Strain identifier

BacDive ID: 7525

Type strain: No

Species: Glutamicibacter nicotianae

Strain history: CIP <- 1994, R. Ruimy, CNRS, Villefranche sur mer, France, Brevibacterium liquefaciens <- ATCC <- Shionogo and Co, Brevibacterium liquefaciens

NCBI tax ID(s): 37929 (species)

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General

@ref: 8929

BacDive-ID: 7525

DSM-Number: 20579

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive

description: Glutamicibacter nicotianae DSM 20579 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sewage.

NCBI tax id

  • NCBI tax id: 37929
  • Matching level: species

strain history

@refhistory
8929<- NCIB <- ATCC <- Shionogo & Co., Ltd
67770ATCC 14929 <-- Shionogi & Co., Ltd..
121293CIP <- 1994, R. Ruimy, CNRS, Villefranche sur mer, France, Brevibacterium liquefaciens <- ATCC <- Shionogo and Co, Brevibacterium liquefaciens

doi: 10.13145/bacdive7525.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Glutamicibacter
  • species: Glutamicibacter nicotianae
  • full scientific name: Glutamicibacter nicotianae (Giovannozzi-Sermanni 1959) Busse 2016

  • synonyms

    @refsynonym
    20215Corynebacterium liquefaciens
    20215Glutamicibacter mysorens
    20215Brevibacterium liquefaciens
    20215Arthrobacter nicotianae
    20215Arthrobacter mysorens

@ref: 8929

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Glutamicibacter

species: Glutamicibacter nicotianae

full scientific name: Glutamicibacter nicotianae (Giovannozzi-Sermanni 1959) Busse 2016

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
121293positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41913MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8929CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
121293CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
8929positivegrowth30mesophilic
41913positivegrowth30mesophilic
55896positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
121293positivegrowth30-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
55896aerobe
121293obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

compound production

@refcompound
8929adenylate cyclase
20216Adenylate cyclase

murein

  • @ref: 8929
  • murein short key: A11.35
  • type: A4alpha L-Lys-L-Ala-L-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-8 (MK-9)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1212934853esculin-hydrolysis
12129317632nitrate+reduction
12129316301nitrite-reduction

metabolite production

  • @ref: 121293
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 121293
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
67770adenylate cyclase4.6.1.1
121293oxidase-
121293beta-galactosidase-3.2.1.23
121293gelatinase+
121293DNase+
121293catalase+1.11.1.6
121293lecithinase-
121293urease-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
121293-+++-+----++---+--+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121293+++++--+++++---+---++++--------+---+-------------+---+------++++--------++-+-+-++-+-----+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8929sewage
55896SewageJapanJPNAsia
67770Sewage
121293Environment, SewageJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_8815.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1446;97_1726;98_2111;99_8815&stattab=map
  • Last taxonomy: Glutamicibacter
  • 16S sequence: AJ251417
  • Sequence Identity:
  • Total samples: 127
  • soil counts: 26
  • aquatic counts: 29
  • animal counts: 63
  • plant counts: 9

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89291Risk group (German classification)
1212931Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Brevibacterium liquefaciens 16S rRNA gene, strain DSM 20579
  • accession: AJ251417
  • length: 1465
  • database: ena
  • NCBI tax ID: 37929

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glutamicibacter nicotianae DSM 20579GCA_016907615contigncbi37929
66792Glutamicibacter nicotianae strain DSM 2057937929.9wgspatric37929
66792Corynebacterium liquefaciens DSM 205792893596632draftimg37929

GC content

  • @ref: 8929
  • GC-content: 62.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes95.669no
anaerobicno99.32yes
halophileyes52.302no
spore-formingno90.794no
glucose-utilyes86.153no
aerobicyes94.417yes
motileno93.331no
flagellatedno95.877no
thermophileno97.882yes
glucose-fermentno85.431no

External links

@ref: 8929

culture collection no.: DSM 20579, ATCC 14929, NCIB 9545, CCUG 43493, CIP 104276, CIP 82.22, JCM 1970, BCRC 12148, KCTC 3129, KCTC 3257, LMG 16159, NCIMB 9545

straininfo link

  • @ref: 76970
  • straininfo: 297021

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism6039354Formation of adenosine cyclic 3',5'-phosphate by nonproliferating cells and cell-free extract of Brevibacterium liquefaciens.Ide M, Yoshimoto A, Okabayashi TJ Bacteriol10.1128/jb.94.2.317-322.19671967Adenine Nucleotides/*biosynthesis, Alanine/pharmacology, Amino Acids/metabolism, Brevibacterium/drug effects/*metabolism, Carbohydrate Metabolism, Chloramphenicol/pharmacology, Chromatography, Thin Layer, Culture Media, Pyruvates/pharmacology, Sulfur/pharmacologyCultivation
Enzymology6243273Mechanism of the adenylate cyclase reaction. Stereochemistry of the reaction catalyzed by the enzyme from Brevibacterium liquefaciens.Gerlt JA, Coderre JA, Wolin MSJ Biol ChemS0021-9258(19)86171-91980Adenylyl Cyclases/*metabolism, Brevibacterium/*enzymology, Cyclic AMP/analogs & derivatives, Magnetic Resonance Spectroscopy, Stereoisomerism, Substrate Specificity, ThionucleotidesMetabolism
Phylogeny15023984Reclassification of Brevibacterium liquefaciens Okabayashi and Masuo 1960 as Arthrobacter nicotianae Giovannozzi-Sermanni 1959.Gelsomino R, Vancanneyt M, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02886-02004Actinomycetales/classification, Arthrobacter/*classification/isolation & purification, Brevibacterium/*classification/isolation & purification, PhylogenyEnzymology
Phylogeny23194805Taxonomic Studies on Arthrobacter nicotianae and Related Taxa: Description of Arthrobacter uratoxydans sp. nov. and Arthrobacter sulfureus sp. nov. and Reclassification of Brevibacterium protophormiae as Arthrobacter protophormiae comb. nov.Stackebrandt E, Fowler VJ, Fiedler F, Seiler HSyst Appl Microbiol10.1016/S0723-2020(83)80005-81983

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8929Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20579)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20579
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41913Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16166
55896Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 43493)https://www.ccug.se/strain?id=43493
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/
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
76970Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297021.1StrainInfo: A central database for resolving microbial strain identifiers
121293Curators of the CIPCollection of Institut Pasteur (CIP 104276)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104276