Strain identifier

BacDive ID: 134220

Type strain: Yes

Species: Marixanthomonas ophiurae

Strain history: CIP <- 2007, JCM <- 2006, M. Uchino, Tokyo Agricult. Univ., Tokyo, Japan <- L.A. Romanenko, Vladivostok, Russia

NCBI tax ID(s): 387659 (species)

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General

@ref: 31925

BacDive-ID: 134220

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

description: Marixanthomonas ophiurae NRIC 0684 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Ophiuroid specimen collected from the Fiji Sea at a depth of 480 m.

NCBI tax id

  • NCBI tax id: 387659
  • Matching level: species

strain history

@refhistory
67770M. Uchino <-- L. A. Romanenko KMM 3046.
121426CIP <- 2007, JCM <- 2006, M. Uchino, Tokyo Agricult. Univ., Tokyo, Japan <- L.A. Romanenko, Vladivostok, Russia

doi: 10.13145/bacdive134220.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Marixanthomonas
  • species: Marixanthomonas ophiurae
  • full scientific name: Marixanthomonas ophiurae Romanenko et al. 2007

@ref: 31925

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Marixanthomonas

species: Marixanthomonas ophiurae

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31925negative2.5 µm0.45 µmrod-shapedno
69480negative99.987
121426negativerod-shapedno

pigmentation

  • @ref: 31925
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37764Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121426CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31925positivegrowth05-32
31925positiveoptimum26.5mesophilic
37764positivegrowth30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31925positivegrowth6.5-8.5alkaliphile
31925positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31925
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31925no
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
31925NaClpositivegrowth1.0-12 %
31925NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3192553424tween 20+carbon source
3192553423tween 40+carbon source
3192553426tween 80+carbon source
12142617632nitrate-reduction
12142616301nitrite-reduction

metabolite production

  • @ref: 121426
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31925catalase+1.11.1.6
31925gelatinase+
31925cytochrome oxidase+1.9.3.1
121426oxidase+
121426catalase+1.11.1.6
121426urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121426-+++-++--+-+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Ophiuroid specimen collected from the Fiji Sea at a depth of 480 m
121426Environment, Deep sea, brittle starFiji SeaFijiFJIAustralia and Oceania

taxonmaps

  • @ref: 69479
  • File name: preview.99_114274.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_38527;97_49040;98_64403;99_114274&stattab=map
  • Last taxonomy: Marixanthomonas ophiurae subclade
  • 16S sequence: AB261012
  • Sequence Identity:
  • Total samples: 1525
  • soil counts: 64
  • aquatic counts: 1240
  • animal counts: 217
  • plant counts: 4

Safety information

risk assessment

  • @ref: 121426
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31925
  • description: Marixanthomonas ophiurae gene for 16S rRNA, partial sequence, strain: KMM 3046
  • accession: AB261012
  • length: 1397
  • database: nuccore
  • NCBI tax ID: 387659

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marixanthomonas ophiurae strain KMM 3046387659.5wgspatric387659
66792Marixanthomonas ophiurae KMM 30462887695450draftimg387659
67770Marixanthomonas ophiurae KMM 3046GCA_003413745contigncbi387659

GC content

@refGC-contentmethod
3192537.3
6777037.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.709yes
anaerobicno99.125yes
halophileyes74.072no
spore-formingno95.958yes
glucose-utilyes78.832no
aerobicyes92.86yes
motileno87.159yes
thermophileno99.564no
flagellatedno95.235yes
glucose-fermentno91.857no

External links

@ref: 31925

culture collection no.: NRIC 0684, JCM 14121, KMM 3046, CIP 109555

straininfo link

  • @ref: 91814
  • straininfo: 297232

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329768Marixanthomonas ophiurae gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star.Romanenko LA, Uchino M, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.64662-02007Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Echinodermata/*microbiology, Fiji, Flavobacteriaceae/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, TemperatureMetabolism
Phylogeny34428132Marixanthomonas spongiae sp. nov., isolated from marine sponge.Zhuang L, Pang H, Xu L, Chen DInt J Syst Evol Microbiol10.1099/ijsem.0.0049682021Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Flavobacteriaceae/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, *Porifera/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34964941Constantimarinum furrinae gen. nov., sp. nov., a marine bacterium isolated from saline volcanic rock aquifer (lava seawater) at Jeju Island, Republic of Korea.Yang SH, Oh HM, Park MJ, Jang D, Kwon KKJ Microbiol10.1007/s12275-022-1468-62021Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Flavobacteriaceae/classification/genetics/*isolation & purification/metabolism, Groundwater/*microbiology, Phylogeny, Republic of Korea, Seawater/*microbiologyMetabolism

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
31925Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172818228776041
37764Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7311
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
91814Reimer, 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-ID297232.1
121426Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109555Collection of Institut Pasteur (CIP 109555)