Strain identifier

BacDive ID: 7582

Type strain: Yes

Species: Glutamicibacter nicotianae

Strain Designation: NANDA-189, A-189

Strain history: CIP <- 1987, NCIB <- K. Nand: strain A-189

NCBI tax ID(s): 1216975 (strain), 257984 (species)

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General

@ref: 4824

BacDive-ID: 7582

DSM-Number: 12798

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, ovoid-shaped, amino acid production

description: Glutamicibacter nicotianae NANDA-189 is an obligate aerobe, mesophilic, Gram-positive bacterium that produces amino acids and was isolated from sewage.

NCBI tax id

NCBI tax idMatching level
257984species
1216975strain

strain history

@refhistory
4824<- NCIMB <- K. Nand
67770LMG 16219 <-- ATCC 33408 <-- NCIB 10583 <-- K. Nand A-189.
121215CIP <- 1987, NCIB <- K. Nand: strain A-189

doi: 10.13145/bacdive7582.20230509.8.1

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: 4824

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Glutamicibacter

species: Glutamicibacter mysorens

full scientific name: Glutamicibacter mysorens (Nand and Rao 1972) Busse 2016 emend. Nouioui et al. 2018

strain designation: NANDA-189, A-189

type strain: yes

Morphology

cell morphology

  • @ref: 121215
  • gram stain: positive
  • cell shape: ovoid-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18370Sand yellow (1002)10-14 daysISP 2
18370Zinc yellow (1018)10-14 daysISP 3
18370Ivory (1014)10-14 daysISP 4
18370Colorless10-14 daysISP 5
18370Honey yellow (1005)10-14 daysISP 6
18370Ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18370noISP 2
18370noISP 3
18370noISP 4
18370noISP 5
18370noISP 6
18370noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4824OXOID NUTRIENT BROTH (DSMZ Medium 948)yeshttps://mediadive.dsmz.de/medium/948Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water
4824RAE MEDIUM (DSMZ Medium 848)yeshttps://mediadive.dsmz.de/medium/848Name: RAE MEDIUM (DSMZ Medium 848) Composition: Glucose 40.0 g/l Yeast extract 10.0 g/l Peptone 10.0 g/l Na2HPO4 x 2 H2O 3.38 g/l Citric acid x H2O 1.5 g/l Glacial acetic acid Absolute ethanol Distilled water
18370ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18370ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
18370ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18370ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18370ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18370ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
37402MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
121215CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121215CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18370positiveoptimum28mesophilic
4824positivegrowth28mesophilic
37402positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121215
  • oxygen tolerance: obligate aerobe

compound production

  • @ref: 4824
  • compound: L glutamic acid

halophily

  • @ref: 18370
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1837017234glucose+
1837022599arabinose-
1837017992sucrose+
1837017268myo-inositol+
1837029864mannitol-
1837028757fructose-
1837026546rhamnose-
1837016634raffinose+
1837062968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12121517632nitrate-reduction
12121516301nitrite-reduction
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6777029985L-glutamateyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12121535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
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+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
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
121215oxidase-
121215catalase+1.11.1.6
121215urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18370+++-++++-++---++-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18370+++-++++-++---++-+-
121215+++-++-+--+---+-+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18370---------++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4824sewageMysoreIndiaINDAsia
67770SewageMysore CityIndiaINDAsia
121215Environment, Sewage

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: AJ639831
  • 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
183701
48241Risk group (German classification)
1212151Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Arthrobacter mysorens partial 16S rRNA gene, type strain DSM 12798TAJ6174821491ena257984
20218Arthrobacter mysorens partial 16S rRNA gene, type strain LMG 16219TAJ6398311478ena257984

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glutamicibacter mysorens NBRC 1030601216975.4wgspatric1216975
66792Glutamicibacter mysorens strain DSM 12798257984.4wgspatric257984
66792Glutamicibacter mysorens NBRC 1030602681812973draftimg1216975
66792Glutamicibacter mysorens DSM 127982627854287draftimg257984
67770Glutamicibacter mysorens NBRC 103060GCA_001552115contigncbi1216975
67770Glutamicibacter mysorens DSM 12798GCA_002797775contigncbi257984

GC content

  • @ref: 67770
  • GC-content: 62
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.795no
gram-positiveyes94.273no
anaerobicno99.376no
aerobicyes96.296no
halophileyes54.791no
spore-formingno89.922no
thermophileno98.067yes
glucose-utilyes85.247yes
flagellatedno96.221no
glucose-fermentno92.779no

External links

@ref: 4824

culture collection no.: DSM 12798, ATCC 33408, NCIMB 10583, JCM 11565, CIP 102716, IAM 14869, KCTC 3381, LMG 16219, NBRC 103060, VTT E-072694

straininfo link

  • @ref: 77026
  • straininfo: 8180

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28056223Glutamicibacter halophytocola sp. nov., an endophytic actinomycete isolated from the roots of a coastal halophyte, Limonium sinense.Feng WW, Wang TT, Bai JL, Ding P, Xing K, Jiang JH, Peng X, Qin SInt J Syst Evol Microbiol10.1099/ijsem.0.0017752017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micrococcaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Plumbaginaceae/*microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32902704Phylogenomic Analysis Reveals That Arthrobacter mysorens Nand and Rao 1972 (Approved Lists 1980) and Glutamicibacter mysorens Busse 2016 are Later Heterotypic Synonyms of Arthrobacter nicotianae Giovannozzi-Sermanni 1959 (Approved Lists 1980) and Glutamicibacter nicotianae Busse 2016.Deb S, Das L, Das SKCurr Microbiol10.1007/s00284-020-02176-z2020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids, Micrococcaceae, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4824Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12798)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12798
18370Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12798.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
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
37402Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14433
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/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
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
77026Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8180.1StrainInfo: A central database for resolving microbial strain identifiers
121215Curators of the CIPCollection of Institut Pasteur (CIP 102716)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102716