Strain identifier

BacDive ID: 276

Type strain: Yes

Species: Aeromonas sobria

Strain history: CIP <- 1974, M.Y. Popoff, Inst. Pasteur, Paris, France: strain 208, Aeromonas fastidiosa

NCBI tax ID(s): 646 (species)

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General

@ref: 7949

BacDive-ID: 276

DSM-Number: 19176

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

description: Aeromonas sobria DSM 19176 is a facultative anaerobe, mesophilic, motile human pathogen that was isolated from fish.

NCBI tax id

  • NCBI tax id: 646
  • Matching level: species

strain history

@refhistory
7949<- CIP <- M. Y. Popoff; Institut Pasteur (Aeromonas fastidiosa); 208
334911974, M.Y. Popoff, Inst. Pasteur, Paris, France: strain 208, Aeromonas fastidiosa
67770M. Popoff 208.
122646CIP <- 1974, M.Y. Popoff, Inst. Pasteur, Paris, France: strain 208, Aeromonas fastidiosa

doi: 10.13145/bacdive276.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Aeromonadales
  • family: Aeromonadaceae
  • genus: Aeromonas
  • species: Aeromonas sobria
  • full scientific name: Aeromonas sobria Popoff and Véron 1981

@ref: 7949

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Aeromonadales

family: Aeromonadaceae

genus: Aeromonas

species: Aeromonas sobria

full scientific name: Aeromonas sobria Popoff and Véron 1981

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.353
6948099.992negative
122646yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7949NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33491MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122646CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122646CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7949positivegrowth28mesophilic
33491positivegrowth30mesophilic
67770positivegrowth30mesophilic
122646positivegrowth5-30
122646nogrowth37mesophilic
122646nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122646
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
122646NaClpositivegrowth0-2 %
122646NaClnogrowth4 %
122646NaClnogrowth6 %
122646NaClnogrowth8 %
122646NaClnogrowth10 %

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
68371cellobiose+builds acid from17057
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
68371D-galactose+builds acid from12936
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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368L-arabinose-fermentation30849
68368amygdalin+fermentation27613
68368melibiose-fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan+energy source27897
68368urea-hydrolysis16199
68368ornithine-degradation18257
68368lysine+degradation25094
68368arginine+hydrolysis29016
122646citrate+carbon source16947
122646esculin-hydrolysis4853
122646glucose+fermentation17234
122646lactose-fermentation17716
122646nitrate+reduction17632
122646nitrite+reduction16301
122646sodium thiosulfate-builds gas from132112
122646nitrate+respiration17632

antibiotic resistance

  • @ref: 122646
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleyes
6836816136hydrogen sulfideno
12264635581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836835581indole+
12264615688acetoin+
12264617234glucose-

