Maribacter maritimus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2018; 68:2431–2436 [View Article] [PubMed]
     [Google Scholar]
  9. Cho KH, Hong SG, Cho HH, Lee YK, Chun J et al. Maribacter arcticus sp. nov., isolated from Arctic marine sediment. Int J Syst Evol Microbiol 2008; 58:1300–1303 [View Article] [PubMed]
     [Google Scholar]
  10. Lo N, Jin HM, Jeon CO. Maribacter aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Maribacter. Int J Syst Evol Microbiol 2013; 63:3409–3414 [View Article]
     [Google Scholar]
  11. Jung YT, Lee JS, Yoon JH. Maribacter caenipelagi sp. nov., a member of the Flavobacteriaceae isolated from a tidal flat sediment of the Yellow Sea in Korea. Antonie Van Leeuwenhoek 2014; 106:733–742 [View Article]
     [Google Scholar]
  12. Park S, Jung YT, Won SM, Yoon JH. Maribacter litorisediminis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2016; 66:4236–4242 [View Article] [PubMed]
     [Google Scholar]
  13. Kim KH, Jin HM, Jeong HI, Jeon CO. Maribacter lutimaris sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:1773–1778 [View Article] [PubMed]
     [Google Scholar]
  14. Thongphrom C, Kim JH, Kim W. Maribacter arenosus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:4826–4831 [View Article] [PubMed]
     [Google Scholar]
  15. Fang C, Wu YH, Xamxidin M, Wang CS, Xu XW. Maribacter cobaltidurans sp. nov., a heavy-metal-tolerant bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:5261–5267 [View Article] [PubMed]
     [Google Scholar]
  16. Lee DW, Lee H, Kwon B-O, Khim JS, Yim UH et al. Maribacter litoralis sp. nov. a marine bacterium isolated from seashore. Int J Syst Evol Microbiol 2018; 68:3471–3478 [View Article] [PubMed]
     [Google Scholar]
  17. Chen C, Su Y, Tao T, Fu G, Zhang C et al. Maripseudobacter aurantiacus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a sedimentation basin. Int J Syst Evol Microbiol 2017; 67:778–783 [View Article]
     [Google Scholar]
  18. Liu A, Zhang YJ, Liu DK, Li XZ. Maribacter luteus sp. nov., a marine bacterium isolated from intertidal sand of the Yellow Sea. Int J Syst Evol Microbiol 2020; 70:3497–3503 [View Article] [PubMed]
     [Google Scholar]
  19. Nedashkovskaya OI, Vancanneyt M, De Vos P, Kim SB, Lee MS et al. Maribacter polysiphoniae sp. nov., isolated from a red alga. Int J Syst Evol Microbiol 2007; 57:2840–2843 [View Article] [PubMed]
     [Google Scholar]
  20. Zhang GI, Hwang CY, Kang SH, Cho BC. Maribacter antarcticus sp. nov., a psychrophilic bacterium isolated from a culture of the Antarctic green alga Pyramimonas gelidicola. Int J Syst Evol Microbiol 2009; 59:1455–1459 [View Article] [PubMed]
     [Google Scholar]
  21. Nedashkovskaya OI, Kim SB, Mikhailov VV. Maribacter stanieri sp. nov., a marine bacterium of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2010; 60:214–218 [View Article] [PubMed]
     [Google Scholar]
  22. Weerawongwiwat V, Kang H, Jung MY, Kim W. Maribacter chungangensis sp. nov., isolated from a green seaweed, and emended descriptions of the genus Maribacter and Maribacter arcticus. Int J Syst Evol Microbiol 2013; 63:2553–2558 [View Article] [PubMed]
     [Google Scholar]
  23. Tang M, Wang G, Xiang W, Chen C, Wu J et al. Maribacter flavus sp. nov., isolated from a cyanobacterial culture pond. Int J Syst Evol Microbiol 2015; 65:3997–4002 [View Article] [PubMed]
     [Google Scholar]
  24. Hu J, Yang Q-Q, Ren Y, Zhang W-W, Zheng G et al. Maribacter thermophilus sp. nov., isolated from an algal bloom in an intertidal zone, and emended description of the genus Maribacter. Int J Syst Evol Microbiol 2015; 65:36–41 [View Article] [PubMed]
     [Google Scholar]
  25. Zhang J-Y, Xia Y, Feng X, Mu D-S, Du Z-J. Maribacter algarum sp. nov., a new member of the family Flavobacteriaceae isolated from the red alga Gelidium amansii. Int J Syst Evol Microbiol 2020; 70:3679–3685 [View Article] [PubMed]
     [Google Scholar]
  26. Khan SA, Jeong SE, Baek JH, Jeon CO. Maribacter algicola sp. nov., isolated from a marine red alga, Porphyridium marinum, and transfer of Maripseudobacter aurantiacus Chen et al. 2017 to the genus Maribacter as Maribacter aurantiacus comb. nov. Int J Syst Evol Microbiol 2020; 70:797–804 [View Article]
     [Google Scholar]
  27. Jackson SA, Kennedy J, Morrissey JP, O’Gara F, Dobson ADW. Maribacter spongiicola sp. nov. and Maribacter vaceletii sp. nov., isolated from marine sponges, and emended description of the genus Maribacter. Int J Syst Evol Microbiol 2015; 65:2097–2103 [View Article]
     [Google Scholar]
  28. Hooper LV, Macpherson AJ. Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat Rev Immunol 2010; 10:159–169 [View Article] [PubMed]
     [Google Scholar]
