Strain identifier

BacDive ID: 7534

Type strain: Yes

Species: Glutamicibacter protophormiae

Strain Designation: M-570

Strain history: CIP <- 2001, JCM <- ATCC <- CCEB <- O. Lysenko: strain M-570

NCBI tax ID(s): 37930 (species)

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General

@ref: 8599

BacDive-ID: 7534

DSM-Number: 20168

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

description: Glutamicibacter protophormiae M-570 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from fly .

NCBI tax id

  • NCBI tax id: 37930
  • Matching level: species

strain history

@refhistory
8599<- ATCC <- CCEB <- O. Lysenko, M-570
67770ATCC 19271 <-- CCEB 282 <-- O. Lysenko M-570.
121974CIP <- 2001, JCM <- ATCC <- CCEB <- O. Lysenko: strain M-570

doi: 10.13145/bacdive7534.20230509.8.1

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 protophormiae
  • full scientific name: Glutamicibacter protophormiae (Lysenko 1959) Busse 2016

  • synonyms

    @refsynonym
    20215Brevibacterium protophormiae
    20215Arthrobacter protophormiae

@ref: 8599

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Glutamicibacter

species: Glutamicibacter protophormiae

full scientific name: Glutamicibacter protophormiae (Lysenko 1959) Busse 2016

strain designation: M-570

type strain: yes

Morphology

cell morphology

  • @ref: 121974
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 121974
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41924MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
8599CORYNEBACTERIUM 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
121974CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8599positivegrowth30mesophilic
41924positivegrowth30mesophilic
67770positivegrowth30mesophilic
121974positivegrowth10-37
121974nogrowth41thermophilic
121974nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121974
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 121974
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 8599
  • 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
12197416947citrate+carbon source
1219744853esculin-hydrolysis
121974606565hippurate+hydrolysis
12197417632nitrate+reduction
12197416301nitrite-reduction
12197417632nitrate-respiration

antibiotic resistance

  • @ref: 121974
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121974
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12197415688acetoin-
12197417234glucose-

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
121974oxidase-
121974beta-galactosidase-3.2.1.23
121974alcohol dehydrogenase-1.1.1.1
121974gelatinase+/-
121974amylase-
121974DNase+
121974caseinase-3.4.21.50
121974catalase+1.11.1.6
121974tween esterase-
121974gamma-glutamyltransferase+2.3.2.2
121974lecithinase-
121974lipase-
121974lysine decarboxylase-4.1.1.18
121974ornithine decarboxylase-4.1.1.17
121974phenylalanine ammonia-lyase-4.3.1.24
121974tryptophan deaminase-
121974urease-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
121974-+++-++++-++---+--+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121974++-------++----+---+-----------+----------------+++--+---+-++++-+---+---+--+---++--+--+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountrycontinent
8599fly (Protophormia terraenovae)Protophormia terraenovae
67770Fly (Protophormia terrae-novae)Protophormia terrae-novaeCzechoslovakiaEurope
121974Fly, Protophormia terraenovae

isolation source categories

  • Cat1: #Host
  • Cat2: #Arthropoda
  • Cat3: #Insecta

taxonmaps

  • @ref: 69479
  • File name: preview.99_53066.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1446;97_1726;98_2111;99_53066&stattab=map
  • Last taxonomy: Glutamicibacter
  • 16S sequence: X80745
  • Sequence Identity:
  • Total samples: 77
  • soil counts: 33
  • aquatic counts: 1
  • animal counts: 39
  • plant counts: 4

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85991Risk group (German classification)
1219741Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: A.protophormiae 16S rDNA
  • accession: X80745
  • length: 1473
  • database: ena
  • NCBI tax ID: 37930

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Glutamicibacter protophormiae DSM 20168GCA_017876615contigncbi37930
66792Glutamicibacter protophormiae JCM 1973GCA_014647495contigncbi37930
66792Glutamicibacter protophormiae strain DSM 2016837930.6wgspatric37930
66792Glutamicibacter protophormiae strain JCM 197337930.4wgspatric37930
66792Glutamicibacter protophormiae DSM 201682918390780draftimg37930

GC content

@refGC-contentmethod
859963.2
6777064.2thermal denaturation, midpoint method (Tm)
6777063.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes92.915no
anaerobicno99.41no
halophileno57.755no
spore-formingno89.777no
glucose-utilyes85.592no
aerobicyes96.063no
motileno94.346no
flagellatedno97.282no
thermophileno98.266yes
glucose-fermentno91.28no

External links

@ref: 8599

culture collection no.: DSM 20168, ATCC 19271, CCEB 282, CIP 106987, JCM 1973, LMG 16324, NBRC 12128, VKM Ac-2104, BCRC 12118, CCM 4749, CGMCC 1.1921, IFO 12128, KACC 10933, KCTC 3385, NCIMB 12765, CCRC 12118

straininfo link

  • @ref: 76979
  • straininfo: 248454

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18337691Arthrobacter soli sp. nov., a novel bacterium isolated from wastewater reservoir sediment.Roh SW, Sung Y, Nam YD, Chang HW, Kim KH, Yoon JH, Jeon CO, Oh HM, Bae JWJ Microbiol10.1007/s12275-007-0239-82008Arthrobacter/classification/genetics/*isolation & purification/physiology, Base Composition, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Waste Disposal, FluidGenetics
Enzymology25345021[Characterization of D-amino acid oxidase and its mutants from Arthrobacter protophormiae].Feng L, Guo J, Li H, Xu S, Ju J, Zhao BWei Sheng Wu Xue Bao2014Arthrobacter/chemistry/*enzymology/genetics, Bacterial Proteins/*chemistry/genetics/isolation & purification/*metabolism, Cloning, Molecular, D-Amino-Acid Oxidase/*chemistry/genetics/isolation & purification/*metabolism, Enzyme Stability, Kinetics, Molecular Sequence Data, Mutation, Substrate SpecificityPhylogeny
Metabolism32571193Two Glycosyl 1-Phosphate Polymers and Teichulosonic Acid from Glutamicibacter protophormiae VKM Ac-2104(T) Cell Wall.Shashkov AS, Tul'skaya EM, Dorofeeva LV, Evtushenko LI, Potekhina NVBiochemistry (Mosc)10.1134/S00062979200501202020Cell Wall/chemistry/*metabolism, Glucosephosphates/chemistry/*metabolism, Magnetic Resonance Spectroscopy/*methods, Micrococcaceae/*metabolism, Polymers/*chemistry, Polysaccharides, Bacterial/chemistry/*metabolism, Teichoic Acids/chemistry/*metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8599Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20168)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20168
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
41924Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19178
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
76979Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID248454.1StrainInfo: A central database for resolving microbial strain identifiers
121974Curators of the CIPCollection of Institut Pasteur (CIP 106987)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106987