Strain identifier

BacDive ID: 140592

Type strain: Yes

Species: Salibacter halophilus

Strain Designation: JZ3C34

Strain history: <- Zongjun Du, Shandong Univ., China

NCBI tax ID(s): 1803916 (species)

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General

@ref: 43263

BacDive-ID: 140592

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, halophilic, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Salibacter halophilus JZ3C34 is a facultative anaerobe, halophilic, mesophilic bacterium that forms circular colonies and was isolated from brine sample from a saltern.

NCBI tax id

  • NCBI tax id: 1803916
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Zongjun Du, Shandong Univ., China

doi: 10.13145/bacdive140592.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Cryomorphaceae
  • genus: Salibacter
  • species: Salibacter halophilus
  • full scientific name: Salibacter halophilus Lu et al. 2017

@ref: 43263

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Cryomorphaceae

genus: Salibacter

species: Salibacter halophilus

strain designation: JZ3C34

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43263negative1.5-2.0 µm0.3-0.4 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative100

colony morphology

  • @ref: 43263
  • colony size: 1 mm
  • colony color: orange
  • colony shape: circular
  • incubation period: 4 days
  • medium used: modified MA

Culture and growth conditions

culture medium

  • @ref: 43263
  • name: modified MA
  • growth: yes
  • composition: sea salt Sigma-Aldrich, 40g/l; NaCl, 30g/l; yeast extract, 1g/l; peptone, 5g/l; ferric citrate, 0.1g/l; and agar, 18g/l

culture temp

@refgrowthtypetemperaturerange
43263positiveoptimum33mesophilic
43263positivegrowth20-50
67771positivegrowth33-37mesophilic

culture pH

@refabilitytypepHPH range
43263positivegrowth6.5-8.5alkaliphile
43263positiveoptimum7.0-8.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43263facultative anaerobe
67771facultative anaerobe

spore formation

@reftype of sporespore formationconfidence
43263endosporeno
69481no100
69480no99.998

halophily

@refhalophily levelsaltgrowthtested relationconcentration
43263halophilicNaClpositivegrowth2.0-18.0 %(w/v)
43263NaClpositiveoptimum6 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4326318420magnesium(2+)+required for growth
4326329108calcium(2+)+required for growth
43263sodium(+)+required for growth
432635291gelatin+hydrolysis
4326353424tween 20+hydrolysis
4326353423tween 40+hydrolysis
4326353426tween 80+hydrolysis
4326328017starch-hydrolysis
432632509agar-hydrolysis
4326358187alginate-hydrolysis
4326317632nitrate-reduction
4326316947citrate-carbon source
4326317634D-glucose+builds acid from
4326330849L-arabinose+builds acid from
4326330911sorbitol+builds acid from
4326317108D-arabinose+builds acid from
4326328066gentiobiose-assimilation
4326315824D-fructose-assimilation
4326317464L-galactonic acid gamma-lactone-assimilation
4326315748D-glucuronate+assimilation
4326362345L-rhamnose-assimilation
4326373706bromosuccinate+assimilation
4326378697D-fructose 6-phosphate+assimilation
4326337684mannose-builds acid from
4326316988D-ribose+builds acid from
4326315824D-fructose+builds acid from
4326317266L-sorbose+builds acid from
432634853esculin+builds acid from
4326327082trehalose+builds acid from
4326316443D-tagatose+builds acid from
4326317234glucose-assimilation
43263potassium 5-dehydro-D-gluconate+builds acid from
4326332528turanose+oxidation
4326375228sodium lactate+oxidation
4326316523D-serine+oxidation
4326378697D-fructose 6-phosphate+oxidation
4326315971L-histidine+oxidation
4326315748D-glucuronate+oxidation
4326332323glucuronamide+oxidation
43263309162-oxoglutarate+oxidation
4326313705acetoacetate+oxidation
4326328066gentiobiose+oxidation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
4326331168acetylspiramycinyesyes30 µg
432633498cefotaxime sodiumyesyes30 µg
4326317698chloramphenicolyesyes30 µg
4326348923erythromycinyesyes15 µg
432636472lincomycinyesyes2 µg
4326317334penicillinyesyes10 µg
4326328077rifampicinyesyes5 µg
4326317076streptomycinyesyes10 µg

