Strain identifier

BacDive ID: 5131

Type strain: Yes

Species: Samsonia erythrinae

Strain Designation: M601

Strain history: CIP <- 2001, CFBP

NCBI tax ID(s): 160434 (species)

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General

@ref: 6486

BacDive-ID: 5131

DSM-Number: 16730

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, plant pathogen

description: Samsonia erythrinae M601 is a facultative anaerobe, mesophilic, motile plant pathogen that was isolated from necrotic lesions of Erythrina sp. bark.

NCBI tax id

  • NCBI tax id: 160434
  • Matching level: species

strain history

@refhistory
6486<- CFBP <- L. Gardan; M601
337662001, CFBP
119130CIP <- 2001, CFBP

doi: 10.13145/bacdive5131.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Yersiniaceae
  • genus: Samsonia
  • species: Samsonia erythrinae
  • full scientific name: Samsonia erythrinae Sutra et al. 2001

@ref: 6486

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Samsonia

species: Samsonia erythrinae

full scientific name: Samsonia erythrinae Sutra et al. 2001

strain designation: M601

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes99.12
6948099.979negative
119130yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6486REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33766MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119130CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6486positivegrowth28mesophilic
33766positivegrowth30mesophilic
119130positivegrowth30-41
119130nogrowth5psychrophilic
119130nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119130
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.943

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
119130mannitol+fermentation29864
119130citrate-carbon source16947
119130glucose+fermentation17234
119130lactose-fermentation17716
119130nitrate+reduction17632
119130nitrite-reduction16301
119130malonate-assimilation15792
119130sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 119130
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119130
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11913015688acetoin+
11913017234glucose-

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
119130oxidase-
119130beta-galactosidase-3.2.1.23
119130alcohol dehydrogenase-1.1.1.1
119130gelatinase-
119130catalase+1.11.1.6
119130lysine decarboxylase-4.1.1.18
119130ornithine decarboxylase-4.1.1.17
119130phenylalanine ammonia-lyase-4.3.1.24
119130tryptophan deaminase-
119130urease-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
119130-+---------+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119130+/---++----+/-+++-+-++---+-++++/----++-----------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119130++-++--+-------+-++++--+-------+++---------++----+-----+---++-+--+----+----+---++-----+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
6486necrotic lesions of Erythrina sp. barkErythrinaMartiniqueFRAMiddle and South America
119130Erythrina sp.FranceFRAEuropeMartinique1995

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Plants#Tree
#Host Body-Site#Other#Wound
#Host Body-Site#Plant#Bark

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
6486yes1Risk group (German classification)
1191301Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6486
  • description: Samsonia erythrinae 16S ribosomal RNA gene, complete sequence
  • accession: AF273037
  • length: 1503
  • database: ena
  • NCBI tax ID: 160434

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Samsonia erythrinae DSM 16730GCA_004342665scaffoldncbi160434
66792Samsonia erythrinae strain DSM 16730160434.3wgspatric160434
66792Samsonia erythrinae DSM 167302791354868draftimg160434

GC content

  • @ref: 6486
  • GC-content: 57
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.929no
flagellatedyes55.737no
gram-positiveno98.083no
anaerobicno97.874no
aerobicyes61.018no
halophileno81.222no
spore-formingno93.768no
glucose-utilyes92.798no
thermophileno97.335yes
glucose-fermentyes93.106no

External links

@ref: 6486

culture collection no.: DSM 16730, CFBP 5236, ICMP 13937, CIP 107322

straininfo link

  • @ref: 74623
  • straininfo: 100946

literature

  • topic: Phylogeny
  • Pubmed-ID: 11491325
  • title: Samsonia erythrinae gen. nov., sp. nov., isolated from bark necrotic lesions of Erythrina sp., and discrimination of plant-pathogenic Enterobacteriaceae by phenotypic features.
  • authors: Sutra L, Christen R, Bollet C, Simoneau P, Gardan L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-4-1291
  • year: 2001
  • mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Enterobacteriaceae/*classification/genetics/*isolation & purification/metabolism/pathogenicity, Erythrina/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Diseases/*microbiology, *Plants, Medicinal, Species Specificity, Terminology as Topic
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
6486Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16730)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16730
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
33766Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4745
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
74623Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100946.1StrainInfo: A central database for resolving microbial strain identifiers
119130Curators of the CIPCollection of Institut Pasteur (CIP 107322)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107322