Strain identifier

BacDive ID: 7566

Type strain: Yes

Species: Paeniglutamicibacter sulfureus

Strain Designation: 8-3

Strain history: CIP <- 2001, JCM <- IAM <- H. Iizuka and K. Komagata: strain 8-3

NCBI tax ID(s): 43666 (species)

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General

@ref: 8598

BacDive-ID: 7566

DSM-Number: 20167

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

description: Paeniglutamicibacter sulfureus 8-3 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from oil brine.

NCBI tax id

  • NCBI tax id: 43666
  • Matching level: species

strain history

@refhistory
8598<- ATCC <- K. Komagata, 8-3 (Brevibacterium sulfureum)
67770IAM 1488 <-- H. Iizuka and K. Komagata 8-3.
123385CIP <- 2001, JCM <- IAM <- H. Iizuka and K. Komagata: strain 8-3

doi: 10.13145/bacdive7566.20230509.8.1

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 sulfureus
  • full scientific name: Paeniglutamicibacter sulfureus (Stackebrandt et al. 1984) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter sulfureus

@ref: 8598

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Paeniglutamicibacter

species: Paeniglutamicibacter sulfureus

full scientific name: Paeniglutamicibacter sulfureus (Stackebrandt et al. 1984) Busse 2016

strain designation: 8-3

type strain: yes

Morphology

cell morphology

  • @ref: 123385
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refcolony colorincubation periodmedium used
18427Lemon yellow (1012)10-14 daysISP 2
18427Zinc yellow (1018)10-14 daysISP 3
18427Ivory (1014)10-14 daysISP 4
18427Golden yellow (1004)10-14 daysISP 6
18427Sand yellow (1002)10-14 daysISP 7
123385

multicellular morphology

@refforms multicellular complexmedium name
18427noISP 2
18427noISP 3
18427noISP 4
18427
18427noISP 6
18427noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18427ISP 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
18427ISP 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:
18427ISP 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
18427ISP 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
18427ISP 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
41919MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
8598CORYNEBACTERIUM 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
123385CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18427positiveoptimum28mesophilic
8598positivegrowth30mesophilic
41919positivegrowth30mesophilic
67770positivegrowth30mesophilic
123385positivegrowth10-30
123385nogrowth37mesophilic
123385nogrowth41thermophilic
123385nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123385
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
18427NaClpositivemaximum7.5 %
123385NaClpositivegrowth0-10 %

murein

  • @ref: 8598
  • murein short key: A11.54
  • type: A4alpha L-Lys-L-Glu

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1842717234glucose+
1842722599arabinose+
1842717992sucrose+
1842718222xylose+
1842717268myo-inositol+
1842729864mannitol+
1842728757fructose+
1842726546rhamnose+
1842716634raffinose-
1842762968cellulose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
12338516947citrate-carbon source
1233854853esculin-hydrolysis
123385606565hippurate+hydrolysis
12338517632nitrate-reduction
12338516301nitrite-reduction
12338517632nitrate-respiration
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

antibiotic resistance

  • @ref: 123385
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12338535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12338515688acetoin-
12338517234glucose-

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+
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)+
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
68368beta-galactosidase+3.2.1.23
123385oxidase+
123385beta-galactosidase+3.2.1.23
123385alcohol dehydrogenase-1.1.1.1
123385gelatinase-
123385amylase-
123385DNase-
123385caseinase-3.4.21.50
123385catalase+1.11.1.6
123385tween esterase-
123385gamma-glutamyltransferase-2.3.2.2
123385lysine decarboxylase-4.1.1.18
123385ornithine decarboxylase-4.1.1.17
123385phenylalanine ammonia-lyase-4.3.1.24
123385tryptophan deaminase-
123385urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18427--+-++++-++---+--+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18427+-+-++++-++---+----
123385++++++++--+---+-----

API 20E

@refONPGLDC LysODCCITH2SURETDA TrpINDVPGEL
18427+----+--+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123385++-+++++-++----+--++------+-+---++-+--+------+---+-+-++--+--+++++-++++-++--+-+-++-----+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
8598oil brine
67770Oil-brine in Yabase oil-field in Akita Pref.JapanJPNAsia
123385Oil-brine in Yabase oil-fieldJapanJPNAsiaAkita

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination#Oil (Fuel)
#Condition#Saline
#Engineered#Food production#Oil (Food)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2676.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_158;97_169;98_188;99_2676&stattab=map
  • Last taxonomy: Paeniglutamicibacter
  • 16S sequence: X83409
  • Sequence Identity:
  • Total samples: 5511
  • soil counts: 2567
  • aquatic counts: 767
  • animal counts: 1632
  • plant counts: 545

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184271
85981Risk group (German classification)
1233851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8598
  • description: A.sulfureus 16S rRNA gene
  • accession: X83409
  • length: 1478
  • database: ena
  • NCBI tax ID: 43666

Genome sequences

  • @ref: 66792
  • description: Paeniglutamicibacter sulfureus DSM 20167
  • accession: 2923482298
  • assembly level: draft
  • database: img
  • NCBI tax ID: 43666

GC content

@refGC-contentmethod
859862.2
6777062.2thermal denaturation, midpoint method (Tm)

External links

@ref: 8598

culture collection no.: DSM 20167, ATCC 19098, NCIB 10355, JCM 1338, CGMCC 1.1898, CIP 106986, IAM 1488, IFO 12678, IMSNU 20369, KCTC 3196, LMG 16694, MTCC 1528, NBRC 12678, NCDO 2403, NCIMB 10355, NRRL B-14730

straininfo link

  • @ref: 77011
  • straininfo: 8190

literature

  • topic: Phylogeny
  • Pubmed-ID: 33555249
  • title: Paeniglutamicibacter terrestris sp. nov., isolated from phenanthrene-degrading consortium enriched from Antarctic soil.
  • authors: Sakdapetsiri C, Kuntaveesuk A, Ngaemthao W, Suriyachadkun C, Muangchinda C, Chavanich S, Viyakarn V, Chen B, Pinyakong O
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004689
  • year: 2021

Reference

@idauthorscataloguedoi/urltitle
8598Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20167)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20167
18427Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20167.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
41919Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19176
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
77011Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8190.1StrainInfo: A central database for resolving microbial strain identifiers
123385Curators of the CIPCollection of Institut Pasteur (CIP 106986)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106986