Strain identifier

BacDive ID: 7524

Type strain: Yes

Species: Glutamicibacter nicotianae

Strain Designation: 94

Strain history: CIP <- 1982, ATCC <- G. Giovannozzi-Sermanni: strain 9-4

NCBI tax ID(s): 37929 (species)

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General

@ref: 8548

BacDive-ID: 7524

DSM-Number: 20123

keywords: genome sequence, 16S sequence, Bacteria, aerobe

description: Glutamicibacter nicotianae 94 is an aerobe bacterium that was isolated from Air of tobacco warehouses.

NCBI tax id

  • NCBI tax id: 37929
  • Matching level: species

strain history

@refhistory
8548<- ATCC <- G. Giovannozzi-Sermanni, 94
67770IAM 12342 <-- CCM 1648 <-- MRI <-- G. Giovannozzi-Sermanni.
121292CIP <- 1982, ATCC <- G. Giovannozzi-Sermanni: strain 9-4

doi: 10.13145/bacdive7524.20240916.9.1

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: 8548

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

strain designation: 94

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive93.847
6948092.1no

colony morphology

@refcolony colorincubation periodmedium used
18623Colorless10-14 daysISP 2
18623Colorless10-14 daysISP 3
18623Ivory (1014)10-14 daysISP 4
18623Colorless10-14 daysISP 5
18623Ivory (1014)10-14 daysISP 6
18623Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18623noISP 2
18623noISP 3
18623noISP 4
18623noISP 5
18623noISP 6
18623noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18623ISP 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
18623ISP 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:
18623ISP 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
18623ISP 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
18623ISP 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
18623ISP 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
41912MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8548CORYNEBACTERIUM 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
121292CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
18623positiveoptimum28
8548positivegrowth30
41912positivegrowth30
47855positivegrowth26
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 47855
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

murein

  • @ref: 8548
  • 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
683794853esculin-hydrolysis
6837916199urea-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

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
68379catalase+1.11.1.6
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
68379pyrrolidonyl arylamidase+3.4.19.3

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
18623--+---+---+------+-
47855++++--+------------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18623+-++++++-++---+--++

Isolation, sampling and environmental information

isolation

@refsample type
67770Air of tobacco warehouses
121292Environment, Air contaminant of tobacco warehouse

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: X80739
  • 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
186231Hazard group
85481Risk group (German classification)
1212921Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Arthrobacter nicotianae partial 16S rRNA gene, type strain CIP 82.107TAM411118174nuccore37929
20218A.nicotianae 16S rDNAX807391472nuccore37929

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glutamicibacter nicotianae strain NBRC 1423437929.5wgspatric37929
67770Glutamicibacter nicotianae NBRC 14234GCA_006539525contigncbi37929

GC content

@refGC-contentmethod
854860.2
6777064Buoyant density centrifugation (BD)
6777060.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes93.847no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.72yes
69480spore-formingspore-formingAbility to form endo- or exosporesno72.666no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.356no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno92.1no

External links

@ref: 8548

culture collection no.: CCUG 23842, DSM 20123, ATCC 15236, CCM 1648, NCIB 9458, JCM 1333, BCRC 11219, CDA 883, CGMCC 1.1895, CIP 82.107, HAMBI 1859, IAM 12342, IFO 14234, IMET 10353, KCTC 3382, LMG 16305, MTCC 21, NBRC 14234, NCDO 2404, NCIMB 9458, NRIC 0153, VKM Ac-1113, VKM Ac-1127

straininfo link

  • @ref: 76969
  • straininfo: 10066

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
9352658Rapid physiological characterization of microorganisms by biosensor technique.Riedel K, Kunze GMicrobiol Res10.1016/S0944-5013(97)80033-X1997*Bacterial Physiological Phenomena, *Biosensing Techniques, Candida/*physiology, Kluyveromyces/*physiology, Pichia/*physiology
28056223Glutamicibacter 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/chemistryPhylogenyTranscriptome
32902704Phylogenomic 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, DNAPhylogenyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8548Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20123)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20123
18623Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20123.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
41912Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11384
47855Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23842)https://www.ccug.se/strain?id=23842
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/
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
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
76969Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10066.1StrainInfo: A central database for resolving microbial strain identifiers
121292Curators of the CIPCollection of Institut Pasteur (CIP 82.107)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2082.107