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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 12

sp. nov. and sp. nov., isolated from the gastrointestinal tract of lake prawn No Access

Abstract

Two novel Gram-stain-positive, non-motile and non-spore-forming bacterial strains, designated J2M5 and J1M15, were isolated from the gastrointestinal tract of a lake prawn . Strain J2M5 was an obligately aerobic bacterium that formed milky-coloured colonies and showed a rod–coccus cell cycle, while strain J1M15 was a facultatively aerobic bacterium that formed orangish-yellow-coloured colonies and showed rod-shaped cells. Strains J2M5 and J1M15 showed the highest 16S rRNA gene sequence similarity to JC2055 (98.63 %) and SST-39 (98.08 %), respectively. The whole-genome sequence of strain J2M5 was 4.52 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J2M5 was 72.5 mol%. The whole-genome sequence of strain J1M15 was 3.20 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J1M15 was 69.6mol %. Strains J2M5 and J1M15 showed high OrthoANI similarity to JC2055 (83.6 %) and (77.2 %), respectively. We analysed the genome sequences of strains J2M5 and J1M15 in terms of carbohydrate-active enzymes, antibiotic resistance genes and virulence factor genes. Strains J2M5 and J1M15 contained MK-8 (H) and MK-9 (H) as the predominant respiratory quinones, respectively. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Additionally, strain J2M5 possessed phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine. The cellular sugar components of strain J2M5 were ribose, mannose, glucose and galactose, and its cellular amino acid components were -alanine and -lysine. The cellular sugar components of strain J1M15 were rhamnose, ribose, mannose and glucose, and its cellular amino acid component was -alanine. The major cellular fatty acids of strains J2M5 and J1M15 were iso-C and anteiso-C, respectively. The multiple taxonomic analyses indicated that strains J2M5 and J1M15 represent novel species of the genus and , respectively. We propose the names sp. nov. and sp. nov. for strain J2M5 (=KCTC 49461=CCUG 74767) and strain J1M15 (=KCTC 49462=CCUG 74766), respectively.

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Keyword(s): Actinomycetota , gut microbiota , lake prawn , Nocardioides , Nocardioides palaemonis , novel species , Tessaracoccus and Tessaracoccus palaemonis
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award NRF-2018R1A5A1025077)
    • Principle Award Recipient: Jin-WooBae
  • National Research Foundation of Korea (Award NRF-2020R1A2C3012797)
    • Principle Award Recipient: Jin-WooBae
© 2022 The Authors
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2022-12-19
2024-04-19
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References

