Strain identifier

BacDive ID: 23924

Type strain: Yes

Species: Phytobacter massiliensis

Strain Designation: JC163

Strain history: CIP <- 2014, DSMZ <- JC Lagier, Timone Hosp., Marseille, France: strain JC163

NCBI tax ID(s): 1485952 (species)

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General

@ref: 20553

BacDive-ID: 23924

DSM-Number: 26120

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

description: Phytobacter massiliensis JC163 is a mesophilic, Gram-negative, motile bacterium that was isolated from human feces of a healthy patient.

NCBI tax id

  • NCBI tax id: 1485952
  • Matching level: species

strain history

@refhistory
20553<- J.-C. Lagier, Timone Hospital, Marseille, France; JC163
120853CIP <- 2014, DSMZ <- JC Lagier, Timone Hosp., Marseille, France: strain JC163

doi: 10.13145/bacdive23924.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Phytobacter
  • species: Phytobacter massiliensis
  • full scientific name: Phytobacter massiliensis (Lagier et al. 2014) Ma et al. 2021

  • synonyms

    @refsynonym
    20215Metakosakonia massiliensis
    20215Enterobacter massiliensis

@ref: 20553

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Enterobacteriaceae

genus: Phytobacter

species: Phytobacter massiliensis

full scientific name: Phytobacter massiliensis (Lagier et al. 2014) Ma et al. 2020

strain designation: JC163

type strain: yes

Morphology

cell morphology

  • @ref: 120853
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20553TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
120853CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

  • @ref: 20553
  • growth: positive
  • type: growth
  • temperature: 37
  • range: mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
6836815688acetoinno
6836835581indoleyes
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 TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
20553+--+----+-+++-++--++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
20553human feces of a healthy patientSenegalSENAfrica
120853Human, FecesSenegalSENAfrica

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
205531Risk group (German classification)
1208531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20553
  • description: Enterobacter massiliensis JC163 16S ribosomal RNA gene, partial sequence
  • accession: JN657217
  • length: 1499
  • database: ena
  • NCBI tax ID: 1095768

GC content

  • @ref: 20553
  • GC-content: 55.1
  • method: sequence analysis

External links

@ref: 20553

culture collection no.: DSM 26120, CSUR P161, CIP 110810

straininfo link

  • @ref: 87925
  • straininfo: 407819

literature

topicPubmed-IDtitleauthorsjournalDOIyeartopic2mesh
Genetics24019988Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov.Lagier JC, El Karkouri K, Mishra AK, Robert C, Raoult D, Fournier PEStand Genomic Sci10.4056/sigs.33968302013Phylogeny
Phylogeny32350604Proposal for Unification of the Genus Metakosakonia and the Genus Phytobacter to a Single Genus Phytobacter and Reclassification of Metakosakonia massiliensis as Phytobacter massiliensis comb. nov.Ma Y, Yao R, Li Y, Wu X, Li S, An QCurr Microbiol10.1007/s00284-020-02004-42020TranscriptomeBacterial Typing Techniques, DNA, Bacterial/genetics, Enterobacteriaceae/*classification, Gammaproteobacteria/*classification, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA

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
20553Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26120Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26120)
68368Automatically annotated from API 20E
87925Reimer, 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-ID407819.1
120853Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110810Collection of Institut Pasteur (CIP 110810)