Strain identifier

BacDive ID: 140651

Type strain: Yes

Species: Arcticibacter svalbardensis

Strain Designation: MN12-7

Strain history: CIP <- 2012, S. Shivaji, CCMB, Hyderabad, India, strain MN12-7

NCBI tax ID(s): 1288027 (species)

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General

@ref: 27122

BacDive-ID: 140651

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

description: Arcticibacter svalbardensis MN12-7 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from surface soil from Ny-Alesund, Svaldbard.

NCBI tax id

  • NCBI tax id: 1288027
  • Matching level: species

strain history

  • @ref: 123394
  • history: CIP <- 2012, S. Shivaji, CCMB, Hyderabad, India, strain MN12-7

doi: 10.13145/bacdive140651.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Arcticibacter
  • species: Arcticibacter svalbardensis
  • full scientific name: Arcticibacter svalbardensis Prasad et al. 2013

@ref: 27122

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Arcticibacter

species: Arcticibacter svalbardensis

strain designation: MN12-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
27122negative3.9 µm1.75 µmrod-shapedno
123394negativerod-shapedno

colony morphology

  • @ref: 27122
  • colony size: 1 mm
  • colony color: light salmon pink
  • colony shape: circular
  • medium used: nutrient agar (Difco)

pigmentation

  • @ref: 27122
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37320MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
27122nutrient agar (Difco)yes
123394CIP Medium 735yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=735
123394CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
123394CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
37320positivegrowth25mesophilic
27122positiveoptimum18psychrophilic
27122positivegrowth4-25

culture pH

@refabilitytypepH
27122positivegrowth7-8
27122positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 27122
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
27122NaClpositivegrowth0-2 M
27122NaClpositiveoptimum0.5-1 M

observation

  • @ref: 27122
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2712215963ribitol-builds acid from
2712215963ribitol-assimilation
2712222599arabinose-assimilation
27122casein-hydrolysis
2712217057cellobiose+assimilation
2712262968cellulose+hydrolysis
2712217029chitin-hydrolysis
2712216947citrate-builds acid from
2712216737creatinine-builds acid from
2712215824D-fructose-builds acid from
2712216899D-mannitol-builds acid from
2712216024D-mannose-builds acid from
2712265327D-xylose-builds acid from
2712216991dna-hydrolysis
2712216813galactitol-assimilation
2712217113erythritol-builds acid from
271224853esculin+hydrolysis
2712228757fructose-assimilation
2712228260galactose+assimilation
271225291gelatin-hydrolysis
271225417glucosamine-assimilation
2712217234glucose+fermentation
2712217234glucose+assimilation
2712217754glycerol-assimilation
2712228087glycogen-builds acid from
2712228304heparin-hydrolysis
2712217268myo-inositol-builds acid from
2712217268myo-inositol-assimilation
2712215443inulin-assimilation
2712230849L-arabinose-builds acid from
2712217716lactose-assimilation
2712217306maltose+assimilation
2712229864mannitol-assimilation
2712237684mannose+assimilation
271226731melezitose-assimilation
2712228053melibiose+assimilation
27122320061methyl alpha-D-glucopyranoside-builds acid from
27122320061methyl alpha-D-glucopyranoside-assimilation
2712243943methyl alpha-D-mannoside-builds acid from
2712243943methyl alpha-D-mannoside-assimilation
2712217632nitrate-reduction
27122O-nitrophenyl-beta-D-galactopyranosid-assimilation
2712218257ornithine-builds acid from
2712217309pectin-hydrolysis
2712215361pyruvate-builds acid from
2712216634raffinose-builds acid from
2712216634raffinose-assimilation
2712226546rhamnose-builds acid from
2712233942ribose-assimilation
2712217814salicin-assimilation
2712284997sodium gluconate-builds acid from
2712284997sodium gluconate-assimilation
2712230911sorbitol-assimilation
2712227922sorbose-builds acid from
2712227922sorbose-assimilation
2712228017starch-hydrolysis
2712228017starch-builds acid from
2712217992sucrose-assimilation
2712227082trehalose+assimilation
2712253426tween 80-hydrolysis
2712217151xylitol-assimilation
2712218222xylose-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
2712271415nitrofurantoinyesyes300 µg (disc)
271223493cefoperazoneyesyes75 µg (disc)
27122204928cefotaximeyesyes30 µg (disc)
271223515cefuroximeyesyes30 µg (disc)
2712217698chloramphenicolyesyes30 µg (disc)
27122116278lomefloxacinyesyes30 µg (disc)
2712248844roxithromycinyesyes30 µg (disc)
2712227902tetracyclineyesyes30 µg (disc)
2712228001vancomycinyesyes30 µg (disc)
2712248923erythromycinyesyes15 µg (disc)
2712228971ampicillinyesyes10 µg (disc)
2712237943colistinyesyes10 µg (disc)
2712218208penicillin gyesyes10 µg (disc)
27122100241ciprofloxacinyesyes5 µg (disc)
271226472lincomycinyesyes2 µg (disc)
271222637amikacinyesyes30 µg (disc)
27122474053cefazolinyesyes30 µg (disc)
271226104kanamycinyesyes30 µg (disc)
27122100147nalidixic acidyesyes30 µg (disc)
2712217076streptomycinyesyes10 µg (disc)
2712228864tobramycinyesyes10 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
2712215688acetoinno
2712216136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
2712217234glucose+
2712215688acetoin-

