Strain identifier

BacDive ID: 14054

Type strain: Yes

Species: Shewanella putrefaciens

Strain Designation: 95

Strain history: CIP <- 1980, C. Richard, Inst. Pasteur, Paris, France: strain 12-80, Alteromonas putrefaciens <- ATCC <- B.W. Hammer: strain 95, Pseudomonas putrefaciens

NCBI tax ID(s): 1236543 (strain), 24 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2428

BacDive-ID: 14054

DSM-Number: 6067

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

description: Shewanella putrefaciens 95 is an aerobe, mesophilic, motile human pathogen that was isolated from Butter.

NCBI tax id

NCBI tax idMatching level
24species
1236543strain

strain history

@refhistory
2428<- ATCC <- B.W. Hammer, 95 (Pseudomonas putrefaciens)
67770IAM 1509 <-- ATCC 8071 <-- B. W. Hammer 95.
122075CIP <- 1980, C. Richard, Inst. Pasteur, Paris, France: strain 12-80, Alteromonas putrefaciens <- ATCC <- B.W. Hammer: strain 95, Pseudomonas putrefaciens

doi: 10.13145/bacdive14054.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Shewanellaceae
  • genus: Shewanella
  • species: Shewanella putrefaciens
  • full scientific name: Shewanella putrefaciens (Lee et al. 1981 ex Derby and Hammer 1931) MacDonell and Colwell 1986
  • synonyms

    • @ref: 20215
    • synonym: Alteromonas putrefaciens

@ref: 2428

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella putrefaciens

full scientific name: Shewanella putrefaciens (Lee et al. 1981) MacDonell and Colwell 1986

strain designation: 95

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.494
6948099.99negative
122075yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2428NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605)yeshttps://mediadive.dsmz.de/medium/605Name: NUTRIENT AGAR (OXOID CM3) (DSMZ Medium 605) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Yeast extract 2.0 g/l Lab-Lemco beef extract 1.0 g/l Distilled water
2428OXOID NUTRIENT BROTH (DSMZ Medium 948)yeshttps://mediadive.dsmz.de/medium/948Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
37718MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122075CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2428positivegrowth26mesophilic
37718positivegrowth25mesophilic
45954positivegrowth30-37mesophilic
67770positivegrowth25mesophilic
122075positivegrowth25-37mesophilic
122075nogrowth5psychrophilic
122075nogrowth41thermophilic
122075nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
45954aerobe
122075obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122075nitrate+reduction17632
122075nitrite+reduction16301
122075sodium thiosulfate+builds gas from132112
122075nitrate+respiration17632

antibiotic resistance

  • @ref: 122075
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

enzymes

@refvalueactivityec
122075oxidase+
122075beta-galactosidase-3.2.1.23
122075alcohol dehydrogenase-1.1.1.1
122075DNase+
122075caseinase+3.4.21.50
122075catalase-1.11.1.6
122075tween esterase-
122075lecithinase+
122075lipase+
122075lysine decarboxylase-4.1.1.18
122075ornithine decarboxylase+4.1.1.17
122075protease+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122075-+++-+++++++-----+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122075-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122075--------------------+----------------------------+---------+---------------+---++--------+-+--+-+-+

Isolation, sampling and environmental information

isolation

@refsample type
45954Butter
67770Butter
122075Surface of tainted butter

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_3799.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_126;97_134;98_151;99_3799&stattab=map
  • Last taxonomy: Shewanella
  • 16S sequence: X81623
  • Sequence Identity:
  • Total samples: 6
  • aquatic counts: 2
  • animal counts: 4

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2428yesyes2Risk group (German classification)
1220751Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Shewanella putrefaciens strain ATCC 8071 16S ribosomal RNA gene, partial sequenceFJ971881797ena24
20218S.putrefaciens 16S rRNA gene (ATCC 8071)X821331436ena24
20218Shewanella putrefaciens strain BCRC 10596 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014563374ena24
20218Shewanella putrefaciens strain BCRC 10596 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014564477ena24
20218Shewanella putrefaciens strain BCRC 10596 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014565326ena24
20218Shewanella putrefaciens strain BCRC 10596 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014566794ena24
20218Shewanella putrefaciens strain BCRC 10596 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014567947ena24
20218Shewanella putrifaciens 16S rRNAD11190165ena24
20218Shewanella putrifaciens 16S rRNAD11239212ena24
20218Shewanella putrifaciens 16S rRNAD11288191ena24
20218S.putrefaciens 16S rRNA geneX816231536ena24
20218Shewanella putrefaciens gene for 16S rRNA, partial sequence, strain: NBRC 3908AB6801671433ena24

