Strain identifier

BacDive ID: 131363

Type strain: Yes

Species: Escherichia marmotae

Strain Designation: HT073016

Strain history: <- S. Liu, Nat. Inst. for Communicable Disease Control and Prevention, Beijing, China; HT073016

NCBI tax ID(s): 1499973 (species)

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General

@ref: 22590

BacDive-ID: 131363

DSM-Number: 28771

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Escherichia marmotae HT073016 is a mesophilic bacterium that was isolated from fresh faeces of wild marmot Marmota himalayana.

NCBI tax id

  • NCBI tax id: 1499973
  • Matching level: species

strain history

  • @ref: 22590
  • history: <- S. Liu, Nat. Inst. for Communicable Disease Control and Prevention, Beijing, China; HT073016

doi: 10.13145/bacdive131363.20230509.8.1

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 marmotae
  • full scientific name: Escherichia marmotae Liu et al. 2015

@ref: 22590

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Escherichia

species: Escherichia marmotae

full scientific name: Escherichia marmotae Liu et al. 2015

strain designation: HT073016

type strain: yes

Morphology

multimedia

  • @ref: 22590
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28771.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 22590
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 22590
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate+reduction
6836830849L-arabinose+fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
22590--+--------++-++---+-+-

Isolation, sampling and environmental information

isolation

  • @ref: 22590
  • sample type: fresh faeces of wild marmot Marmota himalayana
  • host species: Marmota himalayana
  • geographic location: Qinghai province, Yushu Tibetan autonomous prefecture, 4525 m above sea level
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 33.425
  • longitude: 96.375

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Rodentia (Other)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 22590
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22590
  • description: Escherichia marmotae strain HT073016 16S ribosomal RNA gene, partial sequence
  • accession: KJ787692
  • length: 1504
  • database: ena
  • NCBI tax ID: 1499973

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia marmotae HT073016GCA_002900365completencbi1499973
66792Escherichia marmotae HT073016GCA_000807695scaffoldncbi1499973
66792Escherichia marmotae HT0730162917408641completeimg1499973
66792Escherichia marmotae HT0730162630968558draftimg1499973

GC content

  • @ref: 22590
  • GC-content: 53.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno52.723no
gram-positiveno98.379no
anaerobicno95.149no
aerobicyes81.266no
halophileno93.054no
spore-formingno94.344no
glucose-utilyes94.186no
thermophileno98.947no
motileyes89.261no
glucose-fermentyes92.354no

External links

@ref: 22590

culture collection no.: DSM 28771, CGMCC 1.12862

straininfo link

  • @ref: 89802
  • straininfo: 403821

literature

  • topic: Phylogeny
  • Pubmed-ID: 25851592
  • title: Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.
  • authors: Liu S, Jin D, Lan R, Wang Y, Meng Q, Dai H, Lu S, Hu S, Xu J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.000228
  • year: 2015
  • mesh: Animals, 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, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22590Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28771Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28771)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68368Automatically annotated from API 20E
89802Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403821.1