enzymes

@refvalueactivityec
27122catalase+1.11.1.6
27122cytochrome oxidase+1.9.3.1
27122ornithine decarboxylase-4.1.1.17
27122urease-3.5.1.5
27122beta-galactosidase-3.2.1.23
27122lysine decarboxylase-4.1.1.18
27122arginine dihydrolase-3.5.3.6
27122tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
27122surface soil from Ny-Alesund, SvaldbardSvalbardNorwayNOREurope
123394Environment, Soil surface associated with dried vegetationNy Alesund, SpitzbergNorwayNOREurope2010

isolation source categories

Cat1Cat2Cat3
#Climate#Cold#Subarctic
#Environmental#Terrestrial#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_6586.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1702;97_2038;98_2505;99_6586&stattab=map
  • Last taxonomy: Arcticibacter svalbardensis
  • 16S sequence: JQ396621
  • Sequence Identity:
  • Total samples: 36
  • soil counts: 12
  • aquatic counts: 9
  • animal counts: 13
  • plant counts: 2

Safety information

risk assessment

  • @ref: 123394
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 27122
  • description: Arcticibacter svalbardensis MN12-7 16S ribosomal RNA gene, partial sequence
  • accession: JQ396621
  • length: 1499
  • database: nuccore
  • NCBI tax ID: 1150600

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arcticibacter svalbardensis MN12-7GCA_000403135contigncbi1150600
66792Arcticibacter svalbardensis MN12-71150600.3wgspatric1150600
66792Arcticibacter svalbardensis MN12-72541047992draftimg1150600

GC content

  • @ref: 27122
  • GC-content: 38
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.796yes
gram-positiveno96.339no
anaerobicno97.069yes
aerobicyes74.778yes
halophileno93.917no
spore-formingno95.154no
flagellatedno97.549yes
glucose-utilyes90.098yes
thermophileno99.401yes
glucose-fermentno83.216no

External links

@ref: 27122

culture collection no.: KCTC 32015, CIP 110422

straininfo link

  • @ref: 96767
  • straininfo: 388294

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22904219Arcticibacter svalbardensis gen. nov., sp. nov., of the family Sphingobacteriaceae in the phylum Bacteroidetes, isolated from Arctic soil.Prasad S, Manasa BP, Buddhi S, Pratibha MS, Begum Z, Bandi S, Tirunagari P, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.044420-02012Arctic Regions, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Svalbard, Vitamin K 2/analogs & derivatives/analysisGenetics
Genetics23846277Draft Genome Sequence of Arcticibacter svalbardensis Strain MN12-7T, a Member of the Family Sphingobacteriaceae Isolated from an Arctic Soil Sample.Shivaji S, Ara S, Prasad S, Manasa BP, Begum Z, Singh A, Kumar Pinnaka AGenome Announc10.1128/genomeA.00484-132013Phylogeny

Reference

@idauthorstitledoi/urlpubmedcatalogue
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
2712210.1099/ijs.0.044420-022904219
37320Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8279
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
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/
96767Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID388294.1
123394Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110422Collection of Institut Pasteur (CIP 110422)