Strain identifier

BacDive ID: 132975

Type strain: Yes

Species: Proteus terrae subsp. cibarius

Strain Designation: JS9

Strain history: J.-W. Bae; Kyung Hee Univ., South Korea; JS9.

NCBI tax ID(s): 626774 (subspecies)

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General

@ref: 24763

BacDive-ID: 132975

DSM-Number: 100173

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Proteus terrae subsp. cibarius JS9 is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from Jeotgal .

NCBI tax id

  • NCBI tax id: 626774
  • Matching level: subspecies

strain history

@refhistory
24763<- D.-W. Hyun, Kyung Hee Univ., Seoul, Republic of Korea; JS9
67770J.-W. Bae; Kyung Hee Univ., South Korea; JS9.

doi: 10.13145/bacdive132975.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Morganellaceae
  • genus: Proteus
  • species: Proteus terrae subsp. cibarius
  • full scientific name: Proteus terrae subsp. cibarius (Hyun et al. 2016) Behrendt et al. 2021

  • synonyms

    • @ref: 20215
    • synonym: Proteus cibarius

@ref: 24763

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Morganellaceae

genus: Proteus

species: Proteus terrae subsp. cibarius

full scientific name: Proteus terrae subsp. cibarius (Hyun et al. 2016) Behrendt et al. 2021

strain designation: JS9

type strain: yes

Morphology

cell morphology

  • @ref: 43976
  • gram stain: negative
  • cell length: 0.5-2.0 µm
  • cell width: 0.4-0.7 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: peritrichous

colony morphology

  • @ref: 43976
  • colony size: 0.8-1.1 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43976Nutrient agar (NA)yes
24763BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43976positivegrowth10-37
43976positiveoptimum30mesophilic
24763positivegrowth28mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43976positivegrowth5.0-10.0alkaliphile
43976positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43976
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
43976NaClpositivegrowth0-12 %(w/v)
43976NaClpositiveoptimum2 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-8, Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43976168082-dehydro-D-gluconate+builds acid from
4397617108D-arabinose+builds acid from
4397615824D-fructose+builds acid from
4397612936D-galactose+builds acid from
4397617634D-glucose+builds acid from
439766731melezitose+builds acid from
4397616988D-ribose+builds acid from
4397665327D-xylose+builds acid from
4397624265gluconate+builds acid from
4397615978glycerol 3-phosphate+builds acid from
4397617306maltose+builds acid from
43976320061methyl alpha-D-glucopyranoside+builds acid from
43976506227N-acetylglucosamine+builds acid from
4397617992sucrose+builds acid from
4397627082trehalose+builds acid from
4397632528turanose+builds acid from
43976167632-oxobutanoate+energy source
43976309162-oxoglutarate+energy source
43976182404-hydroxy-L-proline+energy source
4397630089acetate+energy source
4397617925alpha-D-glucose+energy source
43976645522-hydroxybutyrate+energy source
4397673706bromosuccinate+energy source
4397617057cellobiose+energy source
4397615570D-alanine+energy source
4397615824D-fructose+energy source
4397612936D-galactose+energy source
439768391D-gluconate+energy source
4397614314D-glucose 6-phosphate+energy source
4397616024D-mannose+energy source
4397616523D-serine+energy source
4397623652dextrin+energy source
4397624996lactate+energy source
4397615740formate+energy source
43976167244-hydroxybutyrate+energy source
4397614336glycerol 1-phosphate+energy source
4397615978glycerol 3-phosphate+energy source
4397628087glycogen+energy source
4397673804glycyl L-aspartic acid+energy source
4397617596inosine+energy source
4397621217L-alaninamide+energy source
43976L-alanine 4-nitroanilide+energy source
4397673786L-alanylglycine+energy source
4397630849L-arabinose+energy source
4397617196L-asparagine+energy source
4397629991L-aspartate+energy source
4397629985L-glutamate+energy source
4397615971L-histidine+energy source
4397615603L-leucine+energy source
4397615729L-ornithine+energy source
4397617295L-phenylalanine+energy source
4397617203L-proline+energy source
4397618183L-pyroglutamic acid+energy source
4397617115L-serine+energy source
4397616857L-threonine+energy source
4397617306maltose+energy source
4397651850methyl pyruvate+energy source
4397675146monomethyl succinate+energy source
4397628037N-acetylgalactosamine+energy source
43976506227N-acetylglucosamine+energy source
4397673784glycyl-l-glutamate+energy source
43976143136succinamate+energy source
4397630031succinate+energy source
4397617992sucrose+energy source
4397617748thymidine+energy source
4397632528turanose+energy source
4397616704uridine+energy source
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

