Name: Sediminibacterium salmoneum NJ-44
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24736

Type strain:

Species: Sediminibacterium salmoneum

Strain Designation: NJ-44

Culture col. no.: DSM 27476, CGMCC 1.6845, NBRC 103935

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

NCBI tax ID(s): 1400522 (strain), 426421 (species)

SI-ID 405286

DSM 27476

Section

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

Gram-negative
motile
rod-shaped
aerobe
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	*Bacteroidota*
	Class	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Sediminibacterium*
	Species	**Sediminibacterium salmoneum**
	Full Scientific Name (LPSN)	Sediminibacterium salmoneum Qu and Yuan 2008

Information on morphological and physiological properties Morphology

[Ref.: #32449]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #32449]	Cell length	1-1.2 µm

[Ref.: #32449]	Cell width	0.2-0.3 µm

[Ref.: #32449]	Cell shape	rod-shaped

[Ref.: #32449]	Motility	yes
[Ref.: #69480]	Motility	no Confidence in %90.706

[Ref.: #32449]	Flagellum arrangement	gliding

[Ref.: #21188]

Incubation period

8-14 days

[Ref.: #32449]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21188]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21188]

Culture medium growth

[Ref.: #21188]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21188]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21188]	growth	28 °C
[Ref.: #32449]	growth	18-37 °C
[Ref.: #32449]	optimum	22-28 °C

[Ref.: #21188]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #32449]			optimum	7
[Ref.: #32449]			growth	6-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32449]

Oxygen tolerance

aerobe

[Ref.: #32449]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32449]		NaCl		growth	0-1	%

[Ref.: #32449]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #32449]	glucose ChEBI	+	carbon source
[Ref.: #68368]	L-arabinose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #32449]	lactose ChEBI	+	carbon source
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #32449]	maltose ChEBI	+	carbon source
[Ref.: #32449]	mannose ChEBI	+	carbon source
[Ref.: #32449]	melibiose ChEBI	+	carbon source
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #32449]	raffinose ChEBI	+	carbon source
[Ref.: #32449]	salicin ChEBI	+	carbon source
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #32449]	sucrose ChEBI	+	carbon source
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #32449]	trehalose ChEBI	+	carbon source
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #32449]	catalase	+	1.11.1.6
[Ref.: #32449]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68368]	cytochrome oxidase	+	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #21188]	16687	+	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #21188]	Sample type/isolated from	sediment from Guanting Reservoir
[Ref.: #21188]	Geographic location (country and/or sea, region)	Beijing
[Ref.: #21188]	Country	China
[Ref.: #21188]	Country ISO 3 Code	CHN
[Ref.: #21188]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	#Container (Reservoir)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #21188]

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.: #21188]	Sediminibacterium salmoneum strain NJ-44 16S ribosomal RNA gene, partial sequence	EF407879	1458	ENA	1400522 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sediminibacterium salmoneum NBRC 103935	GCA_000511175	scaffold	GenBank	1400522 tax ID	*
[Ref.: #66792]	Sediminibacterium salmoneum NBRC 103935	1400522.3	wgs	PATRIC	1400522 tax ID	*
[Ref.: #66792]	Sediminibacterium salmoneum NBRC 103935	2585428137	draft	JGI IMG/M	1400522 tax ID	*

[Ref.: #21188]

GC-content

40.6 mol%

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: Sediminibacterium salmoneum NBRC 103935 NBRC 103935 NCBI: GCA_000511175.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sediminibacterium salmoneum NBRC 103935 NBRC 103935 NCBI: GCA_000511175.1
[Ref.: #69480]	motile	no	94.68	no
[Ref.: #69480]	flagellated	no	97.834	yes
[Ref.: #69480]	gram-positive	no	98.133	yes
[Ref.: #69480]	anaerobic	no	98.659	yes
[Ref.: #69480]	halophile	no	97.69	yes
[Ref.: #69480]	spore-forming	no	96.778	no
[Ref.: #69480]	thermophile	no	92.592	yes
[Ref.: #69480]	glucose-util	yes	84.25	yes
[Ref.: #69480]	aerobic	yes	88.626	yes
[Ref.: #69480]	glucose-ferment	no	90.436	yes

Availability in culture collections External links

[Ref.: #21188]

Culture collection no.

DSM 27476, CGMCC 1.6845, NBRC 103935

[Ref.: #88564]

SI-ID 405286

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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	*
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 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

#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 (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) .

#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 .

#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 )

#88564

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-ID405286.1 )

#28671

IJSEM 2191 2008 ( DOI 10.1099/ijs.0.65514-0 , PubMed 18768628 )

* These data were automatically processed and therefore are not curated

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Sediminibacterium salmoneum NBRC 103935 NBRC 103935

Sediminibacterium salmoneum NBRC 103935 NBRC 103935

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