Strain identifier

BacDive ID: 5470

Type strain: Yes

Species: Reichenbachiella agariperforans

Strain Designation: R3525

Strain history: CIP <- 2003, JCM <- 2001, M. Suzuki: strain R3525 <- KMM 3525 <- O.I. Nedashkovskaya

NCBI tax ID(s): 156994 (species)

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General

@ref: 18167

BacDive-ID: 5470

DSM-Number: 26134

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

description: Reichenbachiella agariperforans R3525 is a mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 156994
  • Matching level: species

strain history

@refhistory
18167<- JCM <- O. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia
67770M. Suzuki R3525 <-- O. I. Nedashkovskaya.
116152CIP <- 2003, JCM <- 2001, M. Suzuki: strain R3525 <- KMM 3525 <- O.I. Nedashkovskaya

doi: 10.13145/bacdive5470.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Reichenbachiellaceae
  • genus: Reichenbachiella
  • species: Reichenbachiella agariperforans
  • full scientific name: Reichenbachiella agariperforans (Nedashkovskaya et al. 2003) Nedashkovskaya et al. 2005

  • synonyms

    • @ref: 20215
    • synonym: Reichenbachia agariperforans

@ref: 18167

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Reichenbachiellaceae

genus: Reichenbachiella

species: Reichenbachiella agariperforans

full scientific name: Reichenbachiella agariperforans (Nedashkovskaya et al. 2003) Nedashkovskaya et al. 2005 emend. Cha et al. 2011

strain designation: R3525

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.986
116152negativerod-shapedno

pigmentation

  • @ref: 116152
  • production: no
  • name: Flexirubin

multimedia

  • @ref: 18167
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_26134.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18167BACTO 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
40726Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116152CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
18167positivegrowth28mesophilic
40726positivegrowth25mesophilic
67770positivegrowth25mesophilic
116152positivegrowth15-30
116152nogrowth5psychrophilic
116152nogrowth37mesophilic
116152nogrowth41thermophilic
116152nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.947

halophily

@refsaltgrowthtested relationconcentration
116152NaClnogrowth0 %
116152NaClnogrowth2 %
116152NaClnogrowth4 %
116152NaClnogrowth6 %
116152NaClnogrowth8 %
116152NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1161524853esculin-hydrolysis
116152606565hippurate-hydrolysis
11615217632nitrate-reduction
11615216301nitrite-reduction
11615215792malonate-assimilation

metabolite production

  • @ref: 116152
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11615215688acetoin-
11615217234glucose-

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
116152oxidase+
116152beta-galactosidase+3.2.1.23
116152alcohol dehydrogenase-1.1.1.1
116152gelatinase+/-
116152amylase+
116152caseinase+3.4.21.50
116152catalase+1.11.1.6
116152tween esterase+
116152gamma-glutamyltransferase-2.3.2.2
116152lecithinase-
116152lipase-
116152lysine decarboxylase-4.1.1.18
116152ornithine decarboxylase-4.1.1.17
116152phenylalanine ammonia-lyase-4.3.1.24
116152protease+
116152tryptophan deaminase-
116152urease-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
116152-++--+++--+--+-+-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116152++-------+------++-----------------------------------------+-------------------+---------++++------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryisolation date
18167seawaterAmursky Bay
67770Seawater collected in the Amursky Bay of the Gulf of Peter the GreatSea of Japan
116152Environment, Sea water sampleSea of Japan2000

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_5242.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_508;96_2546;97_3111;98_3908;99_5242&stattab=map
  • Last taxonomy: Reichenbachiella agariperforans subclade
  • 16S sequence: AB681089
  • Sequence Identity:
  • Total samples: 2542
  • soil counts: 92
  • aquatic counts: 2285
  • animal counts: 149
  • plant counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
181671Risk group (German classification)
1161521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Reichenbachiella agariperforans gene for 16S rRNA, partial sequence, strain: NBRC 16625AB6810891447ena156994
18167Reichenbachia agariperforans gene for 16S rRNA, partial sequenceAB0589191399ena156994

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Reichenbachiella agariperforans strain DSM 26134156994.4wgspatric156994
66792Reichenbachiella agariperforans DSM 261342616644810draftimg156994
67770Reichenbachiella agariperforans DSM 26134GCA_900142205scaffoldncbi156994

GC content

  • @ref: 67770
  • GC-content: 44.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno84.832no
gram-positiveno96.493no
anaerobicno99.368no
aerobicyes91.934no
halophileno69.129no
spore-formingno93.519no
thermophileno99.245yes
glucose-utilyes87.238no
flagellatedno94.38no
glucose-fermentno87.037no

External links

@ref: 18167

culture collection no.: DSM 26134, CIP 107900, JCM 11238, KMM 3525, NBRC 16625, IFO 16625

straininfo link

  • @ref: 74958
  • straininfo: 88307

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656156Reichenbachia agariperforans gen. nov., sp. nov., a novel marine bacterium in the phylum Cytophaga-Flavobacterium-Bacteroides.Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.02128-02003Bacteroides/*classification/genetics/isolation & purification/metabolism, Cytophaga/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/isolation & purification/metabolism, Japan, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiologyEnzymology
Phylogeny20851915Reichenbachiella faecimaris sp. nov., isolated from a tidal flat, and emended descriptions of the genus Reichenbachiella and Reichenbachiella agariperforans.Cha IT, Oh YS, Park SJ, Park BJ, Lee JK, Lim CS, Park AR, Yoo JS, Lee DH, Rhee SK, Roh DHInt J Syst Evol Microbiol10.1099/ijs.0.026849-02010Cytophagaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiologyMetabolism
Phylogeny30231957Reichenbachiella versicolor sp. nov., isolated from red alga.Shi MJ, Wang C, Liu ZY, Jiang LX, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0030232018Bacterial Typing Techniques, Base Composition, China, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodophyta/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18167Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26134)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26134
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
40726Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5463
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/
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
74958Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88307.1StrainInfo: A central database for resolving microbial strain identifiers
116152Curators of the CIPCollection of Institut Pasteur (CIP 107900)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107900