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella putrefaciens ATCC 8071GCA_016406325completencbi24
66792Shewanella putrefaciens JCM 201901236543.3wgspatric1236543
66792Shewanella putrefaciens JCM 20190 = NBRC 39081236543.4wgspatric1236543
66792Shewanella putrefaciens strain ATCC 807124.44completepatric24
66792Shewanella putrefaciens strain JCM 2019024.42wgspatric24
66792Shewanella putrefaciens JCM 201902585427914draftimg1236543
66792Shewanella putrefaciens NBRC 39082731957646draftimg1236543
67770Shewanella putrefaciens JCM 20190 = NBRC 3908GCA_000615005contigncbi1236543
67770Shewanella putrefaciens JCM 20190 = NBRC 3908GCA_001591325contigncbi1236543
67770Shewanella putrefaciens JCM 20190GCA_014647555scaffoldncbi24

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes91.044no
gram-positiveno98.848no
anaerobicno94.88yes
aerobicyes54.392yes
halophileno70.38no
spore-formingno95.728no
thermophileno99.595yes
glucose-utilyes89.617no
motileyes94.075no
glucose-fermentno65.565no

External links

@ref: 2428

culture collection no.: DSM 6067, ATCC 8071, ICPB 352, NCIB 10471, CCUG 13452 D, JCM 20190, CCUG 13452, CECT 331, CIP 80.40, IAM 12079, IAM 1509, IFO 3908, JCM 9294, LMG 2268, NBRC 3908, NCIMB 10471, NCTC 12960

