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Current microbiology
Feb 10, 2025;82 (3): 131.

Comamonas squillarum sp. nov., Isolated from Intestine of Red Swamp Crayfish (Procambarus clarkii).

Shi Shi, Dao-Feng Zhang, Hong-Chuan Wang, Fu-Hui Jiang, Li-Fan Cui, Ying Huang
Author Information
  1. Shi Shi: Jiangsu Province Engineering Research Center for Marine Bio-Resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, China.
  2. Dao-Feng Zhang: Jiangsu Province Engineering Research Center for Marine Bio-Resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, China.
  3. Hong-Chuan Wang: Jiangsu Province Engineering Research Center for Marine Bio-Resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, China.
  4. Fu-Hui Jiang: Jiangsu Province Engineering Research Center for Marine Bio-Resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, China.
  5. Li-Fan Cui: Jiangsu Province Engineering Research Center for Marine Bio-Resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, China.
  6. Ying Huang: Jiangsu Province Engineering Research Center for Marine Bio-Resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, China. huangyingying@hhu.edu.cn.
PMID: 39928163 DOI: 10.1007/s00284-025-04093-5

Abstract

A novel bacterium, designated as strain PR12, was isolated from intestine of red swamp crayfish (Procambarus clarkii), which appeared as creamy white colonies on TSA plates. Growth occurred at temperatures of 4-37 °C (28-30 °C optimal), pH of 6.0-9.0 (7.0-8.5 optimal), and with 0-4.0% (w/v) NaCl (0-1.5% optimal). The cells were Gram-stain-negative, rod-shaped, non-motile, aerobic, oxidase- and catalase-positive, and chemoorganotrophic. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PR12 was related to members of the genus Comamonas and shared the highest sequence similarities with Comamonas koreensis KCTC 12005 (99.0%), Comamonas sediminis S3 (98.8%), and Comamonas piscis CN1 (98.0%). Whole genome size of PR12 was 5,111,300 bp and DNA G + C content was 63.5%. The major cellular fatty acids (> 10%) were C, C cyclo, summed features 3 (Cω6c and/or Cω7c) and summed features 8 (Cω6c and/or Cω7c). The major respiratory quinone was Q-8 and the major polar lipids contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on the digital DNA-DNA hybridization, phylogenetic analysis, average nucleotide identity, average aminoacid identity as well as biochemical characteristics, strain PR12 was clearly distinguishable from all recognized type strains of the genus Comamonas and represents a novel species, for which the name Comamonas squillarum sp. nov. is proposed. The type strain is PR12 (= MCCC 1K08379 = JCM 35896).

