Desulfogranum marinum (DSM 2058, JCM 13489, 3pr10)

Name: Desulfogranum marinum (DSM 2058, JCM 13489, 3pr10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4017

Type strain

Strain Designation 3pr10

Culture col. no. DSM 2058 JCM 13489 3pr10

NCBI tax ID(s) 453220

Special Collections DSMZ JCM

History DSMZ <- F. Widdel, Universität Konstanz, Fakultät für Biologie, Konstanz, Germany; 3pr10 <- F. Widdel {1977} JCM <-- DSM 2058 <-- F. Widdel 3pr10.

Links

Desulfogranum marinum 3pr10 is an anaerobe bacterium that was isolated from marine mud.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 47541

DSM 2058,JCM 13489

@ref 20215

Last LPSN update 2026-05-29 08:25:50

Domain Bacteria

Phylum Thermodesulfobacteriota

Class Desulfobulbia

Order Desulfobulbales

Family Desulfobulbaceae

Genus Desulfogranum

Species Desulfogranum marinum

Full scientific name Desulfogranum marinum (Kuever et al. 2013) Galushko and Kuever 2021

Synonyms (1)

Desulfobulbus marinus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.181
125438	negative	97.422

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
694	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)
694	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

694

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.931

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
694	marine mud	North Sea, Jadebusen	Germany	DEU	Europe
67770	Anaerobic mud flat of the Jadebusen	North Sea

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
694	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	ASM1691856v1 assembly for Desulfogranum marinum DSM 2058	contig	GCA_016918565	453220.3	3000687053	453220	29.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
694	Desulfobulbus marinus strain 3pr10 16S ribosomal RNA gene, partial sequence	M34411	1373		453220

GC content

@ref	GC-content (mol%)	Method
67770	47.3
694	47.3	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: ASM1691856v1 assembly for Desulfogranum marinum DSM 2058
BV-BRC: 453220.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	61.01	no
125439	gram_stain	BacteriaNetⓘ	negative	98.18	no
125439	motility	BacteriaNetⓘ	yes	65.68	no
125439	spore_formation	BacteriaNetⓘ	no	99.93	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfobulbus marinus strain DSM 2058
PATRIC: 453220.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.42	no
125438	anaerobic	anaerobicⓘ	yes	75.88	yes
125438	spore-forming	spore-formingⓘ	no	79.36	no
125438	aerobic	aerobicⓘ	no	75.49	yes
125438	thermophilic	thermophileⓘ	no	89.70	yes
125438	flagellated	motile2+ⓘ	yes	79.54	no

Literature

References

#694	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2058
#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 )
#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) .
#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 )

Rate our new design

Content

About us