straininfo link

  • @ref: 83223
  • straininfo: 4969

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny2391295Classification of the spoilage flora of fish, with special reference to Shewanella putrefaciens.Stenstrom IM, Molin GJ Appl Bacteriol10.1111/j.1365-2672.1990.tb05226.x1990Animals, Bacteria, Aerobic/*classification, Cluster Analysis, Fishes/*microbiology, *Food Microbiology, Pseudomonas/*classificationBiotechnology
Phylogeny7441198Lipid composition and chemotaxonomy of Pseudomonas putrefaciens (Alteromonas putrefaciens).Wilkinson SG, Caudwell PFJ Gen Microbiol10.1099/00221287-118-2-3291980Fatty Acids/analysis, Lipids/*analysis, Lipopolysaccharides/analysis, Phosphatidylethanolamines/analysis, Phosphatidylglycerols/analysis, Phospholipids/analysis, Pseudomonas/analysis/*classification
Metabolism7830320[A simple method for differentiation of hydrogen sulfide-producing bacteria by the pH-dependent EDTA-sensitivity test].Kida N, Matsuzaki M, Matsukawa A, Suzuki S, Ushiama N, Kawahara K, Taguchi FNihon Saikingaku Zasshi10.3412/jsb.49.7691994Bacteria/*classification/*drug effects/metabolism, Edetic Acid/*pharmacology, Hydrogen Sulfide/*metabolism, Hydrogen-Ion Concentration, Microbial Sensitivity Tests/methodsPhylogeny
Biotechnology8486552Production and specificity of poly- and monoclonal antibodies raised against Shewanella putrefaciens.Fonnesbech B, Frokiaer H, Gram L, Jespersen CMJ Appl Bacteriol10.1111/j.1365-2672.1993.tb05152.x1993Animals, Antibodies, Bacterial/analysis/*biosynthesis, Antibodies, Monoclonal/analysis/*biosynthesis, Antibody Specificity, Enzyme-Linked Immunosorbent Assay, Immunoblotting, Mice, Pseudomonas/*immunology, Rabbits, Vibrionaceae/*immunology
Phylogeny9172338Differentiation of Shewanella putrefaciens and Shewanella alga on the basis of whole-cell protein profiles, ribotyping, phenotypic characterization, and 16S rRNA gene sequence analysis.Vogel BF, Jorgensen K, Christensen H, Olsen JE, Gram LAppl Environ Microbiol10.1128/aem.63.6.2189-2199.19971997Animals, Bacterial Proteins/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, Fishes/microbiology, Fuel Oils, Genes, Bacterial, Gram-Negative Facultatively Anaerobic Rods/chemistry/*classification/genetics, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, Species Specificity, Water MicrobiologyPathogenicity
Biotechnology15163589New method for rapid and sensitive quantification of sulphide-producing bacteria in fish from arctic and temperate waters.Skjerdal OT, Lorentzen G, Tryland I, Berg JDInt J Food Microbiol10.1016/j.ijfoodmicro.2003.11.0162004Animals, Colony Count, Microbial, Color, Fishes/*microbiology, Fluorescence, Food Microbiology, Food Preservation/*methods, Hydrogen Sulfide/*analysis, Iron/chemistry/metabolism, Odorants/analysis, Predictive Value of Tests, Regression Analysis, Sensitivity and Specificity, Shewanella putrefaciens/*isolation & purification/metabolism, Temperature, Time FactorsMetabolism
Phylogeny15653901Shewanella decolorationis sp. nov., a dye-decolorizing bacterium isolated from activated sludge of a waste-water treatment plant.Xu M, Guo J, Cen Y, Zhong X, Cao W, Sun GInt J Syst Evol Microbiol10.1099/ijs.0.63157-02005Bacterial Typing Techniques, China, Coloring Agents/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, Shewanella/*classification/genetics/isolation & purification/physiology, *Textile Industry, Waste Disposal, Fluid/*methodsGenetics
Phylogeny16403893Shewanella hafniensis sp. nov. and Shewanella morhuae sp. nov., isolated from marine fish of the Baltic Sea.Satomi M, Vogel BF, Gram L, Venkateswaran KInt J Syst Evol Microbiol10.1099/ijs.0.63931-02006Animals, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/chemistry, Denmark, Flounder/*microbiology, Gadiformes/*microbiology, Molecular Sequence Data, Oceans and Seas, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Shewanella/chemistry/*classification/isolation & purification/physiology, Species SpecificityGenetics
Metabolism21482426How does organic matter constrain the nature, size and availability of Fe nanoparticles for biological reduction?Pedrot M, Le Boudec A, Davranche M, Dia A, Henin OJ Colloid Interface Sci10.1016/j.jcis.2011.03.0672011Benzopyrans/chemistry/*metabolism, Colloids/chemistry/metabolism, *Humic Substances, Hydrogen-Ion Concentration, Iron/chemistry/*metabolism, Oxidation-Reduction, Particle Size, Shewanella putrefaciens/chemistry/*metabolism, Surface Properties
Phylogeny35849218Shewanella azerbaijanica sp. nov. a novel aquatic species with high bioremediation abilities.Nouioui I, Tarhriz V, Kim HM, Montazersaheb S, Hejazi MA, Jeon CO, Klenk HP, Hejazi MSArch Microbiol10.1007/s00203-022-03112-42022Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/genetics, Fatty Acids, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Shewanella/genetics, *Sodium ChlorideTranscriptome
Phylogeny35861494Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss).Altun S, Duman M, Ay H, Saticioglu IBInt J Syst Evol Microbiol10.1099/ijsem.0.0054602022Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Oncorhynchus mykiss, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, *Shewanella, UbiquinoneTranscriptome
35996024Antimicrobial Effect of Epigallocatechin Gallate Against Shewanella putrefaciens ATCC 8071: A Study Based on Cell Membrane and Biofilm.Pei J, Yu H, Qiu W, Mei J, Xie JCurr Microbiol10.1007/s00284-022-02978-32022Animals, *Anti-Infective Agents/pharmacology, Biofilms, Catechin/analogs & derivatives, Cell Membrane, *Shewanella putrefaciens
Metabolism36512125Study on spoilage potential and its molecular basis of Shewanella putrefaciens in response to cold conditions by Label-free quantitative proteomic analysis.Qian YF, Cheng Y, Xie J, Yang SPWorld J Microbiol Biotechnol10.1007/s11274-022-03479-y2022*Shewanella putrefaciens/metabolism, Cold Temperature, Proteomics, Biogenic Amines/analysis/metabolism, Nitrogen/metabolism, Peptide Hydrolases/metabolism, *Shewanella/metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2428Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6067)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6067
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
37718Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11135
45954Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 13452 D)https://www.ccug.se/strain?id=13452
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/
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
83223Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4969.1StrainInfo: A central database for resolving microbial strain identifiers
122075Curators of the CIPCollection of Institut Pasteur (CIP 80.40)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.40