References

  1. Davis GHG, Park RWA (1962) A taxonomic study of certain bacteria currently classified as Vibrio species. Microbiology 27:101–119. https://doi.org/10.1099/00221287-27-1-101 [DOI: 10.1099/00221287-27-1-101]
  2. Wauters G, De Baere T, Willems A, Falsen E, Vaneechoutte M (2003) Description of Comamonas aquatica comb. nov. and Comamonas kerstersii sp. nov. for two subgroups of Comamonas terrigena and emended description of Comamonas terrigena. Int J Syst Evol Microbiol 53:859–862. https://doi.org/10.1099/ijs.0.02450-0 [DOI: 10.1099/ijs.0.02450-0]
  3. De Vos P, Kersters K, Falsen E, Pot B, Gillis M, Segers P, De Ley J (1985) Comamonas Davis and Park 1962 gen. nov., nom. rev. emend., and Comamonas terrigena hugh 1962 sp. nov., nom. rev. Int J Syst Evol Microbiol 35:443–453. https://doi.org/10.1099/00207713-35-4-443 [DOI: 10.1099/00207713-35-4-443]
  4. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70:5607–5612. https://doi.org/10.1099/ijsem.0.004332 [DOI: 10.1099/ijsem.0.004332]
  5. Chang Y-H, Han J-i, Chun J, Lee KC, Rhee M-S, Kim Y-B, Bae KS (2002) Comamonas koreensis sp. nov., a non-motile species from wetland in Woopo. Korea Int J Syst Evol Microbiol 52:377–381. https://doi.org/10.1099/00207713-52-2-377 [DOI: 10.1099/00207713-52-2-377]
  6. Kang W, Soo Kim P, Hyun D-W, Lee J-Y, Sik Kim H, Joon OhS, Shin N-R, Bae J-W (2016) Comamonas piscis sp. nov., isolated from the intestine of a Korean rockfish, Sebastes schlegelii. Int J Syst Evol Microbiol 66:780–785. https://doi.org/10.1099/ijsem.0.000790 [DOI: 10.1099/ijsem.0.000790]
  7. Kämpfer P, Busse H-J, Baars S, Wilharm G, Glaeser SP (2018) Comamonas aquatilis sp. nov., isolated from a garden pond. Int J Syst Evol Microbiol 68:1210–1214. https://doi.org/10.1099/ijsem.0.002652 [DOI: 10.1099/ijsem.0.002652]
  8. Park K-H, Yu Z, Dong K, Lee S-S (2021) Comamonas suwonensis sp. Nov., isolated from stream water in the Republic of Korea. Int J Syst Evol Microbiol 71:004681. https://doi.org/10.1099/ijsem.0.004681 [DOI: 10.1099/ijsem.0.004681]
  9. Xu M, Li F, Zhang X, Chen B, Geng Y, Ouyang P, Chen D, Li L, Huang X (2024) Microbiome analysis reveals the intestinal microbiota characteristics and potential impact of Procambarus clarkii. Appl Microbiol Biotechnol 108:77. https://doi.org/10.1007/s00253-023-12914-5 [DOI: 10.1007/s00253-023-12914-5]
  10. Alvanou MV, Feidantsis K, Staikou A, Apostolidis AP, Michaelidis B, Giantsis IA (2023) Probiotics, prebiotics, and synbiotics utilization in crayfish aquaculture and factors affecting gut microbiota. Microorganisms 11:1232. https://doi.org/10.3390/microorganisms11051232 [DOI: 10.3390/microorganisms11051232]
  11. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703. https://doi.org/10.1128/jb.173.2.697-703.1991 [DOI: 10.1128/jb.173.2.697-703.1991]
  12. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) Mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096 [DOI: 10.1093/molbev/msy096]
  13. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/bf01731581 [DOI: 10.1007/bf01731581]
  14. Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. https://doi.org/10.1371/journal.pcbi.1005595 [DOI: 10.1371/journal.pcbi.1005595]
  15. Golosova O, Henderson R, Vaskin Y, Gabrielian A, Grekhov G, Nagarajan V, Oler AJ, Nones MQ, Hurt D, Fursov M, Huyen Y (2014) Unipro UGENE NGS pipelines and components for variant calling, Rna-seq and ChIP-seq data analyses. PeerJ. https://doi.org/10.7717/peerj.644.10.7717/peerj.644 [DOI: 10.7717/peerj.644.10.7717/peerj.644]
  16. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA (2013) Assembling single-cell genomes and mini-metagenomes from chimeric mda products. J Comput Biol 20:714–737. https://doi.org/10.1089/cmb.2013.0084 [DOI: 10.1089/cmb.2013.0084]
  17. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114 [DOI: 10.1101/gr.186072.114]
  18. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2021) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucl Acids Res 50:D801–D807. https://doi.org/10.1093/nar/gkab902 [DOI: 10.1093/nar/gkab902]
  19. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4 [DOI: 10.1007/s10482-017-0844-4]
  20. Kim D, Park S, Chun J (2021) Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 59:476–480. https://doi.org/10.1007/s12275-021-1154-0 [DOI: 10.1007/s12275-021-1154-0]
  21. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt K, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucl Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569 [DOI: 10.1093/nar/gkw569]
  22. Zhang DF, He W, Shao ZZ, Ahmed I, Zhang YQ, Li WJ, Zhao Z (2023) Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae. Int J Syst Evol Microbiol 73:006156. https://doi.org/10.1099/ijsem.0.006156 [DOI: 10.1099/ijsem.0.006156]
  23. Zhang DF, He W, Shao ZZ, Ahmed I, Zhang YQ, Li WJ, Zhao Z (2023) EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets. BMC Bioinf 24:390. https://doi.org/10.1186/s12859-023-05527-2 [DOI: 10.1186/s12859-023-05527-2]
  24. Athalye M, Noble WC, Minnikin DE (1985) Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 58:507–512. https://doi.org/10.1111/j.1365-2672.1985.tb01491.x [DOI: 10.1111/j.1365-2672.1985.tb01491.x]
  25. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6 [DOI: 10.1016/0167-7012(84)90018-6]
  26. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469. https://doi.org/10.2323/jgam.42.457 [DOI: 10.2323/jgam.42.457]
  27. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Nat Acad Sci 106:19126–19131. https://doi.org/10.1073/pnas.0906412106 [DOI: 10.1073/pnas.0906412106]
  28. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu X-W, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516 [DOI: 10.1099/ijsem.0.002516]

Grants

  1. No. 32002423/National Natural Science Foundation of China

MeSH Term

Animals
Astacoidea
Phylogeny
RNA, Ribosomal, 16S
Base Composition
DNA, Bacterial
Fatty Acids
Intestines
Comamonas
Bacterial Typing Techniques
Phospholipids
Sequence Analysis, DNA
Genome, Bacterial

Chemicals

RNA, Ribosomal, 16S
DNA, Bacterial
Fatty Acids
Phospholipids
Journal Article
Article has an altmetric score of 1

Word Cloud

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