  29. Lee WJ, Hase K. Gut microbiota-generated metabolites in animal health and disease. Nat Chem Biol 2014; 10:416–424 [View Article] [PubMed]
     [Google Scholar]
  30. Verschuere L, Rombaut G, Sorgeloos P, Verstraete W. Probiotic bacteria as biological control agents in aquaculture. Microbiol Mol Biol Rev 2000; 64:655–671 [View Article] [PubMed]
     [Google Scholar]
  31. Knipe H, Temperton B, Lange A, Bass D, Tyler CR. Probiotics and competitive exclusion of pathogens in shrimp aquaculture. Rev Aquacult 2021; 13:324–352 [View Article]
     [Google Scholar]
  32. Englen MD, Kelley LC. A rapid DNA isolation procedure for the identification of Campylobacter jejuni by the polymerase chain reaction. Lett Appl Microbiol 2000; 31:421–426 [View Article]
     [Google Scholar]
  33. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Good-fellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991
     [Google Scholar]
  34. Sayers EW, Bolton EE, Brister JR, Canese K, Chan J et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2022; 50:D20–D26 [View Article]
     [Google Scholar]
  35. 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]
  36. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
     [Google Scholar]
  38. 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]
  39. Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 2018; 34:i142–i150 [View Article] [PubMed]
     [Google Scholar]
  40. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V et al. Twelve years of SAMtools and BCFtools. Gigascience 2021; 10:giab008 [View Article]
     [Google Scholar]
  41. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  42. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
     [Google Scholar]
  43. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article]
     [Google Scholar]
  44. 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]
  45. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article]
     [Google Scholar]
  46. 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]
  47. 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]
  48. McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B et al. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009; 75:6864–6875 [View Article] [PubMed]
     [Google Scholar]
  49. Merhan O, Nikolić GS. The biochemistry and antioxidant properties of carotenoids. In Cvetković DJ, Nikolić GS. eds Carotenoids Rijeka: InTech; 2017 pp 52–66 [View Article]
     [Google Scholar]
  50. Fawzy S, Wang W, Zhou Y, Xue Y, Yi G et al. Can dietary β-carotene supplementation provide an alternative to astaxanthin on the performance of growth, pigmentation, biochemical, and immuno-physiological parameters of Litopenaeus vannamei?. Aquaculture Reports 2022; 23:101054 [View Article]
     [Google Scholar]
  51. Escamilla-Montes R, Barraza A, Luna-González A, Angulo C, Fierro-Coronado JA et al. Effect of dietary inulin in the gut microbiota of whiteleg shrimp Penaeus vannamei. Lat Am J Aquat Res 2021; 49:418–430 [View Article]
     [Google Scholar]
  52. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article]
     [Google Scholar]
  53. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd. Baltimore: Williams & Wilkins; 1967
     [Google Scholar]
  54. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G. eds Methods for General and Molecular Microbiology American Society of Microbiology; 2007 pp 330–393
     [Google Scholar]
  55. Gosink JJ, Woese CR, Staley JT. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of “Flectobacillus glomeratus” as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 1998; 48:223–235 [View Article]
     [Google Scholar]
  56. Chen W-P, Kuo T-T. A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res 1993; 21:2260 [View Article]
     [Google Scholar]
  57. Smibert R, Krieg N. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  58. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  59. Lányi B. Classical and rapid identification methods for medically important bacteria. In Colwell R. eds Methods in Microbiology vol 19 Academic Press; 1988 pp 1–67
     [Google Scholar]
  60. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article] [PubMed]
     [Google Scholar]
  61. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acids Methyl Esters (GC-FAME) Newark, NY: Microbial ID; 2006
     [Google Scholar]
  62. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  63. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
     [Google Scholar]
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Maribacter litopenaei sp. nov., isolated from the intestinal tract of the Pacific white shrimp Litopenaeus vannamei
Int J Syst Evol Microbiol 73, 005786 (2023); https://doi.org/10.1099/ijsem.0.005786
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