Demequina sediminicola (DSM 24867, NBRC 105855, HR08-43)

Name: Demequina sediminicola (DSM 24867, NBRC 105855, HR08-43)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17841

Type strain

Strain Designation HR08-43

Culture col. no. DSM 24867 NBRC 105855 HR08-43

NCBI tax ID(s) 1095026

Special Collections DSMZ Literature strains

Links

Demequina sediminicola HR08-43 is an anaerobe, mesophilic, Gram-positive prokaryote that was isolated from marine sediment.

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

Name and taxonomic classification

SI-ID 406360

NBRC 105855,DSM 24867

@ref 20215

Last LPSN update 2025-12-16 09:51:12

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Demequinaceae

Genus Demequina

Species Demequina sediminicola

Full scientific name Demequina sediminicola Hamada et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30586	positive	3 µm	0.65 µm	rod-shaped
125438					92.5
125438	positive				91.686
125439	positive				93.9

Colony morphology

17792

Incubation period3-7 days

Pigmentation

30586

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17792	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17792	positive	growth	28	mesophilic
30586	positive	growth	10-28
30586	positive	optimum	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30586	positive	optimum	7.5
30586	positive	growth	07-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30586	anaerobe
125439	obligate aerobe	93.6

Spore formation

30586

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30586	NaCl	positive	growth	0-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30586	17057 ChEBI	cellobiose	+	carbon source
30586	4853 ChEBI	esculin	+	hydrolysis
30586	28757 ChEBI	fructose	+	carbon source
30586	28260 ChEBI	galactose	+	carbon source
30586	17234 ChEBI	glucose	+	carbon source
30586	17716 ChEBI	lactose	+	carbon source
30586	17306 ChEBI	maltose	+	carbon source
30586	29864 ChEBI	mannitol	+	carbon source
30586	37684 ChEBI	mannose	+	carbon source
30586	26546 ChEBI	rhamnose	+	carbon source
30586	17814 ChEBI	salicin	+	carbon source
30586	17992 ChEBI	sucrose	+	carbon source
30586	27082 ChEBI	trehalose	+	carbon source
30586	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30586	acid phosphatase	+	3.1.3.2
30586	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
17792	marine sediment	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB674957 (>99% sequence identity) for Demequina sediminicola subclade from Microbeatlas

Aquatic Samples	46
Soil Samples	60
Animal Samples	134
Plant Samples	19
Total Samples	259

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17792	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	ASM97505v1 assembly for Demequina sediminicola NBRC 105855	scaffold	GCA_000975055	1095026.3	2690315958	1095026	76.33

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17792	Demequina sediminicola gene for 16S rRNA, partial sequence	AB674957	1476		1095026

GC content

@ref	GC-content (mol%)	Method
17792	62.4	high performance liquid chromatography (HPLC)
30586	62.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Demequina sediminicola NBRC 105855
NCBI: GCA_000975055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.60	no
125439	gram_stain	BacteriaNetⓘ	positive	93.90	no
125439	motility	BacteriaNetⓘ	no	75.20	no
125439	spore_formation	BacteriaNetⓘ	no	87.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Demequina sediminicola NBRC 105855
NCBI: GCA_000975055.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.69	yes
125438	anaerobic	anaerobicⓘ	no	85.59	yes
125438	aerobic	aerobicⓘ	yes	51.37	yes
125438	spore-forming	spore-formingⓘ	no	75.27	yes
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	92.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment.	Hamada M, Tamura T, Yamamura H, Suzuki KI, Hayakawa M	Int J Syst Evol Microbiol	10.1099/ijs.0.039297-0	2012

References

#17792	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24867
#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 )
#30586	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 #26917 (see below)
#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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Demequina sediminicola (DSM 24867, NBRC 105855, HR08-43)

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

Halophily

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_000975055

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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