Desulfogranum japonicum (DSM 18378, JCM 14043, Pro1)

Name: Desulfogranum japonicum (DSM 18378, JCM 14043, Pro1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4015

Type strain

Strain Designation Pro1

Culture col. no. DSM 18378 JCM 14043 Pro1

NCBI tax ID(s) 1121403 231447

Special Collections DSMZ JCM Literature strains

History <- A. Ueki, Yamagata Univ., Tsuruoka, Japan; Pro1 <- A. Ueki; {1999} A. Ueki Pro1.

Links

Desulfogranum japonicum Pro1 is an anaerobe, Gram-negative, motile bacterium that was isolated from estuarine sediment.

Gram-negative motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 302753

DSM 18378,JCM 14043

@ref 20215

Last LPSN update 2026-02-09 11:18:37

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfobulbia

Order Desulfobulbales

Family Desulfobulbaceae

Genus Desulfogranum

Species Desulfogranum japonicum

Full scientific name Desulfogranum japonicum (Suzuki et al. 2007) Galushko and Kuever 2021

Synonyms (1)

Desulfobulbus japonicus

BacDive ID	Other strains from **Desulfogranum japonicum** (1)	Type strain
4016	D. japonicum Pro16, DSM 18379, JCM 14044

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32038	negative	2.15 µm	1.2 µm	rod-shaped
125438	negative				97.422
125439	negative				99.6

Pigmentation

32038

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7362	DESULFOBULBUS SP. MEDIUM (MARINE) (DSMZ Medium 195b)		Medium recipe at MediaDive	Name: DESULFOBULBUS SP. MEDIUM (MARINE) (DSMZ Medium 195b) Composition: NaCl 20.9372 g/l Na2SO4 2.99103 g/l MgCl2 x 6 H2O 2.99103 g/l Na2CO3 1.49551 g/l Na-propionate 1.49551 g/l KCl 0.498504 g/l Na2S x 9 H2O 0.398804 g/l NH4Cl 0.299103 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l NaOH 0.000498504 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7362	positive	growth	35
32038	positive	growth	15-35
32038	positive	optimum	35
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
32038	positive	optimum	6.7
32038	positive	growth	6.1-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7362	anaerobe
32038	anaerobe

Spore formation

@ref	Spore formation	Confidence
32038
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32038	NaCl	positive	growth	01-07 %
32038	NaCl	positive	optimum	3 %

Observation

67770

Observationquinones: MK-5(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32038	16449 ChEBI	alanine	+	carbon source
32038	28885 ChEBI	butanol	+	carbon source
32038	16236 ChEBI	ethanol	+	carbon source
32038	15740 ChEBI	formate	+	carbon source
32038	28757 ChEBI	fructose	+	carbon source
32038	17234 ChEBI	glucose	+	carbon source
32038	17754 ChEBI	glycerol	+	carbon source
32038	24996 ChEBI	lactate	+	carbon source
32038	25115 ChEBI	malate	+	carbon source
32038	17272 ChEBI	propionate	+	carbon source
32038	15361 ChEBI	pyruvate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Brackish

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7362	estuarine sediment	Yamagata	Japan	JPN	Asia
67770	Estuarine sediment in the Sea of Japan of the Japanese Islands

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7362	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
67770	ASM42994v1 assembly for Desulfogranum japonicum DSM 18378	scaffold	GCA_000429945	1121403.3	2524614762	1121403	49.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7362	Desulfobulbus japonicus gene for 16S ribosomal RNA, partial sequence, strain: Pro1 (= JCM 14043, = DSM 18378)	AB110549	1485		231447

GC content

@ref	GC-content (mol%)	Method
7362	48.6
67770	48.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfogranum japonicum DSM 18378
NCBI: GCA_000429945

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	54.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	motility	BacteriaNetⓘ	yes	65.00	no
125439	spore_formation	BacteriaNetⓘ	no	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfobulbus japonicus DSM 18378
PATRIC: 1121403.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.42	yes
125438	anaerobic	anaerobicⓘ	yes	68.04	yes
125438	spore-forming	spore-formingⓘ	no	81.63	yes
125438	aerobic	aerobicⓘ	no	76.88	yes
125438	thermophilic	thermophileⓘ	no	91.96	no
125438	flagellated	motile2+ⓘ	yes	81.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development.	Kuhl M, Ruckert C, Glaser L, Beganovic S, Luzhetskyy A, Kalinowski J, Wittmann C.	Biotechnol Bioeng	10.1002/bit.27818	2021
Enzymology	"Candidatus Desulfobulbus rimicarensis," an Uncultivated Deltaproteobacterial Epibiont from the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata.	Jiang L, Liu X, Dong C, Huang Z, Cambon-Bonavita MA, Alain K, Gu L, Wang S, Shao Z.	Appl Environ Microbiol	10.1128/aem.02549-19	2020
	Ecophysiological Features Shape the Distribution of Prophages and CRISPR in Sulfate Reducing Prokaryotes.	Orellana R, Arancibia A, Badilla L, Acosta J, Arancibia G, Escar R, Ferrada G, Seeger M.	Microorganisms	10.3390/microorganisms9050931	2021
Phylogeny	Desulfobulbus japonicus sp. nov., a novel Gram-negative propionate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan.	Suzuki D, Ueki A, Amaishi A, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.64855-0	2007

References

#7362	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18378
#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 )
#28288	IJSEM 849 2007 ( DOI 10.1099/ijs.0.64855-0 , PubMed 17392218 )
#32038	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28288
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Desulfogranum japonicum (DSM 18378, JCM 14043, Pro1)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000429945

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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