Sediminibacterium salmoneum (DSM 27476, CGMCC 1.6845, NBRC 103935)

Name: Sediminibacterium salmoneum (DSM 27476, CGMCC 1.6845, NBRC 103935)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24736

Type strain

Strain Designation NJ-44

Culture col. no. DSM 27476 CGMCC 1.6845 NBRC 103935 NJ-44

NCBI tax ID(s) 1400522 426421

Special Collections DSMZ Literature strains

History DSMZ <- NBRC <- China General Microbiological Culture Collection Center, CGMCC <- J.-H. Qu, China Agric. Univ., College Biol. Sci., Beijing; NJ-44

Links

Sediminibacterium salmoneum NJ-44 is an aerobe, Gram-negative, motile bacterium that was isolated from sediment from Guanting Reservoir.

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

Name and taxonomic classification

SI-ID 405286

NBRC 103935,DSM 27476

@ref 20215

Last LPSN update 2026-05-29 08:30:40

Domain Bacteria

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Sediminibacterium

Species Sediminibacterium salmoneum

Full scientific name Sediminibacterium salmoneum Qu and Yuan 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
32449	negative	1-1.2 µm	0.2-0.3 µm	rod-shaped	gliding
125438						90.75
125438	negative					90.554
125439	negative					99.574

Colony morphology

21188

Incubation period8-14 days

Pigmentation

32449

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21188	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21188	positive	growth	28
32449	positive	growth	18-37
32449	positive	optimum	22-28

Culture pH

@ref	Ability	Type	PH
32449	positive	optimum	7
32449	positive	growth	6-7.5

Physiology and metabolism

Oxygen tolerance

32449

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
32449
125439		99.814
125438		92.976

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32449	NaCl	positive	growth	0-1 %

Observation

32449

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	-	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
32449	17234 ChEBI	glucose	+	carbon source
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
32449	17716 ChEBI	lactose	+	carbon source
68368	25094 ChEBI	lysine	-	degradation	from API 20E
32449	17306 ChEBI	maltose	+	carbon source
32449	37684 ChEBI	mannose	+	carbon source
32449	28053 ChEBI	melibiose	+	carbon source
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
32449	16634 ChEBI	raffinose	+	carbon source
32449	17814 ChEBI	salicin	+	carbon source
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
32449	17992 ChEBI	sucrose	+	carbon source
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
32449	27082 ChEBI	trehalose	+	carbon source
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
32449	catalase	+	1.11.1.6
32449	cytochrome oxidase	+	1.9.3.1
68368	cytochrome oxidase	+	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
21188	+	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	#Container (Reservoir)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21188	sediment from Guanting Reservoir	Beijing	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF407879 (>99% sequence identity) for Sediminibacterium salmoneum subclade from Microbeatlas

Aquatic Samples	2905
Soil Samples	190
Animal Samples	572
Plant Samples	89
Total Samples	3756

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21188	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM51117v1 assembly for Sediminibacterium salmoneum NBRC 103935	scaffold	GCA_000511175	1400522.3	2585428137	1400522	52.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21188	Sediminibacterium salmoneum strain NJ-44 16S ribosomal RNA gene, partial sequence	EF407879	1458		1400522
124043	Sediminibacterium salmoneum gene for 16S rRNA, partial sequence, strain: NBRC 103935.	AB682145	1456		1400522

GC content

21188

GC-content (mol%)40.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM51117v1 assembly for Sediminibacterium salmoneum NBRC 103935
BV-BRC: 1400522.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.09	no
125439	gram_stain	BacteriaNetⓘ	negative	99.57	no
125439	motility	BacteriaNetⓘ	no	79.17	no
125439	spore_formation	BacteriaNetⓘ	no	99.81	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sediminibacterium salmoneum NBRC 103935 NBRC 103935
NCBI: GCA_000511175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	90.55	yes
125438	anaerobic	anaerobicⓘ	no	96.52	yes
125438	aerobic	aerobicⓘ	yes	87.98	no
125438	spore-forming	spore-formingⓘ	no	92.98	no
125438	thermophilic	thermophileⓘ	no	95.38	yes
125438	flagellated	motile2+ⓘ	no	90.75	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Whole-Genome Sequence of Sediminibacterium sp. Strain TEGAF015, Isolated from a Shallow Eutrophic Freshwater Lake in Japan.	Ogata Y, Watanabe K, Takemine S, Shindo C, Kurokawa R, Suda W.	Microbiol Resour Announc	10.1128/mra.00882-22	2022
Genetics	Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge.	Ayarza JM, Figuerola EL, Erijman L	Genome Announc	10.1128/genomeA.01073-13	2014
Phylogeny	Sediminibacterium soli sp. nov., isolated from soil.	Wu S, Zhong L, Liao S, Li T, Zhou Z, Wang G	Arch Microbiol	10.1007/s00203-020-02089-2	2020
Phylogeny	Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water.	Eder W, Peplies J, Wanner G, Fruhling A, Verbarg S	Int J Syst Evol Microbiol	10.1099/ijs.0.000040	2015
Phylogeny	Sediminibacterium goheungense sp. nov., isolated from a freshwater reservoir.	Kang H, Kim H, Lee BI, Joung Y, Joh K	Int J Syst Evol Microbiol	10.1099/ijs.0.055137-0	2014
Phylogeny	Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water.	Albert RA, Zitomer D, Dollhopf M, Schauer-Gimenez AE, Struble C, King M, Son S, Langer S, Busse HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.056663-0	2013
Phylogeny	Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum.	Kim YJ, Nguyen NL, Weon HY, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.038554-0	2012
Phylogeny	Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.	Kampfer P, Lodders N, Falsen E	Int J Syst Evol Microbiol	10.1099/ijs.0.023002-0	2010
Phylogeny	Solibius ginsengiterrae gen. nov., sp. nov., isolated from soil of a ginseng field, and emended description of the genus Sediminibacterium and of Sediminibacterium salmoneium.	Kim YJ, Kim MK, Bui TP, Kim HB, Srinivasan S, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.011882-0	2010
Phylogeny	Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir.	Qu JH, Yuan HL	Int J Syst Evol Microbiol	10.1099/ijs.0.65514-0	2008

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 )
#21188	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27476
#28671	IJSEM 2191 2008 ( DOI 10.1099/ijs.0.65514-0 , PubMed 18768628 )
#32449	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 #28671
#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) .
#68368	Automatically annotated from API 20E .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Sediminibacterium salmoneum (DSM 27476, CGMCC 1.6845, NBRC 103935)

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

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000511175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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