Strain identifier

BacDive ID: 3791

Type strain: Yes

Species: Bernardetia litoralis

Strain Designation: Fx l1, Sio-4

Strain history: CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- NCIMB <- R.A Lewin: strain SIO-4

NCBI tax ID(s): 880071 (strain), 999 (species)

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General

@ref: 2822

BacDive-ID: 3791

DSM-Number: 6794

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

description: Bernardetia litoralis Fx l1 is a Gram-negative bacterium that was isolated from sea-water aquarium.

NCBI tax id

NCBI tax idMatching level
999species
880071strain

strain history

@refhistory
2822<- H. Reichenbach, Fx l1 <- ATCC <- R.A. Lewin, SIO-4
120628CIP <- 2000, J.F. Bernardet, INRA, Jouy-en-Josas, France <- NCIMB <- R.A Lewin: strain SIO-4

doi: 10.13145/bacdive3791.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Bernardetiaceae
  • genus: Bernardetia
  • species: Bernardetia litoralis
  • full scientific name: Bernardetia litoralis (Lewin 1969) Hahnke et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Flexibacter litoralis

@ref: 2822

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Bernardetiaceae

genus: Bernardetia

species: Bernardetia litoralis

full scientific name: Bernardetia litoralis (Lewin 1969) Hahnke et al. 2017

strain designation: Fx l1, Sio-4

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120628negativerod-shapedno
69480negative96.5

pigmentation

  • @ref: 120628
  • production: no
  • name: Flexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_6794_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2822CYTOPHAGA (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
42263Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
2822BACTO 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
120628CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
2822positivegrowth30
42263positivegrowth25
120628positivegrowth15-25
120628nogrowth5
120628nogrowth30
120628nogrowth37
120628nogrowth41
120628nogrowth45

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 99

halophily

@refsaltgrowthtested relationconcentration
120628NaClnogrowth0 %
120628NaClnogrowth2 %
120628NaClnogrowth4 %
120628NaClnogrowth6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1206284853esculin-hydrolysis
120628606565hippurate-hydrolysis
12062817632nitrate-reduction
12062816301nitrite-reduction
12062815792malonate-assimilation

metabolite production

  • @ref: 120628
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12062815688acetoin-
12062817234glucose-

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
120628oxidase+
120628beta-galactosidase-3.2.1.23
120628alcohol dehydrogenase-1.1.1.1
120628gelatinase+
120628amylase-
120628caseinase+3.4.21.50
120628catalase+1.11.1.6
120628tween esterase+
120628gamma-glutamyltransferase-2.3.2.2
120628lecithinase+
120628lipase+
120628lysine decarboxylase-4.1.1.18
120628ornithine decarboxylase-4.1.1.17
120628phenylalanine ammonia-lyase-4.3.1.24
120628protease+
120628tryptophan deaminase-
120628urease-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
120628-+++-+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2822sea-water aquariumCalifornia, La JollaUSAUSANorth America
120628Marine aquarium outflowLa Jolla, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Water reservoir (Aquarium/pool)
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1138.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17088;96_666;97_770;98_892;99_1138&stattab=map
  • Last taxonomy: Bernardetia litoralis subclade
  • 16S sequence: NR_102950
  • Sequence Identity:
  • Total samples: 8447
  • soil counts: 409
  • aquatic counts: 5955
  • animal counts: 1962
  • plant counts: 121

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
28221Risk group (German classification)
1206281Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Flexibacter litoralis gene for 16S rRNA, strain:IFO 15988AB0780561483nuccore880071
20218Flexibacter litoralis gene for 16S rRNA, partial sequence, strain: NBRC 15988AB6810191453nuccore999
20218Flexibacter litoralis 16S ribosomal RNAM587841501nuccore999
2822Bernardetia litoralis DSM 6794 16S ribosomal RNA, partial sequenceNR_1029501516nuccore880071

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bernardetia litoralis DSM 6794GCA_000265505completencbi880071
66792Flexibacter litoralis DSM 6794880071.3completepatric880071
66792Bernardetia litoralis DSM 67942509276059completeimg880071

GC content

  • @ref: 2822
  • GC-content: 30.3

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno99no
69480gram-positivegram-positivePositive reaction to Gram-stainingno96.5no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.281no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes82.589no
69480spore-formingspore-formingAbility to form endo- or exosporesno89.977no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno87.255no
69480flagellatedmotile2+Ability to perform flagellated movementno88no

External links

@ref: 2822

culture collection no.: DSM 6794, ATCC 23117, IFO 15988, NBRC 15988, CIP 106402, NCIMB 1366

straininfo link

  • @ref: 73303
  • straininfo: 92086

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2822Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6794)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6794
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
42263Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18528
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
73303Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92086.1StrainInfo: A central database for resolving microbial strain identifiers
120628Curators of the CIPCollection of Institut Pasteur (CIP 106402)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106402