Strain identifier

BacDive ID: 133367

Type strain: Yes

Species: Arcticibacterium luteifluviistationis

Strain Designation: SM1504

Strain history: <- Yu-Zhong Zhang, Shandong Univ.

NCBI tax ID(s): 1784714 (species)

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General

@ref: 25217

BacDive-ID: 133367

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

description: Arcticibacterium luteifluviistationis SM1504 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Arctic seawater .

NCBI tax id

  • NCBI tax id: 1784714
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Yu-Zhong Zhang, Shandong Univ.

doi: 10.13145/bacdive133367.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Arcticibacterium
  • species: Arcticibacterium luteifluviistationis
  • full scientific name: Arcticibacterium luteifluviistationis Li et al. 2017

@ref: 25217

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Cytophagaceae

genus: Arcticibacterium

species: Arcticibacterium luteifluviistationis

strain designation: SM1504

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25217negative1.5-3.0 µm0.3-0.4 µmrod-shapedno
67771no
67771negative
69480no93.793
69480negative99.991

colony morphology

  • @ref: 25217
  • colony size: 1.0-2.0 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: tryptic soy agar (TSA)

pigmentation

  • @ref: 25217
  • production: no
  • name: Flexirubin-type

Culture and growth conditions

culture medium

  • @ref: 25217
  • name: tryptic soy agar (TSA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
25217positivegrowth4.0-30.0
25217positiveoptimum20psychrophilic
67771positivegrowth20psychrophilic

culture pH

@refabilitytypepH
25217positivegrowth6.0-7.5
25217positiveoptimum6.5-7.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
25217aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

halophily

@refsalttested relationconcentrationgrowth
25217NaCloptimum0 %
25217NaClgrowth0.0-4.0 %(w/v)positive

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
252172509agar-hydrolysis
2521758187alginate-hydrolysis
25217casein-hydrolysis
2521762968cellulose-hydrolysis
2521717029chitin-hydrolysis
2521727689decanoate-assimilation
2521716991dna-hydrolysis
252174767elastin-hydrolysis
2521761995lecithin-hydrolysis
2521717632nitrate-reduction
2521728017starch-hydrolysis
2521753426tween 80-hydrolysis
2521737166xylan-hydrolysis
25217168082-dehydro-D-gluconate+assimilation
25217581435-dehydro-D-gluconate+assimilation
2521717128adipate+assimilation
2521718305arbutin+assimilation
2521717057cellobiose+assimilation
2521715824D-fructose+assimilation
2521717634D-glucose+assimilation
2521716899D-mannitol+assimilation
2521716024D-mannose+assimilation
2521717924D-sorbitol+assimilation
2521765327D-xylose+assimilation
252174853esculin+hydrolysis
252174853esculin+assimilation
2521716813galactitol+assimilation
252175291gelatin+hydrolysis
2521717234glucose+builds acid from
2521717754glycerol+assimilation
2521717268myo-inositol+assimilation
2521730849L-arabinose+assimilation
2521762345L-rhamnose+assimilation
2521725115malate+assimilation
2521717306maltose+assimilation
25217320061methyl alpha-D-glucopyranoside+assimilation
25217506227N-acetylglucosamine+assimilation
2521718401phenylacetate+assimilation
2521732032potassium gluconate+assimilation
2521753258sodium citrate+assimilation
2521728017starch+assimilation
2521717992sucrose+assimilation
2521727082trehalose+assimilation
2521727897tryptophan+energy source
2521732528turanose+assimilation
2521753424tween 20+hydrolysis
2521753423tween 40+hydrolysis
2521753425tween 60+hydrolysis
2521718186tyrosine+hydrolysis
2521716199urea+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
2521728971ampicillinyesyes10 µg
252173393carbenicillinyesyes100 µg
2521717698chloramphenicolyesyes30 µg
2521748923erythromycinyesyes15 µg
2521717833gentamicinyesyes10 µg
252176472lincomycinyesyes15 µg
2521718208penicillin gyesyes10 µg
2521728077rifampicinyesyes5 µg
2521737943colistinyesyes10 µg
252176104kanamycinyesyes30 µg
252178309polymyxin byesyes300 Unit
2521727902tetracyclineyesyes30 µg
2521728001vancomycinyesyes30 µg
2521717076streptomycinyesyes30 µg

