Name: Geomicrobium sediminis DSM 25540
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24784

Type strain:

Species: Geomicrobium sediminis

Culture col. no.: DSM 25540, CCTCC AB 2013245, JCM 18144, YIM M13075

Strain history: S.-K. Tang YIM M13075.

NCBI tax ID(s): 1347788 (species)

SI-ID 405688

DSM 25540

Other strains from Geomicrobium sediminis

G. sediminis DSM 23309, CPCC 100153 (type strain)
G. sediminis JMAK1, DSM 24526

Section

Geomicrobium sediminis DSM 25540 is a spore-forming, mesophilic, motile bacterium that was isolated from marine sediment.

motile
spore-forming
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Geomicrobium*
	Species	**Geomicrobium sediminis**
	Full Scientific Name (LPSN)	Geomicrobium sediminis Xiong et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #69480]	Motility	yes Confidence in %91.978

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21206]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #21206]

Culture medium growth

[Ref.: #21206]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21206]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21206]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #21206]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %97
[Ref.: #69480]	Ability of spore formation	yes Confidence in %100

[Ref.: #67770]

Observation

quinones: MK-7, MK-6

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21206]	Sample type/isolated from	marine sediment
[Ref.: #21206]	Geographic location (country and/or sea, region)	South China Sea (113°29.704E, 18°32.409 N at a depth of 1468 m)
[Ref.: #21206]	Country	China
[Ref.: #21206]	Country ISO 3 Code	CHN
[Ref.: #21206]	Continent	Asia
[Ref.: #21206]	Geographic location	18.5401°/113.4950°

[Ref.: #67770]	Sample type/isolated from	Marine sediment sample collected from the South China Sea (18° 32.409' N 113° 29.704' E)
[Ref.: #67770]	Geographic location	18.5401°/113.4950°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KF040368 (>99% sequence identity) for Geomicrobium from Microbeatlas

Aquatic Samples	242
Soil Samples	871
Animal Samples	455
Plant Samples	278
Total Samples	1846

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21206]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #21206]	Geomicrobium sediminis strain YIM M13075 16S ribosomal RNA gene, partial sequence	KF040368	1536	ENA	1347788 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Geomicrobium sediminis DSM 25540	GCA_016908595	contig	GenBank	1347788 tax ID	*
[Ref.: #66792]	Geomicrobium sediminis strain DSM 25540	1347788.3	wgs	PATRIC	1347788 tax ID	*
[Ref.: #66792]	Geomicrobium sediminis DSM 25540	2901154911	draft	JGI IMG/M	1347788 tax ID	*

[Ref.: #21206]

GC-content

42.7 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Geomicrobium sediminis strain DSM 25540 PATRIC: 1347788.3
[Ref.: #69481]	spore-forming	yes	97	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geomicrobium sediminis strain DSM 25540 PATRIC: 1347788.3
[Ref.: #69480]	motile	yes	87.416	no
[Ref.: #69480]	gram-positive	yes	89.525	no
[Ref.: #69480]	anaerobic	no	98.65	no
[Ref.: #69480]	halophile	yes	89.517	no
[Ref.: #69480]	spore-forming	yes	88.969	no
[Ref.: #69480]	thermophile	no	99.332	yes
[Ref.: #69480]	glucose-util	yes	83.191	no
[Ref.: #69480]	aerobic	yes	94.699	no
[Ref.: #69480]	flagellated	yes	56.114	no
[Ref.: #69480]	glucose-ferment	no	92.941	no

Availability in culture collections External links

[Ref.: #21206]

Culture collection no.

DSM 25540, CCTCC AB 2013245, JCM 18144, YIM M13075

[Ref.: #88608]

SI-ID 405688

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Geomicrobium sediminis sp. nov., a novel bacterium isolated from a sediment sample collected from the South China Sea, and emended description of the genus Geomicrobium.	Xiong ZJ, Zhang YG, Zhang DF, Liu BB, Li L, Zhang XM, Xu LH, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-013-0039-6	2013	*

References

#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 )

#21206

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25540

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88608

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID405688.1 )

* These data were automatically processed and therefore are not curated

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Geomicrobium sediminis strain DSM 25540

Geomicrobium sediminis strain DSM 25540

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