Granulibacter bethesdensis (DSM 17861, ATCC BAA-1260, CGDNIH1)

Name: Granulibacter bethesdensis (DSM 17861, ATCC BAA-1260, CGDNIH1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 80

Type strain

Strain Designation CGDNIH1

Culture col. no. DSM 17861 ATCC BAA-1260 CGDNIH1

NCBI tax ID(s) 364410

Special Collections DSMZ Literature strains

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

Links

Granulibacter bethesdensis CGDNIH1 is an obligate aerobe, Gram-negative, coccus-shaped bacterium that has a yellow pigmentation and was isolated from lymph node cultures from a chronic granulomatous disease patient.

Gram-negative coccus-shaped pigmented obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 292928

DSM 17861,ATCC BAA-1260,LMG 24392

@ref 20215

Last LPSN update 2026-05-29 08:24:56

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 (1)

"Granulobacter bethesdensis"

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
22963	negative	coccus-shaped
125438	negative		97.36
125439	negative		96.455

Colony morphology

22963

Medium usedmodifed glucose-yeast extract-CaCO3 Acetobacter medium

Pigmentation

@ref	Production	Color
22963		yellow

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7145	GRANULIBACTER MEDIUM (DSMZ Medium 1186)	Medium recipe at MediaDive	Name: 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
22963	glutamate agar
22963	mannitol agar
22963	modified glucose-yeast extract-CaCO3 Acetobacter medium		glucose 50.0;CaCO3 12.5; autolysed yeast 5.0 and agar 15.0 ( g l -1)

Culture temp

@ref	Growth	Type	Temperature (°C)
7145	positive	growth	35
22963	positive	optimum	35.0-37.0

Culture pH

@ref	Ability	Type	PH
22963	positive	optimum	5.0-6.5

Physiology and metabolism

Oxygen tolerance

22963

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.064
125439		99.62

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
22963	30089 ChEBI	acetate	+	oxidation
22963	16236 ChEBI	ethanol	+	builds acid from
22963	16813 ChEBI	galactitol	-	builds acid from
22963	17234 ChEBI	glucose	+	builds acid from
22963	17234 ChEBI	glucose	+	growth
22963	17754 ChEBI	glycerol	+/-	builds acid from
22963	24996 ChEBI	lactate	+	oxidation
22963	17716 ChEBI	lactose	-	builds acid from
22963	17306 ChEBI	maltose	-	builds acid from
22963	29864 ChEBI	mannitol	-	builds acid from
22963	17790 ChEBI	methanol	+	carbon source
22963	30911 ChEBI	sorbitol	-	builds acid from
22963	17992 ChEBI	sucrose	-	builds acid from
22963	18222 ChEBI	xylose	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
22963	16016 ChEBI	dihydroxyacetone

Enzymes

@ref	Value	Activity	Ec
22963	catalase	+	1.11.1.6
22963	cytochrome oxidase	-	1.9.3.1
22963	urease	+/-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Organ	#Lymph node
#Infection	#Patient	-

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
7145	lymph node cultures from a chronic granulomatous disease patient	Homo sapiens	Maryland, Bethesda	USA	USA	North America
22963	three patients with chronic granulomatous disease	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence AY788950 (>99% sequence identity) for Granulibacter bethesdensis subclade from Microbeatlas

Aquatic Samples	1723
Soil Samples	3219
Animal Samples	677
Plant Samples	954
Total Samples	6573

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
7145	yes, in single cases	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1428v2 assembly for Granulibacter bethesdensis CGDNIH1	complete	GCA_000014285	391165.9	637000123	391165	99.69

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7145	Granulibacter bethesdensis CGDNIH1 16S ribosomal RNA gene, partial sequence	AY788950	1491		391165

GC content

7145

GC-content (mol%)59.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1428v2 assembly for Granulibacter bethesdensis CGDNIH1
BV-BRC: 391165.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	70.30	no
125439	gram_stain	BacteriaNetⓘ	negative	96.46	no
125439	motility	BacteriaNetⓘ	yes	77.29	no
125439	spore_formation	BacteriaNetⓘ	no	99.62	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Granulibacter bethesdensis CGDNIH1 CGDNIH1
NCBI: GCA_000014285.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.36	yes
125438	anaerobic	anaerobicⓘ	no	92.43	yes
125438	aerobic	aerobicⓘ	yes	78.18	yes
125438	spore-forming	spore-formingⓘ	no	91.06	no
125438	thermophilic	thermophileⓘ	no	94.70	yes
125438	flagellated	motile2+ⓘ	no	68.24	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Serologic reactivity to the emerging pathogen Granulibacter bethesdensis.	Greenberg DE, Shoffner AR, Marshall-Batty KR, Arora K, Zhao M, Martin R, Ding L, Hammer CH, Shaw PA, Kuhns DB, Malech HL, Gallin JI, Zarember KA, Holland SM.	J Infect Dis	10.1093/infdis/jis431	2012
	Acidomonas methanolica-associated necrotizing lymphadenitis in a patient with chronic granulomatous disease.	Chase JM, Holland SM, Greenberg DE, Marshall-Batty K, Zelazny AM, Church JA.	J Clin Immunol	10.1007/s10875-012-9728-6	2012
Enzymology	The structure of allophanate hydrolase from Granulibacter bethesdensis provides insights into substrate specificity in the amidase signature family.	Lin Y, St Maurice M.	Biochemistry	10.1021/bi301242m	2013
	Innate immunity against Granulibacter bethesdensis, an emerging gram-negative bacterial pathogen.	Zarember KA, Marshall-Batty KR, Cruz AR, Chu J, Fenster ME, Shoffner AR, Rogge LS, Whitney AR, Czapiga M, Song HH, Shaw PA, Nagashima K, Malech HL, DeLeo FR, Holland SM, Gallin JI, Greenberg DE.	Infect Immun	10.1128/iai.05557-11	2012
Enzymology	The urea carboxylase and allophanate hydrolase activities of urea amidolyase are functionally independent.	Lin Y, Boese CJ, St Maurice M.	Protein Sci	10.1002/pro.2990	2016
Metabolism	IrrE, a global regulator of extreme radiation resistance in Deinococcus radiodurans, enhances salt tolerance in Escherichia coli and Brassica napus.	Pan J, Wang J, Zhou Z, Yan Y, Zhang W, Lu W, Ping S, Dai Q, Yuan M, Feng B, Hou X, Zhang Y, Ma R, Liu T, Feng L, Wang L, Chen M, Lin M.	PLoS One	10.1371/journal.pone.0004422	2009
Metabolism	Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.	Shen YQ, Bonnot F, Imsand EM, RoseFigura JM, Sjolander K, Klinman JP.	Biochemistry	10.1021/bi201763d	2012
Phylogeny	Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil.	Ramirez-Bahena MH, Tejedor C, Martin I, Velazquez E, Peix A	Int J Syst Evol Microbiol	10.1099/ijs.0.041368-0	2012
Phylogeny	Granulibacter 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 AM	Int J Syst Evol Microbiol	10.1099/ijs.0.64412-0	2006

References

#7145	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17861
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#22963	David E. Greenberg,Stephen F. Porcella,Frida Stock,Alexandra Wong,Patricia S. Conville,Patrick R. Murray,Steven M. Holland, Adrian M. Zelazny: Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae. IJSEM 56: 2609 - 2616 2006 ( DOI 10.1099/ijs.0.64412-0 , PubMed 17082400 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#69479	João 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.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Granulibacter bethesdensis (DSM 17861, ATCC BAA-1260, CGDNIH1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000014285

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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