  1. Chiu S-T, Chu T-W, Simangunsong T, Ballantyne R, Chiu C-S et al. Probiotic, Lactobacillus pentosus BD6 boost the growth and health status of white shrimp, Litopenaeus vannamei via oral administration. Fish Shellfish Immunol 2021; 117:124–135 [View Article]
     [Google Scholar]
  2. Dai W, Yu W, Zhang J, Zhu J, Tao Z et al. The gut eukaryotic microbiota influences the growth performance among cohabitating shrimp. Appl Microbiol Biotechnol 2017; 101:6447–6457 [View Article] [PubMed]
     [Google Scholar]
  3. Dai W-F, Zhang J-J, Qiu Q-F, Chen J, Yang W et al. Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities. Fish Shellfish Immunol 2018; 80:191–199 [View Article] [PubMed]
     [Google Scholar]
  4. Li E, Xu C, Wang X, Wang S, Zhao Q et al. Gut microbiota and its modulation for healthy farming of pacific white shrimp Litopenaeus vannamei. Rev Fisher Sci Aquacult 2018; 26:381–399 [View Article]
     [Google Scholar]
  5. Nelson TM, Rogers TL, Brown MV. The gut bacterial community of mammals from marine and terrestrial habitats. PLoS One 2013; 8:e83655 [View Article] [PubMed]
     [Google Scholar]
  6. Park W. Gut microbiomes and their metabolites shape human and animal health. J Microbiol 2018; 56:151–153 [View Article] [PubMed]
     [Google Scholar]
  7. Xiong J, Dai W, Zhu J, Liu K, Dong C et al. The underlying ecological processes of gut microbiota among cohabitating retarded, overgrown and normal shrimp. Microb Ecol 2017; 73:988–999 [View Article]
     [Google Scholar]
  8. Abt MC, Pamer EG. Commensal bacteria mediated defenses against pathogens. Curr Opin Immunol 2014; 29:16–22 [View Article] [PubMed]
     [Google Scholar]
  9. Mallon CA, Elsas JD van, Salles JF. Microbial invasions: the process, patterns, and mechanisms. Trends Microbiol 2015; 23:719–729 [View Article] [PubMed]
     [Google Scholar]
  10. Chen WY, Ng TH, Wu JH, Chen JW, Wang HC. Microbiome dynamics in a shrimp grow-out pond with possible outbreak of acute hepatopancreatic necrosis disease. Sci Rep 2017; 7:9395 [View Article]
     [Google Scholar]
  11. Holt CC, Bass D, Stentiford GD, van der Giezen M. Understanding the role of the shrimp gut microbiome in health and disease. J Invertebr Pathol 2021; 186:107387 [View Article] [PubMed]
     [Google Scholar]
  12. Xiong J, Zhu J, Dai W, Dong C, Qiu Q et al. Integrating gut microbiota immaturity and disease-discriminatory taxa to diagnose the initiation and severity of shrimp disease. Environ Microbiol 2017; 19:1490–1501 [View Article] [PubMed]
     [Google Scholar]
  13. Tzeng T-D, Pao Y-Y, Chen P-C, Weng FC-H, Jean WD et al. Effects of host phylogeny and habitats on gut microbiomes of oriental river prawn (Macrobrachium nipponense). PLoS One 2015; 10:e0132860 [View Article]
     [Google Scholar]
  14. Zhao Y, Duan C, Zhang X, Chen H, Ren H et al. Insights into the gut microbiota of freshwater shrimp and its associations with the surrounding microbiota and environmental factors. J Microbiol Biotechnol 2018; 28:946–956 [View Article]
     [Google Scholar]
  15. Lee SD. Nocardioides furvisabuli sp. nov., isolated from black sand. Int J Syst Evol Microbiol 2007; 57:35–39 [View Article] [PubMed]
     [Google Scholar]
  16. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Nocardioides glacieisoli sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2015; 65:4845–4849 [View Article] [PubMed]
     [Google Scholar]
  17. Prauser H. Nocardioides, a new genus of the order actinomycetales. Int J Syst Bacteriol 1976; 26:58–65 [View Article]
     [Google Scholar]
  18. Schippers A, Schumann P, Spröer C. Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium. Int J Syst Evol Microbiol 2005; 55:1501–1504 [View Article] [PubMed]
     [Google Scholar]
  19. Wang L, Li J, Zhang G. Nocardioides rotundus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:1932–1936 [View Article] [PubMed]
     [Google Scholar]
  20. Wang S, Zhou Y, Zhang G. Nocardioides flavus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:5275–5280 [View Article] [PubMed]
     [Google Scholar]
  21. Yi H, Chun J. Nocardioides ganghwensis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2004; 54:1295–1299 [View Article] [PubMed]
     [Google Scholar]
  22. Zhang D-C, Schumann P, Redzic M, Zhou Y-G, Liu H-C et al. Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:445–450 [View Article] [PubMed]
     [Google Scholar]
  23. Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YH. Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China. Int J Syst Evol Microbiol 2019; 69:2329–2334 [View Article] [PubMed]
     [Google Scholar]
  24. Maszenan AM, Seviour RJ, Patel BKC, Schumann P, Rees GN. Tessaracoccus bendigoensis gen nov.sp. nov., a gram-positive coccus occurring in regular packages or tetrads, isolated from activated sludge biomass. Int J Syst Bacteriol 1999; 49 Pt 2:459–468 [View Article]
     [Google Scholar]
  25. Cai M, Wang L, Cai H, Li Y, Wang Y-N et al. Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil. Int J Syst Evol Microbiol 2011; 61:1767–1775 [View Article] [PubMed]
     [Google Scholar]
  26. Chaudhary DK, Kim J. Tessaracoccus terricola sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:529–535 [View Article] [PubMed]
     [Google Scholar]
  27. Hyun D-W, Sung H, Kim PS, Lee J-Y, Jeong Y-S et al. Tessaracoccus coleopterorum sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  28. Lee DW, Lee SD. Tessaracoccus flavescens sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2008; 58:785–789 [View Article] [PubMed]
     [Google Scholar]
