Strain identifier

BacDive ID: 5733

Type strain: Yes

Species: Salinimicrobium catena

Strain Designation: HY1

Strain history: S. Liu HY1.

NCBI tax ID(s): 390640 (species)

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General

@ref: 17282

BacDive-ID: 5733

DSM-Number: 23553

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Salinimicrobium catena HY1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment from oilfield.

NCBI tax id

  • NCBI tax id: 390640
  • Matching level: species

strain history

@refhistory
17282<- JCM; JCM 14015 <- S. Liu
67770S. Liu HY1.

doi: 10.13145/bacdive5733.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Salinimicrobium
  • species: Salinimicrobium catena
  • full scientific name: Salinimicrobium catena (Ying et al. 2007) Lim et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Salegentibacter catena

@ref: 17282

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Salinimicrobium

species: Salinimicrobium catena

full scientific name: Salinimicrobium catena (Ying et al. 2007) Lim et al. 2008 emend. Nedashkovskaya et al. 2010

strain designation: HY1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31923negative2-6 µm0.5-0.8 µmrod-shapedno
125438no93
125438negative98.5
125439negative99.8

Culture and growth conditions

culture medium

  • @ref: 17282
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperature
17282positivegrowth28
31923positivegrowth15-42
31923positiveoptimum33
67770positivegrowth30

culture pH

@refabilitytypepHPH range
31923positivegrowth6.5-9.0alkaliphile
31923positiveoptimum7.85

Physiology and metabolism

oxygen tolerance

  • @ref: 31923
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31923no
125438no93.5
125439no99

halophily

@refsaltgrowthtested relationconcentration
31923NaClpositivegrowth0.1-10 %
31923NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3192317234glucose+carbon source
319234853esculin+hydrolysis

metabolite production

  • @ref: 31923
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31923acid phosphatase+3.1.3.2
31923alkaline phosphatase+3.1.3.1
31923catalase+1.11.1.6
31923gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17282sediment from oilfieldXijiang, South China SeaChinaCHNAsia
67770Sediment of Xijiang oilfield in the South China Sea

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_14037.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_7243;97_8687;98_10648;99_14037&stattab=map
  • Last taxonomy: Salinimicrobium catena subclade
  • 16S sequence: DQ640642
  • Sequence Identity:
  • Total samples: 410
  • soil counts: 100
  • aquatic counts: 285
  • animal counts: 16
  • plant counts: 9

Safety information

risk assessment

  • @ref: 17282
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17282
  • description: Salinimicrobium catena strain HY1 16S ribosomal RNA gene, partial sequence
  • accession: DQ640642
  • length: 1487
  • database: nuccore
  • NCBI tax ID: 390640

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinimicrobium catena strain CGMCC 1.6101390640.6wgspatric390640
66792Salinimicrobium catena strain DSM 23553390640.7wgspatric390640
66792Salinimicrobium catena CGMCC 1.61012617270763draftimg390640
66792Salinimicrobium catena DSM 235532622736500draftimg390640
67770Salinimicrobium catena CGMCC 1.6101GCA_900102915scaffoldncbi390640
67770Salinimicrobium catena DSM 23553GCA_900107495scaffoldncbi390640

GC content

@refGC-contentmethod
1728244.4thermal denaturation, midpoint method (Tm)
3192344.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.614yes
125438spore-formingspore-formingAbility to form endo- or exosporesno93.5yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.188no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.851yes
125438motile2+flagellatedAbility to perform flagellated movementno93yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99
125439BacteriaNetmotilityAbility to perform movementno71.8
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative aerobe60.8

External links

@ref: 17282

culture collection no.: DSM 23553, CGMCC 1.6101, JCM 14015, CIP 109554

straininfo link

  • @ref: 75213
  • straininfo: 297329

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267953Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter.Ying JY, Liu ZP, Wang BJ, Dai X, Yang SS, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64658-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, Base Sequence, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flavobacteriaceae/*classification/cytology/*isolation & purification/physiology, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Locomotion, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Water MicrobiologyGenetics
Phylogeny18218946Reclassification of Salegentibacter catena Ying et al. 2007 as Salinimicrobium catena gen. nov., comb. nov. and description of Salinimicrobium xinjiangense sp. nov., a halophilic bacterium isolated from Xinjiang province in China.Lim JM, Jeon CO, Lee SS, Park DJ, Xu LH, Jiang CL, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65297-02008Bacterial Typing Techniques, China, DNA, Bacterial/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Fresh Water/chemistry/*microbiology, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium ChlorideGenetics
Phylogeny21685257Salinimicrobium gaetbulicola sp. nov., isolated from tidal flat sediment.Lee SY, Park S, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.033399-02011Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17282Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23553)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23553
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31923Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2818028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75213Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297329.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1