Strain identifier

BacDive ID: 5613

Type strain: Yes

Species: Maribacter arcticus

Strain history: CIP <- 2014, KCTC

NCBI tax ID(s): 561365 (species)

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General

@ref: 17277

BacDive-ID: 5613

DSM-Number: 23546

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

description: Maribacter arcticus DSM 23546 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 561365
  • Matching level: species

strain history

@refhistory
415932014, KCTC
17277<- KCTC <- S. G. Hong, Korea Polar Research Institute, Incheon
67770S. G. Hong KOPRI 20941.
67771<- SK Hong, KOPRI
116478CIP <- 2014, KCTC

doi: 10.13145/bacdive5613.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Maribacter
  • species: Maribacter arcticus
  • full scientific name: Maribacter arcticus Cho et al. 2008

@ref: 17277

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Maribacter

species: Maribacter arcticus

full scientific name: Maribacter arcticus Cho et al. 2008 emend. Weerawongwiwat et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32476negative2.15 µm0.4 µmrod-shapedno
67771rod-shapedno
67771negative
116478negativerod-shapedyes
125438no95.5
125438negative97.5
125439negative99

pigmentation

  • @ref: 32476
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17277BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
41593Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116478CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
17277positivegrowth20
32476positivegrowth04-30
32476positiveoptimum21
41593positivegrowth20
67770positivegrowth20
67771positivegrowth20-22

culture pH

@refabilitytypepHPH range
32476positivegrowth05-10alkaliphile
32476positiveoptimum6

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32476aerobe
67771aerobe
125439obligate aerobe95.6

spore formation

@refspore formationconfidence
125438no91.973
125439no96.4

halophily

  • @ref: 32476
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 2.35 %

observation

@refobservation
67770quinones: MK-6
67771quinones: MK-6

enzymes

@refvalueactivityec
32476acid phosphatase+3.1.3.2
32476alkaline phosphatase+3.1.3.1
32476catalase+1.11.1.6
32476cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17277marine sedimentSpitsbergen, Ny-ÅlesundNorwayNOREurope
67770Marine sediment sample collected at Ny-ÅlesundSpitsbergen IslandsNorwayNOREurope
67771From marine sediment from Ny-A° lesundSpitsbergenNorwayNOREurope
116478Environment, Sample of marine sedimentNy-Alesund, Spitsbergen Islands, NorwayNorwayNOREurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_7442.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_141;96_1222;97_1721;98_5453;99_7442&stattab=map
  • Last taxonomy: Maribacter arcticus subclade
  • 16S sequence: AY771762
  • Sequence Identity:
  • Total samples: 520
  • soil counts: 21
  • aquatic counts: 487
  • animal counts: 11
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
172771Risk group (German classification)
1164781Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17277
  • description: Maribacter arcticus strain KOPRI 20941 16S ribosomal RNA gene, partial sequence
  • accession: AY771762
  • length: 1490
  • database: nuccore
  • NCBI tax ID: 561365

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Maribacter arcticus DSM 23546GCA_900167935scaffoldncbi561365
66792Maribacter arcticus strain DSM 23546561365.3wgspatric561365
66792Maribacter arcticus DSM 235462595698209draftimg561365

GC content

@refGC-contentmethod
1727736thermal denaturation, midpoint method (Tm)
3247636
6777136.0

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.278no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.872no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.973no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.322yes
125438motile2+flagellatedAbility to perform flagellated movementno95.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno96.4
125439BacteriaNetmotilityAbility to perform movementno69.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative99
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.6

External links

@ref: 17277

culture collection no.: DSM 23546, JCM 14790, KCTC 22053, KOPRI 20941, CIP 110780

straininfo link

@refstraininfo
75095406972
75096413392

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18523168Maribacter arcticus sp. nov., isolated from Arctic marine sediment.Cho KH, Hong SG, Cho HH, Lee YK, Chun J, Lee HKInt J Syst Evol Microbiol10.1099/ijs.0.65549-02008Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Norway, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny19502334Maribacter antarcticus sp. nov., a psychrophilic bacterium isolated from a culture of the Antarctic green alga Pyramimonas gelidicola.Zhang GI, Hwang CY, Kang SH, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.006056-02009Antarctic Regions, Bacterial Typing Techniques, Base Composition, Chlorophyta/growth & development/*microbiology, Culture Media, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacteriaceae/classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityCultivation
Phylogeny23243094Maribacter chungangensis sp. nov., isolated from a green seaweed, and emended descriptions of the genus Maribacter and Maribacter arcticus.Weerawongwiwat V, Kang H, Jung MY, Kim WInt J Syst Evol Microbiol10.1099/ijs.0.039628-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seaweed/*microbiology, Sequence Analysis, DNA, Undaria/*microbiologyGenetics
Phylogeny25090958Maribacter caenipelagi sp. nov., a member of the Flavobacteriaceae isolated from a tidal flat sediment of the Yellow Sea in Korea.Jung YT, Lee JS, Yoon JHAntonie Van Leeuwenhoek10.1007/s10482-014-0243-z2014Bacterial 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, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics
Phylogeny28879842Maribacter pelagius sp. nov., isolated from seawater.Jin M, Kim M, Kim JY, Song HS, Cha IT, Roh SW, Lee SJInt J Syst Evol Microbiol10.1099/ijsem.0.0022032017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17277Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23546)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23546
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
32476Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2869628776041
41593Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30592
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75095Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406972.1StrainInfo: A central database for resolving microbial strain identifiers
75096Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID413392.1StrainInfo: A central database for resolving microbial strain identifiers
116478Curators of the CIPCollection of Institut Pasteur (CIP 110780)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110780
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