Strain identifier

BacDive ID: 5166

Type strain: Yes

Species: Serratia ureilytica

Strain history: CIP <- 2005, CCUG <- 2005, B. Bhadra, North Bengal Univ., Siliguri, India: strain NiVa 51

NCBI tax ID(s): 300181 (species)

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General

@ref: 6664

BacDive-ID: 5166

DSM-Number: 16952

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Serratia ureilytica DSM 16952 is an aerobe, Gram-negative, motile bacterium that was isolated from water from Torsa River.

NCBI tax id

  • NCBI tax id: 300181
  • Matching level: species

strain history

@refhistory
6664<- R. Chakraborty,Univ. North Bengal; NiVa51
67770B. Bhadra Niva 51.
123743CIP <- 2005, CCUG <- 2005, B. Bhadra, North Bengal Univ., Siliguri, India: strain NiVa 51

doi: 10.13145/bacdive5166.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Yersiniaceae
  • genus: Serratia
  • species: Serratia ureilytica
  • full scientific name: Serratia ureilytica Bhadra et al. 2005

@ref: 6664

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Serratia

species: Serratia ureilytica

full scientific name: Serratia ureilytica Bhadra et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31489negative0.9 µm0.85 µmrod-shapedyes
123743negativerod-shapedyes

colony morphology

  • @ref: 123743
  • hemolysis ability: 1

pigmentation

  • @ref: 31489
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33270MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123743CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
31489positivegrowth08-43
31489positiveoptimum25.5mesophilic
33270positivegrowth30mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
31489positivegrowth05-11alkaliphile
31489positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31489aerobe
123743facultative anaerobe

spore formation

  • @ref: 31489
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31489NaClpositivegrowth0-1.4 %
31489NaClpositiveoptimum0.7 %

observation

  • @ref: 31489
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3148930089acetate+carbon source
3148915963ribitol+carbon source
3148916449alanine+carbon source
3148929016arginine+carbon source
3148927570histidine+carbon source
31489182404-hydroxy-L-proline+carbon source
3148928053melibiose+carbon source
3148918257ornithine+carbon source
3148928044phenylalanine+carbon source
3148926271proline+carbon source
3148917822serine+carbon source
3148930911sorbitol+carbon source
3148930031succinate+carbon source
3148926986threonine+carbon source
3148918222xylose+carbon source
314894853esculin+hydrolysis
3148917632nitrate+reduction
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate+builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol+builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol+builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol+builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol+builds acid from
6837117754glycerol+builds acid from
12374317632nitrate+reduction
12374316301nitrite-reduction

metabolite production

  • @ref: 123743
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31489catalase+1.11.1.6
31489urease+3.5.1.5
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
123743oxidase-
123743alcohol dehydrogenase-1.1.1.1
123743catalase+1.11.1.6
123743lysine decarboxylase+4.1.1.18
123743ornithine decarboxylase+4.1.1.17
123743urease+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
123743-++++++-+-++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123743++--+--+-++++---+++--+-++++/-+--++-----+--+----++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6664water from Torsa RiverJalpaiguri, West BengalIndiaINDAsia
67770Torsa Rivernorthern West BengalIndiaINDAsia
123743Environment, Water, riverTorsa River, Hasimara, West BengalIndiaINDAsia2002

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #River (Creek)

taxonmaps

  • @ref: 69479
  • File name: preview.99_289.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_244;99_289&stattab=map
  • Last taxonomy: Serratia marcescens
  • 16S sequence: LC507943
  • Sequence Identity:
  • Total samples: 22704
  • soil counts: 1270
  • aquatic counts: 2336
  • animal counts: 18103
  • plant counts: 995

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66641Risk group (German classification)
1237431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
31489Serratia ureilytica 16S rRNA gene, type strain NiVa 51TAJ8540621505nuccore300181
67770Serratia ureilytica JCM 13046 gene for 16S rRNA, partial sequenceLC5079431464ena300181

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Serratia ureilytica strain CCUG:50595300181.29wgspatric300181
67770Serratia ureilytica CCUG:50595GCA_013375155contigncbi300181

GC content

@refGC-contentmethod
3148960
6777060high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.158yes
anaerobicno98.255no
halophileno94.13yes
spore-formingno95.469yes
glucose-utilyes94.748no
flagellatedno59.423no
aerobicyes91.916yes
motileyes87.491yes
thermophileno99.503yes
glucose-fermentyes90.982no

External links

@ref: 6664

culture collection no.: DSM 16952, CCUG 50595, LMG 22860, NIVA NiVa51, JCM 13046, BCRC 17594, CCM 7336, CIP 108937, JCM 16474, NiVa 51

straininfo link

  • @ref: 74658
  • straininfo: 136003

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166724Serratia ureilytica sp. nov., a novel urea-utilizing species.Bhadra B, Roy P, Chakraborty RInt J Syst Evol Microbiol10.1099/ijs.0.63674-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Serratia/*classification/genetics/isolation & purification/physiology, Urea/*metabolismGenetics
Phylogeny19578149Serratia nematodiphila sp. nov., associated symbiotically with the entomopathogenic nematode Heterorhabditidoides chongmingensis (Rhabditida: Rhabditidae).Zhang CX, Yang SY, Xu MX, Sun J, Liu H, Liu JR, Liu H, Kan F, Sun J, Lai R, Zhang KYInt J Syst Evol Microbiol10.1099/ijs.0.65718-02009Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Fluorescence, Genes, rRNA, Genotype, Intestines/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhabditoidea/*microbiology, Sequence Analysis, DNA, Serratia/*classification/genetics/isolation & purification/physiology, Species Specificity, *SymbiosisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6664Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16952)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16952
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
31489Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2778728776041
33270Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6622
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
74658Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID136003.1StrainInfo: A central database for resolving microbial strain identifiers
123743Curators of the CIPCollection of Institut Pasteur (CIP 108937)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108937