Geomicrobium halophilum (DSM 21769, JCM 15647, BH1)

Name: Geomicrobium halophilum (DSM 21769, JCM 15647, BH1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18133

Type strain

Strain Designation BH1

Culture col. no. DSM 21769 JCM 15647 BH1

NCBI tax ID(s) 549000

Special Collections DSMZ JCM Literature strains

History <- A. Echigo, Toyo Univ., Bio-Nano Electronics Res. Ctr., Kawago, Saitama, Japan; BH1 A. Echigo BH1.

Links

Geomicrobium halophilum BH1 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from non-saline soil from a forest.

Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402467

JCM 15647,DSM 21769

@ref 20215

Last LPSN update 2026-02-09 11:22:23

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Geomicrobium

Species Geomicrobium halophilum

Full scientific name Geomicrobium halophilum Echigo et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29446	positive	1.1 µm	0.6 µm	rod-shaped

Pigmentation

29446

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15936	HALOBACTERIA MEDIUM (DSMZ Medium 372)		Medium recipe at MediaDive	Name: HALOBACTERIA MEDIUM (DSMZ Medium 372; with strain-specific modifications) Composition: NaCl 100.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15936	positive	growth	35	mesophilic
29446	positive	growth	20-40
29446	positive	optimum	30	mesophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29446	positive	optimum	8.75
29446	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

29446

Oxygen toleranceaerobe

Spore formation

29446

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29446	NaCl	positive	growth	05-25 %
29446	NaCl	positive	optimum	12.5 %

Observation

@ref	Observation
29446	aggregates in clumps
67770	quinones: MK-6, MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29446	17057 ChEBI	cellobiose	+	carbon source
29446	17754 ChEBI	glycerol	+	carbon source
29446	17716 ChEBI	lactose	+	carbon source
29446	29864 ChEBI	mannitol	+	carbon source
29446	16634 ChEBI	raffinose	+	carbon source
29446	30911 ChEBI	sorbitol	+	carbon source
29446	17992 ChEBI	sucrose	+	carbon source
29446	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29446	catalase	+	1.11.1.6
29446	cytochrome oxidase	+	1.9.3.1
29446	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15936	non-saline soil from a forest	Saitama Prefecture, Kawagoe City, Toyo University campus	Japan	JPN	Asia
67770	Forest soil	Kawagoe, Saitama Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB449106 (>99% sequence identity) for Geomicrobium halophilum subclade from Microbeatlas

Aquatic Samples	19
Soil Samples	26
Animal Samples	134
Plant Samples	8
Total Samples	187

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15936	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	ASM1420765v1 assembly for Geomicrobium halophilum DSM 21769	scaffold	GCA_014207655	549000.3	2861595016	549000	71.79

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15936	Geomicrobium halophilum gene for 16S rRNA, partial sequence	AB449106	1479		549000

GC content

@ref	GC-content (mol%)	Method
15936	45	high performance liquid chromatography (HPLC)
29446	45

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geomicrobium halophilum DSM 21769
NCBI: GCA_014207655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	75.80	no
125439	motility	BacteriaNetⓘ	yes	69.70	no
125439	gram_stain	BacteriaNetⓘ	variable	81.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	75.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Geomicrobium halophilum DSM 21769
NCBI: GCA_014207655.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.99	yes
125438	anaerobic	anaerobicⓘ	no	98.38	no
125438	aerobic	aerobicⓘ	yes	80.99	yes
125438	spore-forming	spore-formingⓘ	yes	82.06	no
125438	thermophilic	thermophileⓘ	no	89.90	yes
125438	flagellated	motile2+ⓘ	yes	60.52	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Screening and isolation of halophilic bacteria producing industrially important enzymes.	Kumar S, Karan R, Kapoor S, S P S, S K K.	Braz J Microbiol	10.1590/s1517-838220120004000044	2012
Enzymology	Unmasking the measles-like parchment discoloration: molecular and microanalytical approach.	Pinar G, Sterflinger K, Pinzari F.	Environ Microbiol	10.1111/1462-2920.12471	2015
Phylogeny	Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi.	Jang JY, Oh YJ, Lim SK, Park HK, Lee C, Kim JY, Lee MA, Choi HJ.	J Microbiol	10.1007/s12275-018-8518-0	2018
Phylogeny	Geomicrobium halophilum gen. nov., sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from soil.	Echigo A, Minegishi H, Mizuki T, Kamekura M, Usami R	Int J Syst Evol Microbiol	10.1099/ijs.0.013268-0	2009

References

#15936	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21769
#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 )
#25852	IJSEM 990 2010 ( DOI 10.1099/ijs.0.013268-0 , PubMed 19666816 )
#29446	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 #25852
#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;
#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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Geomicrobium halophilum (DSM 21769, JCM 15647, BH1)

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

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014207655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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