  29. Seck E, Traore SI, Khelaifia S, Beye M, Michelle C et al. Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut. New Microbes New Infect 2016; 13:3–12 [View Article] [PubMed]
     [Google Scholar]
  30. Tak EJ, Kim HS, Lee J-Y, Kang W, Hyun D-W et al. Tessaracoccus aquimaris sp. nov., isolated from the intestine of a Korean rockfish, Sebastes schlegelii, from a marine aquaculture pond. Int J Syst Evol Microbiol 2018; 68:1065–1072 [View Article] [PubMed]
     [Google Scholar]
  31. Thongphrom C, Kim JH, Bora N, Kim W. Tessaracoccus arenae sp. nov., isolated from sea sand. Int J Syst Evol Microbiol 2017; 67:2008–2013 [View Article] [PubMed]
     [Google Scholar]
  32. Srinivasan S, Sundararaman A, Lee SS. Tessaracoccus defluvii sp. nov., isolated from an aeration tank of a sewage treatment plant. Antonie Van Leeuwenhoek 2017; 110:1–9 [View Article] [PubMed]
     [Google Scholar]
  33. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article] [PubMed]
     [Google Scholar]
  34. Hyun D-W, Jeong Y-S, Lee J-Y, Sung H, Lee S-Y et al. Description of Nocardioides piscis sp nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish). J Microbiol 2021; 59:552–562 [View Article]
     [Google Scholar]
  35. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley & Sons; 1991 pp 115–175
     [Google Scholar]
  36. 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]
  37. 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]
  38. 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]
     [Google Scholar]
  39. 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]
  40. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Biol 1969; 18:1–32 [View Article]
     [Google Scholar]
  41. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  42. 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] [PubMed]
     [Google Scholar]
  43. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
     [Google Scholar]
  44. 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]
  45. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  46. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  47. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
     [Google Scholar]
  48. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article] [PubMed]
     [Google Scholar]
  49. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
     [Google Scholar]
  50. Ha SM, Kim CK, Roh J, Byun JH, Yang SJ et al. Application of the whole genome-based bacterial identification system, TrueBac ID, using clinical isolates that were not identified with three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems. Ann Lab Med 2019; 39:530–536 [View Article]
     [Google Scholar]
  51. Jeong Y-S, Kang W, Lee J-Y, Sung H, Kim HS et al. Pseudorhodobacter turbinis sp. nov., isolated from the gut of the Korean turban shell, Turbo cornutus. Int J Syst Evol Microbiol 2019; 71: [View Article]
     [Google Scholar]
  52. 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]
  53. Biebl H, Pukall R, Lünsdorf H, Schulz S, Allgaier M et al. Description of Labrenzia alexandrii gen. nov., sp. nov.,a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense. Int J Syst Evol Microbiol 2007; 57:1095–1107 [View Article]
     [Google Scholar]
  54. Jeong S-W, Han JE, Lee J-Y, Yoo J-H, Kim D-Y et al. Description of Polaribacter batillariae sp nov.Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish. J Microbiol 2022; 60:576–584 [View Article]
     [Google Scholar]
  55. Shindo K, Kikuta K, Suzuki A, Katsuta A, Kasai H et al. Rare carotenoids, (3R)-saproxanthin and (3R,2’S)-myxol, isolated from novel marine bacteria (Flavobacteriaceae) and their antioxidative activities. Appl Microbiol Biotechnol 2007; 74:1350–1357 [View Article] [PubMed]
     [Google Scholar]
  56. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580 [View Article]
     [Google Scholar]
  57. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article]
     [Google Scholar]
  58. Jouanneau S, Recoules L, Durand MJ, Boukabache A, Picot V et al. Methods for assessing biochemical oxygen demand (BOD): a review. Water Res 2014; 49:62–82 [View Article] [PubMed]
     [Google Scholar]
  59. Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019; 47:D666–D677 [View Article] [PubMed]
     [Google Scholar]
  60. 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]
  61. 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]
  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 Meth 1984; 2:233–241 [View Article]
     [Google Scholar]
  63. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial systematics. Meth Microbiol 1988; 19:161–207
     [Google Scholar]
  64. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
     [Google Scholar]
  65. Partridge SM. Aniline hydrogen phthalate as a spraying reagent for chromatography of sugars. Nature 1949; 164:443 [View Article]
     [Google Scholar]
  66. MIDI Sherlock Microbial Identification System Operating Manual, version 3.0 Newark, DE: MIDI; 1999
     [Google Scholar]
  67. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids MIDI inc; 1990
     [Google Scholar]
  68. Lee S-Y, Kim PS, Sung H, Hyun D-W, Bae J-W. Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork. J Microbiol 2022; 60:469–477 [View Article] [PubMed]
     [Google Scholar]
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Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
Int J Syst Evol Microbiol 72, 005643 (2023); https://doi.org/10.1099/ijsem.0.005643
/content/journal/ijsem/10.1099/ijsem.0.005643
/content/journal/ijsem/10.1099/ijsem.0.005643
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