Strain identifier

BacDive ID: 7610

Type strain: Yes

Species: Paeniglutamicibacter gangotriensis

Strain Designation: Lz1y

Strain history: CIP <- 2005, JCM <- S. Shivaji: strain Lz1y

NCBI tax ID(s): 254787 (species)

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General

@ref: 6108

BacDive-ID: 7610

DSM-Number: 15796

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

description: Paeniglutamicibacter gangotriensis Lz1y is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 254787
  • Matching level: species

strain history

@refhistory
6108<- S. Shivaji; LZ1Y
67770S. Shivaji strain Lz1y.
119532CIP <- 2005, JCM <- S. Shivaji: strain Lz1y

doi: 10.13145/bacdive7610.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Paeniglutamicibacter
  • species: Paeniglutamicibacter gangotriensis
  • full scientific name: Paeniglutamicibacter gangotriensis (Gupta et al. 2004) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter gangotriensis

@ref: 6108

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Paeniglutamicibacter

species: Paeniglutamicibacter gangotriensis

full scientific name: Paeniglutamicibacter gangotriensis (Gupta et al. 2004) Busse 2016 emend. Nouioui et al. 2018

strain designation: Lz1y

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31239positiverod-shapedno
119532positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18396Zinc yellow (1018)10-14 daysISP 2
18396Zinc yellow (1018)10-14 daysISP 3
18396Zinc yellow (1018)10-14 daysISP 4
18396Zinc yellow (1018)10-14 daysISP 5
18396Zinc yellow (1018)10-14 daysISP 6
18396Zinc yellow (1018)10-14 daysISP 7
119532

multicellular morphology

@refforms multicellular complexmedium name
18396noISP 2
18396noISP 3
18396noISP 4
18396noISP 5
18396noISP 6
18396noISP 7

pigmentation

  • @ref: 31239
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6108TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18396ISP 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
18396ISP 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:
18396ISP 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
18396ISP 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
18396ISP 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
18396ISP 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
37307MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119532CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119532CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
18396positiveoptimum28mesophilic
6108positivegrowth22psychrophilic
31239positivegrowth04-30
31239positiveoptimum22psychrophilic
37307positivegrowth22psychrophilic
67770positivegrowth22psychrophilic
119532positivegrowth10-30
119532nogrowth37mesophilic
119532nogrowth41thermophilic
119532nogrowth45thermophilic

culture pH

  • @ref: 31239
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31239aerobe
119532obligate aerobe

spore formation

  • @ref: 31239
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
119532NaClpositivegrowth0-2 %
119532NaClnogrowth4 %
119532NaClnogrowth6 %
119532NaClnogrowth8 %
119532NaClnogrowth10 %

murein

  • @ref: 6108
  • murein short key: A11.33
  • type: A4alpha L-Lys-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10, MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1839617234glucose+
1839622599arabinose+/-
1839617992sucrose+
1839618222xylose-
1839617268myo-inositol-
1839629864mannitol+
1839628757fructose+
1839626546rhamnose-
1839616634raffinose-
1839662968cellulose+/-
3123915963ribitol+carbon source
3123922599arabinose+carbon source
3123929016arginine+carbon source
3123922653asparagine+carbon source
3123917057cellobiose+carbon source
3123928757fructose+carbon source
3123928260galactose+carbon source
3123917234glucose+carbon source
3123915428glycine+carbon source
3123917716lactose+carbon source
3123917306maltose+carbon source
3123937684mannose+carbon source
3123928053melibiose+carbon source
3123928044phenylalanine+carbon source
3123915361pyruvate+carbon source
3123933942ribose+carbon source
3123930911sorbitol+carbon source
3123917992sucrose+carbon source
3123917151xylitol+carbon source
3123918222xylose+carbon source
119532606565hippurate-hydrolysis
11953217632nitrate+reduction
11953216301nitrite-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose+fermentation

metabolite production

  • @ref: 119532
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11953215688acetoin-
11953217234glucose-

enzymes

@refvalueactivityec
31239catalase+1.11.1.6
31239gelatinase+
31239cytochrome oxidase+1.9.3.1
31239urease+3.5.1.5
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
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
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
119532oxidase+
119532beta-galactosidase-3.2.1.23
119532alcohol dehydrogenase-1.1.1.1
119532gelatinase+
119532amylase-
119532DNase-
119532caseinase+3.4.21.50
119532catalase+1.11.1.6
119532tween esterase-
119532gamma-glutamyltransferase-2.3.2.2
119532lecithinase-
119532lipase-
119532lysine decarboxylase-4.1.1.18
119532ornithine decarboxylase-4.1.1.17
119532phenylalanine ammonia-lyase-4.3.1.24
119532tryptophan deaminase-
119532urease+3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18396+++--+--+++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18396+++-++++-+----+--+-
119532++++++++-++---+--+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119532++--+----++----+---------------+-+---------------+---+---++-+++++-+-++-++--+--+++-++------+++++-++-

Isolation, sampling and environmental information

isolation

@refsample typecontinentgeographic locationcountryorigin.country
6108soilAustralia and Oceania
67770Penguin rookery soilAntarcticaDakshin GangotriAntarcticaATA
119532Environment, Soil, Penguin rookeryAntarcticaDakshin GangotriAntarcticaATA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61081Risk group (German classification)
183961
1195321Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6108
  • description: Arthrobacter gangotriensis 16S rRNA gene, type strain Lz1Y
  • accession: AJ606061
  • length: 1454
  • database: ena
  • NCBI tax ID: 1276920

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paeniglutamicibacter gangotriensis Lz1y2537561926draftimg1276920
67770Paeniglutamicibacter gangotriensis Lz1yGCA_000348945contigncbi1276920

GC content

@refGC-contentmethod
610864-66
3123966
6777063genome sequence analysis
6777058
6777063.9genome sequence analysis

External links

@ref: 6108

culture collection no.: DSM 15796, JCM 12166, CIP 108630

straininfo link

  • @ref: 77054
  • straininfo: 134411

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545486
  • title: Arthrobacter gangotriensis sp. nov. and Arthrobacter kerguelensis sp. nov. from Antarctica.
  • authors: Gupta P, Reddy GSN, Delille D, Shivaji S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63110-0
  • year: 2004
  • mesh: Antarctic Regions, Arthrobacter/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/chemistry/isolation & purification, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry/isolation & purification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis/chemistry/isolation & purification, Water Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6108Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15796)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15796
18396Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15796.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
31239Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2756328776041
37307Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6280
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
77054Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134411.1StrainInfo: A central database for resolving microbial strain identifiers
119532Curators of the CIPCollection of Institut Pasteur (CIP 108630)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108630