metabolite production

@refChebi-IDmetaboliteproduction
4326316136hydrogen sulfideno
4326335581indoleno
4326315688acetoinno

metabolite tests

  • @ref: 43263
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
43263beta-galactosidase-3.2.1.23
43263cytochrome oxidase-1.9.3.1
43263catalase+1.11.1.6
43263alkaline phosphatase+3.1.3.1
43263leucine arylamidase+3.4.11.1
43263acid phosphatase+3.1.3.2
43263esterase (C 4)+
43263esterase Lipase (C 8)+
43263valine arylamidase-
43263naphthol-AS-BI-phosphohydrolase-
43263cystine arylamidase-3.4.11.3
43263lipase (C 14)-
43263trypsin-3.4.21.4
43263chymotrypsin-3.4.4.5
43263alpha-glucosidase-3.2.1.20
43263beta-glucosidase-3.2.1.21
43263alpha-mannosidase-3.2.1.24
43263beta-D-fucosidase-3.2.1.38
43263alpha-galactosidase-3.2.1.22
43263beta-glucuronidase-3.2.1.31
43263N-acetyl-beta-glucosaminidase-3.2.1.52

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43263C15:0 iso59
    43263C15:1 iso G14.9
  • type of FA analysis: whole cell analysis
  • incubation medium: modified MA
  • agar/liquid: liquid
  • incubation temperature: 33
  • incubation time: 4
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43263brine sample from a salternFeicheng, ChinaChinaCHNAsia
67771From marine solar salternFeicheng, the coastal area of WeihaiChinaCHNAsia

isolation source categories

Cat1Cat2
#Condition#Saline
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_100052.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16866;96_40637;97_51863;98_68418;99_100052&stattab=map
  • Last taxonomy: Salibacter halophilus subclade
  • 16S sequence: KU726562
  • Sequence Identity:
  • Total samples: 666
  • soil counts: 52
  • aquatic counts: 546
  • animal counts: 54
  • plant counts: 14

Sequence information

16S sequences

  • @ref: 43263
  • description: 16S rRNA gene sequences
  • accession: KU726562
  • length: 1448
  • database: ena
  • NCBI tax ID: 1803916

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salibacter halophilus KCTC 52047GCA_008806325contigncbi1803916
66792Halospina sp. K52047b2614160.3wgspatric2614160
66792Salibacter halophilus strain KCTC 520471803916.3wgspatric1803916
66792Salibacter halophilus KCTC 520472886991845draftimg1803916

GC content

@refGC-contentmethod
4326339.6high performance liquid chromatography (HPLC)
6777139.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.311yes
gram-positiveno98.769no
anaerobicno96.818no
aerobicyes83.478no
halophileyes95.922yes
spore-formingno96.069no
glucose-utilno50.98no
flagellatedyes57.675yes
thermophileno98.503no
glucose-fermentno87.996no

External links

@ref: 43263

culture collection no.: KCTC 52047, MCCC 1K02288

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28593834Salibacter halophilus gen. nov., sp. nov., isolated from a saltern.Lu DC, Xia J, Dunlap CA, Rooney AP, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0018072017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome
Phylogeny33847553Croceimicrobium hydrocarbonivorans gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate.Liu R, Lai Q, Gu L, Yan P, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0047702021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Geologic Sediments/*microbiology, *Microbial Consortia, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyethylene Terephthalates/*metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43263De-Chen Lu, Jun Xia, Christopher A. Dunlap, Alejandro P. Rooney and Zong-Jun DuSalibacter halophilus gen. nov., sp. nov., isolated from a saltern10.1099/ijsem.0.001807IJSEM 67: 1784-1788 201728593834
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1