Strain identifier

BacDive ID: 5473

Type strain: Yes

Species: Marivirga tractuosa

Strain Designation: H-43

Strain history: CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- NCIMB <- R.A. Lewin: strain H-43 <- N. Thach

NCBI tax ID(s): 643867 (strain), 1006 (species)

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General

@ref: 1594

BacDive-ID: 5473

DSM-Number: 4126

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Marivirga tractuosa H-43 is a mesophilic, Gram-negative bacterium that was isolated from beach sand.

NCBI tax id

NCBI tax idMatching level
643867strain
1006species

strain history

@refhistory
1594<- NCMB <- R.A. Lewin, H-43 (Microscilla tractuosa)
123573CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- NCIMB <- R.A. Lewin: strain H-43 <- N. Thach

doi: 10.13145/bacdive5473.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Marivirgaceae
  • genus: Marivirga
  • species: Marivirga tractuosa
  • full scientific name: Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010

  • synonyms

    @refsynonym
    20215Flexibacter tractuosus
    20215Microscilla tractuosa

@ref: 1594

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Marivirgaceae

genus: Marivirga

species: Marivirga tractuosa

full scientific name: Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010

strain designation: H-43

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.859
123573negativerod-shapedno

pigmentation

  • @ref: 123573
  • production: no
  • name: Flexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_4126_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1594CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172)yeshttps://mediadive.dsmz.de/medium/172Name: CYTOPHAGA (marine) MEDIUM (DSMZ Medium 172) Composition: NaCl 24.7 g/l Agar 15.0 g/l MgSO4 x 7 H2O 6.3 g/l MgCl2 x 6 H2O 4.6 g/l CaCl2 x 2 H2O 1.2 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KCl 0.7 g/l NaHCO3 0.2 g/l Distilled water
40308Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
123573CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
1594positivegrowth25mesophilic
40308positivegrowth25mesophilic
123573positivegrowth15-37
123573nogrowth5psychrophilic
123573nogrowth41thermophilic
123573nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1235734853esculin+hydrolysis
123573606565hippurate-hydrolysis
12357317632nitrate-reduction
12357316301nitrite-reduction
12357315792malonate-assimilation

metabolite production

  • @ref: 123573
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12357315688acetoin-
12357317234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123573oxidase-
123573beta-galactosidase-3.2.1.23
123573alcohol dehydrogenase-1.1.1.1
123573gelatinase+
123573amylase-
123573caseinase+3.4.21.50
123573catalase-1.11.1.6
123573tween esterase+
123573gamma-glutamyltransferase+2.3.2.2
123573lecithinase+
123573lipase+
123573lysine decarboxylase-4.1.1.18
123573ornithine decarboxylase-4.1.1.17
123573phenylalanine ammonia-lyase+4.3.1.24
123573protease+
123573tryptophan deaminase-
123573urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123573-+++-+++-+++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1594beach sandNhatrang, South China SeaVietnamVNMAsia
123573Environment, Beach sandNhatrangVietnamVNMAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_5068.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_500;96_2470;97_3014;98_3782;99_5068&stattab=map
  • Last taxonomy: Marivirga tractuosa
  • 16S sequence: AB078072
  • Sequence Identity:
  • Total samples: 153
  • soil counts: 19
  • aquatic counts: 106
  • animal counts: 25
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
15941Risk group (German classification)
1235731Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flexibacter tractuosus 16S ribosomal RNAM587891475ena1006
1594Flexibacter tractuosus gene for 16S rRNA, strain:IFO 15989AB0780721476ena643867

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Marivirga tractuosa DSM 4126GCA_000183425completencbi643867
66792Marivirga tractuosa DSM 4126643867.13plasmidpatric643867
66792Marivirga tractuosa DSM 4126643867.3completepatric643867
66792Marivirga tractuosa H-43, DSM 4126649633065completeimg643867

GC content

  • @ref: 1594
  • GC-content: 36.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno90.418no
flagellatedno95.474no
gram-positiveno98.265no
anaerobicno98.371no
aerobicyes90.627no
halophileyes51.64no
spore-formingno94.961no
thermophileno99.011no
glucose-utilyes80.669no
glucose-fermentno89.769no

External links

@ref: 1594

culture collection no.: DSM 4126, ATCC 23168, CIP 106410, IFO 15989, KCTC 2958, NBRC 15989, NCIMB 1408, VKM B-1430

straininfo link

  • @ref: 74961
  • straininfo: 10282

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19767357Reclassification of Flexibacter tractuosus (Lewin 1969) Leadbetter 1974 and 'Microscilla sericea' Lewin 1969 in the genus Marivirga gen. nov. as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov.Nedashkovskaya OI, Vancanneyt M, Kim SB, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.016121-02009Bacteroidetes/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flexibacter/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Genetics21677852Complete genome sequence of Marivirga tractuosa type strain (H-43).Pagani I, Chertkov O, Lapidus A, Lucas S, Del Rio TG, Tice H, Copeland A, Cheng JF, Nolan M, Saunders E, Pitluck S, Held B, Goodwin L, Liolios K, Ovchinikova G, Ivanova N, Mavromatis K, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Detter JC, Han C, Tapia R, Ngatchou-Djao OD, Rohde M, Goker M, Spring S, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NCStand Genomic Sci10.4056/sigs.16239412011
Phylogeny22904215Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil.Zhang L, Shen X, Liu Y, Li SInt J Syst Evol Microbiol10.1099/ijs.0.044651-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Polyenes/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny25500205Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea.Xu Y, Zhang R, Li Q, Liu K, Jiao NInt J Syst Evol Microbiol10.1099/ijs.0.066027-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phosphatidylcholines/chemistry, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28646633Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae.Muramatsu Y, Kamakura Y, Takahashi M, Nakagawa YInt J Syst Evol Microbiol10.1099/ijsem.0.0018902017Bacterial Typing Techniques, Bacteroidetes/*classification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flexibacter/*classification, Phosphatidylethanolamines/chemistry, *Phylogeny, Queensland, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1594Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4126)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4126
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40308Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18538
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74961Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10282.1StrainInfo: A central database for resolving microbial strain identifiers
123573Curators of the CIPCollection of Institut Pasteur (CIP 106410)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106410