metabolite production

  • @ref: 25217
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 25217
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
25217acid phosphatase+3.1.3.2
25217alkaline phosphatase+3.1.3.1
25217alpha-chymotrypsin+3.4.21.1
25217alpha-fucosidase-3.2.1.51
25217alpha-galactosidase-3.2.1.22
25217alpha-glucosidase+3.2.1.20
25217alpha-mannosidase+3.2.1.24
25217arginine dihydrolase-3.5.3.6
25217beta-galactosidase+3.2.1.23
25217beta-glucosidase+3.2.1.21
25217beta-glucuronidase-3.2.1.31
25217catalase+1.11.1.6
25217cystine arylamidase+3.4.11.3
25217esterase (C 4)+
25217esterase Lipase (C 8)+
25217gelatinase+
25217leucine arylamidase+3.4.11.1
25217lipase (C 14)-
25217N-acetyl-beta-glucosaminidase-3.2.1.52
25217naphthol-AS-BI-phosphohydrolase+
25217trypsin+3.4.21.4
25217tryptophan deaminase+4.1.99.1
25217urease+3.5.1.5
25217valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25217C15:0 anteiso5
    25217C15:1ω6c1.4
    25217C16:1ω7c / iso-C15 2-OH46.1
    25217C18:1ω7c1.2
    25217C13:0 iso1.1
    25217C15:0 iso24.9
    25217C15:0 iso 3OH2.3
    25217C15:1 iso h / C13:0 3OH3.7
    25217C17:0 iso 3OH1.4
    25217C17:1 iso I /C17:1 anteiso B7.7
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy
  • incubation temperature: 20
  • incubation time: 3
  • software version: Sherlock 4.5
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
25217Arctic seawater (surface sample)King’s Fjord, SvalbardNorwayNOREuropetryptic soy agar (TSA)0.5 % tryptone (Oxoid), 0.1 % yeast extract (Oxoid), 1.5 % agar and artificial seawater14 days15
67771From arctic sea waterChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Condition#Psychrophilic (<10°C)
#Climate#Cold#Polar

taxonmaps

  • @ref: 69479
  • File name: preview.99_11356.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16802;96_5687;97_6847;98_8488;99_11356&stattab=map
  • Last taxonomy: Arcticibacterium luteifluviistationis subclade
  • 16S sequence: KU529276
  • Sequence Identity:
  • Total samples: 1159
  • soil counts: 15
  • aquatic counts: 1029
  • animal counts: 31
  • plant counts: 84

Sequence information

16S sequences

  • @ref: 25217
  • description: Lacihabitans sp. SM1504 16S ribosomal RNA gene, partial sequence
  • accession: KU529276
  • length: 1439
  • database: nuccore
  • NCBI tax ID: 1784714

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcticibacterium luteifluviistationis SM1504TGCA_003258705completencbi1784714
66792Arcticibacterium luteifluviistationis SM15042887088641completeimg1784714

GC content

@refGC-contentmethod
2521740.8thermal denaturation, midpoint method (Tm)
6777140.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.207no
gram-positiveno97.738no
anaerobicno99.501yes
aerobicyes91.313yes
halophileno91.262no
spore-formingno96.676no
glucose-utilyes85.292no
thermophileno98.623yes
motileno92.021yes
glucose-fermentno92.355no

External links

@ref: 25217

culture collection no.: KCTC 42716, CCTCC AB 2015348

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902275Arcticibacterium luteifluviistationis gen. nov., sp. nov., isolated from Arctic seawater.Li DD, Peng M, Wang N, Wang XJ, Zhang XY, Chen XL, Su HN, Zhang YZ, Shi MInt J Syst Evol Microbiol10.1099/ijsem.0.0016902017Arctic Regions, Bacterial Typing Techniques, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Genetics30505389Complete genome sequence of Arcticibacterium luteifluviistationis SM1504(T), a cytophagaceae bacterium isolated from Arctic surface seawater.Li Y, Guo XH, Dang YR, Sun LL, Zhang XY, Chen XL, Qin QL, Wang PStand Genomic Sci10.1186/s40793-018-0335-x2018
Metabolism31253686A Novel Subfamily of Endo-beta-1,4-Glucanases in Glycoside Hydrolase Family 10.Zhao F, Cao HY, Zhao LS, Zhang Y, Li CY, Zhang YZ, Li PY, Wang P, Chen XLAppl Environ Microbiol10.1128/AEM.01029-192019Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/metabolism, Cellulase/chemistry/*genetics/metabolism, Cytophagaceae/*genetics/metabolism, Escherichia coli/genetics, *Gene Expression Regulation, Bacterial, Phylogeny, Sequence AlignmentPhylogeny
Enzymology34058201Active site architecture of an acetyl xylan esterase indicates a novel cold adaptation strategy.Zhang Y, Ding HT, Jiang WX, Zhang X, Cao HY, Wang JP, Li CY, Huang F, Zhang XY, Chen XL, Zhang YZ, Li PYJ Biol Chem10.1016/j.jbc.2021.1008412021Acetylesterase/antagonists & inhibitors/*chemistry/genetics/*metabolism, *Adaptation, Physiological, Amino Acid Sequence, Bacteria/enzymology, Catalytic Domain, *Cold Temperature, Enzyme Inhibitors/pharmacology, Enzyme Stability/drug effects, Kinetics, Metals/pharmacology, Models, Molecular, Molecular Dynamics Simulation, Mutation/genetics, Phylogeny, Protein Multimerization, Substrate Specificity/drug effects, TemperaturePathogenicity

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
25217D. D. P. Li, M.,Wang, N.,Wang, X. J.,Zhang, X. Y.,Chen, X. L.,Su, H. N.,Zhang, Y. Z.,Shi, M.Arcticibacterium luteifluviistationis gen. nov., sp. nov., isolated from Arctic seawater10.1099/ijsem.0.001690IJSEM 67: 664-669 201727902275
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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