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantresistance conc.
439766104kanamycinyesyes100 µg/mL
4397628971ampicillinyesyes200 µg/mL
4397627902tetracyclineyesyes30 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinyes
6836835581indoleyes

metabolite tests

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

enzymes

@refvalueactivityec
43976catalase+1.11.1.6
43976alpha-glucosidase+3.2.1.20
43976alkaline phosphatase+3.1.3.1
43976protease+
43976leucine arylamidase+3.4.11.1
43976acid phosphatase+3.1.3.2
43976valine arylamidase+
43976naphthol-AS-BI-phosphohydrolase+
43976trypsin+3.4.21.4
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43976C14:07.5
    43976C14:0 3OH / C16:1 iso I6.8
    43976C16:028.2
    43976C16:12.1
    43976C16:1ω7c / C16:1ω6c24.3
    43976C17:00.5
    43976C17:0 cyclo7.7
    43976C17:1ω8c0.6
    43976C18:00.5
    43976C18:1ω7c / C18:1ω6c19.1
    43976C18:1ω9c0.5
    43976C19:0ω8c cyclo0.6
  • type of FA analysis: whole cell analysis
  • incubation medium: Nutrient agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.2
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Agilent 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
24763------++++++----+------
24763-----+++++++----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
24763Jeotgal (Korean traditional fermented seafood)Republic of KoreaKORAsia
43976Korean fermented seafood, JeotgalNutrient agar3 days25
67770Korean fermented seafood, JeotgalRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Seafood
#Engineered#Food production#Fermented

taxonmaps

  • @ref: 69479
  • File name: preview.99_739.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_12;97_12;98_14;99_739&stattab=map
  • Last taxonomy: Proteus
  • 16S sequence: FJ796245
  • Sequence Identity:
  • Total samples: 89
  • soil counts: 4
  • aquatic counts: 10
  • animal counts: 74
  • plant counts: 1

Safety information

risk assessment

  • @ref: 24763
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24763
  • description: Proteus cibarius strain JS9 16S ribosomal RNA gene, partial sequence
  • accession: FJ796245
  • length: 1476
  • database: ena
  • NCBI tax ID: 626774

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Proteus cibarius strain JCM 30699626774.3wgspatric626774
66792Proteus cibarius JCM 306992905324704draftimg626774
67770Proteus terrae subsp. cibarius JCM 30699GCA_003144495contigncbi626774

GC content

@refGC-contentmethod
4397639real time PCR (RTD-PCR)
2476339.0fluorimetric
6777039thermal denaturation, midpoint method (Tm)
6777037.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.677no
anaerobicno96.894no
halophileno90.099no
spore-formingno96.314no
glucose-utilyes90.268no
thermophileno99.077yes
flagellatedyes73.271yes
aerobicno57.136yes
motileyes88.975yes
glucose-fermentyes88.529yes

External links

@ref: 24763

culture collection no.: DSM 100173, JCM 30699, KACC 18404

straininfo link

  • @ref: 91251
  • straininfo: 402545

literature

  • topic: Phylogeny
  • Pubmed-ID: 26944634
  • title: Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus.
  • authors: Hyun DW, Jung MJ, Kim MS, Shin NR, Kim PS, Whon TW, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001002
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Proteus/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Seafood/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24763Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100173Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100173)
43976Dong-Wook Hyun, Mi-Ja Jung, Min-Soo Kim, Na-Ri Shin, Pil Soo Kim, Tae Woong Whon, Jin-Woo BaeProteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus10.1099/ijsem.0.001002IJSEM 66: 2158-2164 201626944634
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91251Reimer, 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-ID402545.1