Strain identifier

BacDive ID: 80

Type strain: Yes

Species: Granulibacter bethesdensis

Strain Designation: CGDNIH1

Strain history: <- P. R. Murray, Natl. Inst. Health (NIH), US Dept. Health and Human Services, Bethesda; CGDNIH1

NCBI tax ID(s): 364410 (species)

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General

@ref: 7145

BacDive-ID: 80

DSM-Number: 17861

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, coccus-shaped, pigmented, human pathogen

description: Granulibacter bethesdensis CGDNIH1 is an obligate aerobe, mesophilic, Gram-negative human pathogen that has a yellow pigmentation and was isolated from lymph node cultures from a chronic granulomatous disease patient.

NCBI tax id

  • NCBI tax id: 364410
  • Matching level: species

strain history

  • @ref: 7145
  • history: <- P. R. Murray, Natl. Inst. Health (NIH), US Dept. Health and Human Services, Bethesda; CGDNIH1

doi: 10.13145/bacdive80.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Granulibacter
  • species: Granulibacter bethesdensis
  • full scientific name: Granulibacter bethesdensis Greenberg et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Granulobacter bethesdensis

@ref: 7145

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Granulibacter

species: Granulibacter bethesdensis

full scientific name: Granulibacter bethesdensis Greenberg et al. 2006

strain designation: CGDNIH1

type strain: yes

Morphology

cell morphology

  • @ref: 22963
  • gram stain: negative
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 22963
  • medium used: modifed glucose-yeast extract-CaCO3 Acetobacter medium

pigmentation

  • @ref: 22963
  • production: yes
  • color: yellow

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7145GRANULIBACTER MEDIUM (DSMZ Medium 1186)yeshttps://mediadive.dsmz.de/medium/1186Name: GRANULIBACTER MEDIUM (DSMZ Medium 1186) Composition: Glucose 50.0 g/l Agar 15.0 g/l CaCO3 12.5 g/l Yeast extract 5.0 g/l Distilled water
22963glutamate agaryes
22963mannitol agaryes
22963modified glucose-yeast extract-CaCO3 Acetobacter mediumyesglucose 50.0;CaCO3 12.5; autolysed yeast 5.0 and agar 15.0 ( g l -1)

culture temp

@refgrowthtypetemperaturerange
7145positivegrowth35mesophilic
22963positiveoptimum35.0-37.0mesophilic

culture pH

  • @ref: 22963
  • ability: positive
  • type: optimum
  • pH: 5.0-6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 22963
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2296316813galactitol-builds acid from
2296317716lactose-builds acid from
2296317306maltose-builds acid from
2296329864mannitol-builds acid from
2296330911sorbitol-builds acid from
2296317992sucrose-builds acid from
2296318222xylose-builds acid from
2296316236ethanol+builds acid from
2296317234glucose+builds acid from
2296317790methanol+carbon source
2296317234glucose+growth
2296330089acetate+oxidation
2296324996lactate+oxidation
2296317754glycerol+/-builds acid from

metabolite production

  • @ref: 22963
  • Chebi-ID: 16016
  • metabolite: dihydroxyacetone
  • production: no

enzymes

@refvalueactivityec
22963catalase+1.11.1.6
22963cytochrome oxidase-1.9.3.1
22963urease+/-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7145lymph node cultures from a chronic granulomatous disease patientMaryland, BethesdaUSAUSANorth America
22963three patients with chronic granulomatous disease

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Lymph node
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_65.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_52;97_55;98_60;99_65&stattab=map
  • Last taxonomy: Granulibacter bethesdensis subclade
  • 16S sequence: AY788950
  • Sequence Identity:
  • Total samples: 6573
  • soil counts: 3219
  • aquatic counts: 1723
  • animal counts: 677
  • plant counts: 954

Safety information

risk assessment

  • @ref: 7145
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7145
  • description: Granulibacter bethesdensis CGDNIH1 16S ribosomal RNA gene, partial sequence
  • accession: AY788950
  • length: 1491
  • database: ena
  • NCBI tax ID: 391165

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Granulibacter bethesdensis CGDNIH1GCA_000014285completencbi391165
66792Granulibacter bethesdensis CGDNIH1391165.9completepatric391165
66792Granulibacter bethesdensis CGDNIH1637000123completeimg391165

GC content

  • @ref: 7145
  • GC-content: 59.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.755no
motileno89.755no
flagellatedno96.057yes
flagellatedno96.057yes
gram-positiveno98.325no
gram-positiveno98.325no
anaerobicno97.328yes
anaerobicno97.328yes
halophileno91.195no
halophileno91.195no
spore-formingno93.984no
spore-formingno93.984no
thermophileno89.3yes
glucose-utilyes87.901yes
glucose-utilyes87.901yes
aerobicyes74.845yes
aerobicyes74.845yes
thermophileno89.3yes
glucose-fermentno88.968no
glucose-fermentno88.968no

External links

@ref: 7145

culture collection no.: DSM 17861, ATCC BAA 1260

straininfo link

  • @ref: 69763
  • straininfo: 292928

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17082400Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae.Greenberg DE, Porcella SF, Stock F, Wong A, Conville PS, Murray PR, Holland SM, Zelazny AMInt J Syst Evol Microbiol10.1099/ijs.0.64412-02006Acetates/metabolism, Acetobacteraceae/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA, Ribosomal Spacer, Ethanol/metabolism, Fatty Acids/analysis/chemistry, Genes, rRNA, Granulomatous Disease, Chronic/*microbiology, Humans, Hydrogen-Ion Concentration, Lactic Acid/metabolism, Methanol/metabolism, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Sequence Analysis, DNA, Temperature, United StatesMetabolism
Phylogeny23002052Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil.Ramirez-Bahena MH, Tejedor C, Martin I, Velazquez E, Peix AInt J Syst Evol Microbiol10.1099/ijs.0.041368-02012Acetobacteraceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/analysis, Medicago sativa/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Spain, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7145Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17861)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17861
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
22963David E. Greenberg,Stephen F. Porcella,Frida Stock,Alexandra Wong,Patricia S. Conville,Patrick R. Murray,Steven M. Holland, Adrian M. Zelazny10.1099/ijs.0.64412-0Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family AcetobacteraceaeIJSEM 56: 2609-2616 200617082400
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)
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
69763Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292928.1StrainInfo: A central database for resolving microbial strain identifiers