Strain identifier

BacDive ID: 4927

Type strain: Yes

Species: Escherichia hermannii

Strain Designation: 980-72

Strain history: CIP <- 1988, ATCC <- CDC: strain 980-72 <- Louisiana State Hlth. Dept., USA

NCBI tax ID(s): 1115512 (strain), 565 (species)

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General

@ref: 1719

BacDive-ID: 4927

DSM-Number: 4560

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

description: Escherichia hermannii 980-72 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from Toe of 17-year old female.

NCBI tax id

NCBI tax idMatching level
565species
1115512strain

strain history

@refhistory
1719<- ATCC <- B.R. Davis, CDC, 980-72
67770Y. Kosako 83024 <-- R. Sakazaki 82073 <-- D. J. Brenner CDC 980-72 <-- Louisiana State Health Dept., USA.
119884CIP <- 1988, ATCC <- CDC: strain 980-72 <- Louisiana State Hlth. Dept., USA

doi: 10.13145/bacdive4927.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Escherichia
  • species: Escherichia hermannii
  • full scientific name: Escherichia hermannii Brenner et al. 1983

  • synonyms

    • @ref: 20215
    • synonym: Atlantibacter hermannii

@ref: 1719

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Escherichia

species: Escherichia hermannii

full scientific name: Escherichia hermannii Brenner et al. 1983

strain designation: 980-72

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.458
6948099.955negative
119884yesnegativerod-shaped

colony morphology

  • @ref: 119884

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1719COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
1719NUTRIENT 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
40553MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119884CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119884CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1719positivegrowth37mesophilic
40553positivegrowth30mesophilic
67770positivegrowth37mesophilic
119884positivegrowth30-41
119884nogrowth5psychrophilic
119884nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119884
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.269

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
68371turanose-builds acid from32528
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
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
68371erythritol-builds acid from17113
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
68368citrate-assimilation16947
68368ornithine+degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
119884mannitol+fermentation29864
119884citrate-carbon source16947
119884glucose+fermentation17234
119884lactose-fermentation17716
119884nitrate+reduction17632
119884nitrite-reduction16301
119884malonate-assimilation15792
119884sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 119884
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno
11988435581indoleyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole+
11988415688acetoin-
11988417234glucose+

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
119884oxidase-
119884beta-galactosidase+3.2.1.23
119884alcohol dehydrogenase-1.1.1.1
119884gelatinase-
119884catalase+1.11.1.6
119884lysine decarboxylase-4.1.1.18
119884ornithine decarboxylase+4.1.1.17
119884phenylalanine ammonia-lyase-4.3.1.24
119884tryptophan deaminase-
119884urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46327C14:02.414
    46327C16:034.116
    46327C18:00.818
    46327C11:0 ISO 3OH712.09
    46327C14:0 3OH/C16:1 ISO I1015.485
    46327C16:1 ω7c1715.819
    46327C17:0 CYCLO7.116.888
    46327C18:1 ω7c /12t/9t18.417.824
    46327C19:0 ISO0.918.633
    46327unknown 13.961113.961
    46327unknown 14.5031.314.503
  • 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
119884-+++-++-+-++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1719+--+----++-++--+--++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119884+/--+/-+++---++++-++-+---+-+-+/-++---+------+/--+/------++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119884+++++----++----+++++++-+-----+-+-+-----+---++----+---++++--++--------------+---++-+---+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1719Toe of 17-year old femaleLouisiana State Health Dept.USAUSANorth America
46327Human infected toe,17-yr-old femaleLouisianaUSAUSANorth America
67770Infected toe of a 17-year-old femaleLAUSAUSANorth America
119884Human, Female, toe

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Limb#Foot
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_3894.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_88;99_3894&stattab=map
  • Last taxonomy: Enterobacteriaceae
  • 16S sequence: JN175345
  • Sequence Identity:
  • Total samples: 253
  • soil counts: 10
  • aquatic counts: 6
  • animal counts: 232
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17192Risk group (German classification)
1198841Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
1719Escherichia hermannii strain CIP 103176 16S ribosomal RNA gene, complete sequenceJN1753451478ena565
67770Escherichia hermannii gene for 16S rRNA, partial sequence, strain: NBRC 105704AB6822761467ena565

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Atlantibacter hermannii NCTC12129GCA_900635495completencbi565
66792Atlantibacter hermannii strain FDAARGOS_888565.17completepatric565
66792Atlantibacter hermannii strain NCTC12129565.8completepatric565
66792Escherichia hermannii NBRC 1057041115512.3wgspatric1115512
66792Atlantibacter hermannii NBRC 1057042514752030draftimg1115512
67770Atlantibacter hermannii NBRC 105704GCA_000248015contigncbi1115512

GC content

  • @ref: 67770
  • GC-content: 52.4
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno58.974no
gram-positiveno97.758no
anaerobicno95.429no
aerobicyes77.328no
halophileno88.123no
spore-formingno94.097no
thermophileno99.098yes
glucose-utilyes94.79no
motileyes88.609no
glucose-fermentyes92.65yes

External links

@ref: 1719

culture collection no.: DSM 4560, ATCC 33650, CIP 103176, CCUG 15714, CDC 980-72, JCM 1473, BCRC 13982, CGMCC 1.3439, CGMCC 1.6766, HAMBI 1693, LMG 7867, NBRC 105704, NCTC 12129

straininfo link

  • @ref: 74424
  • straininfo: 13668

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
15225064Benzylidene acetal fragmentation route to 6-deoxy sugars: direct reductive cleavage in the presence of ether protecting groups, permitting the efficient, highly stereocontrolled synthesis of beta-D-rhamnosides from D-mannosyl glycosyl donors. Total synthesis of alpha-D-Gal-(1-->3)-alpha-D-Rha-(1-->3)- beta-D-Rha-(1-->4)-beta-D-Glu-OMe, the repeating unit of the antigenic lipopolysaccharide from Escherichia hermannii ATCC 33650 and 33652.Crich D, Yao QJ Am Chem Soc10.1021/ja048070j2004Benzylidene Compounds/*chemistry, Escherichia/*chemistry, Glycosylation, Lipopolysaccharides/*chemistry, Mannosides/*chemistry, Molecular Structure, Oligosaccharides/*chemical synthesis/chemistry, Rhamnose/*chemical synthesis/chemistry
25851592Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.Liu S, Jin D, Lan R, Wang Y, Meng Q, Dai H, Lu S, Hu S, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.0002282015Animals, Base Composition, China, DNA, Bacterial/genetics, Escherichia/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Feces/*microbiology, Marmota/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPhylogenyGenetics

Reference

@idauthorscataloguedoi/urltitle
1719Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4560)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4560
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
40553Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14944
46327Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15714)https://www.ccug.se/strain?id=15714
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
74424Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13668.1StrainInfo: A central database for resolving microbial strain identifiers
119884Curators of the CIPCollection of Institut Pasteur (CIP 103176)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103176