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
68368cytochrome oxidase+1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
122646oxidase+
122646beta-galactosidase+3.2.1.23
122646alcohol dehydrogenase+1.1.1.1
122646gelatinase+
122646amylase+
122646DNase+
122646caseinase+3.4.21.50
122646catalase+1.11.1.6
122646tween esterase-
122646gamma-glutamyltransferase-2.3.2.2
122646lecithinase+
122646lipase+
122646lysine decarboxylase-4.1.1.18
122646ornithine decarboxylase-4.1.1.17
122646phenylalanine ammonia-lyase+4.3.1.24
122646tryptophan deaminase-
122646urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46162C12:06.512
    46162C13:00.313
    46162C14:04.314
    46162C15:01.215
    46162C16:014.116
    46162C17:00.417
    46162C18:00.318
    46162C12:0 3OH0.213.455
    46162C13:0 3OH/C15:1 i I/H0.314.469
    46162C13:0 iso1.312.612
    46162C13:0 ISO 2OH0.413.814
    46162C14:0 3OH/C16:1 ISO I7.715.485
    46162C15:0 ISO1.714.621
    46162C15:0 ISO 3OH216.135
    46162C16:0 anteiso0.215.717
    46162C16:0 iso0.415.626
    46162C16:0 N alcohol115.549
    46162C16:1 ω7c38.415.819
    46162C16:1 ω7c alcohol2.115.386
    46162C17:0 10-methyl0.917.41
    46162C17:0 iso1.516.629
    46162C17:1 ω6c0.316.862
    46162C17:1 ω8c1.216.792
    46162C17:1 ω9c ISO1.616.416
    46162C18:1 ω7c /12t/9t7.317.824
    46162C18:1 ω9c0.417.769
    46162C18:2 ω6,9c/C18:0 ANTE2.517.724
    46162C18:3 ω6,9,12c0.417.577
    46162Unidentified0.413.94
    46162Unidentified0.215.28
    46162Unidentified0.717.327
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122646-+++++-++-+--+-+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7949+++-----+-+++---+-+-+
7949+++-+---+++++---+-+-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122646+--+/-+----++++----+--++----++--++---++---------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122646+++++--+-++----+-+-+--+--------+-+-------+-------++--+----+++-----------------+++-+---+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7949fishFranceFRAEurope
46162Carp,Cyprinus carpio
67770Fish
122646Animal, Fish

isolation source categories

  • Cat1: #Host
  • Cat2: #Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_3322.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_11;96_15;97_15;98_18;99_3322&stattab=map
  • Last taxonomy: Aeromonas
  • 16S sequence: X60412
  • Sequence Identity:
  • Total samples: 39
  • aquatic counts: 24
  • animal counts: 12
  • plant counts: 3

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
7949yesyes2Risk group (German classification)
1226461Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Aeromonas sobria gene for 16S rRNA, partial sequence, strain: JCM 2139AB4729421414ena646
20218Aeromonas sobria strain ATCC 43979 clone 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceEF373994517ena646
20218Aeromonas sobria strain ATCC 43979 clone 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceEF373995513ena646
20218Aeromonas sobria 16S rRNA gene, strain NCIMB 12065X604121503ena646
7949A.sobria (ATCC 43979T) gene for 16S ribosomal RNAX746831460ena646

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aeromonas sobria CIP 74.33GCA_018359945contigncbi646
66792Aeromonas sobria CECT 4245646.4wgspatric646
66792Aeromonas sobria strain CIP 74.33646.37wgspatric646
66792Aeromonas sobria CECT 42452639763156draftimg646
67770Aeromonas sobria CECT 4245GCA_000820145scaffoldncbi646

GC content

  • @ref: 67770
  • GC-content: 58.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.89no
anaerobicno95.07no
halophileno88.149no
spore-formingno95.782no
glucose-utilyes90.31no
flagellatedyes89.567no
aerobicyes82.127no
thermophileno99.196yes
motileyes91.154no
glucose-fermentyes90.8no

External links

@ref: 7949

culture collection no.: DSM 19176, ATCC 43979, CCM 2807, CCUG 14830, CECT 4245, CIP 74.33, JCM 2139, LMG 3783, NCIMB 12065, NCTC 12979, CIP 74-33, BCRC 13066, CECT 837, HAMBI 1974, LMG 12159, VTT E-032002

straininfo link

  • @ref: 69958
  • straininfo: 389399

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902029Aeromonas sharmana sp. nov., isolated from a warm spring.Saha P, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.63972-02006Aeromonas/chemistry/*classification/isolation & purification/physiology, India, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, *Water MicrobiologyGenetics
29276504Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex.Gauthier J, Vincent AT, Charette SJ, Derome NFront Microbiol10.3389/fmicb.2017.024342017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7949Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19176)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19176
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
33491Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10726
46162Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 14830)https://www.ccug.se/strain?id=14830
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
69958Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389399.1StrainInfo: A central database for resolving microbial strain identifiers
122646Curators of the CIPCollection of Institut Pasteur (CIP 74.33)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2074.33