Name: Sphingobacterium alimentarium DSM 22362
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14130

Type strain:

Species: Sphingobacterium alimentarium

Culture col. no.: DSM 22362, LMG 25273, WCC 4521

Strain history: <- S. Scherer, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC4521 <- V. Schmidt

NCBI tax ID(s): 797292 (species)

SI-ID 361451

LMG 25273, DSM 22362, DSM 22632

Section

Sphingobacterium alimentarium DSM 22362 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from dairy environment.

Gram-negative
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	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Sphingobacterium*
	Species	**Sphingobacterium alimentarium**
	Full Scientific Name (LPSN)	Sphingobacterium alimentarium Schmidt et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30447]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #30447]	Cell length	1.75 µm

[Ref.: #30447]	Cell width	0.8 µm

[Ref.: #30447]	Cell shape	rod-shaped

[Ref.: #30447]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.513

[Ref.: #30447]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16184]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #16184]

Culture medium growth

[Ref.: #16184]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16184]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #16184]			growth	28 °C
[Ref.: #30447]			growth	10-41 °C

[Ref.: #16184]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #30447]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30447]

Oxygen tolerance

aerobe

[Ref.: #30447]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30447]		NaCl		growth	0-3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30447]	cellobiose ChEBI	+	carbon source
[Ref.: #30447]	esculin ChEBI	+	hydrolysis
[Ref.: #30447]	fructose ChEBI	+	carbon source
[Ref.: #30447]	glucose ChEBI	+	carbon source
[Ref.: #30447]	glycogen ChEBI	+	carbon source
[Ref.: #30447]	lactose ChEBI	+	carbon source
[Ref.: #30447]	maltose ChEBI	+	carbon source
[Ref.: #30447]	mannose ChEBI	+	carbon source
[Ref.: #30447]	melibiose ChEBI	+	carbon source
[Ref.: #30447]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30447]	raffinose ChEBI	+	carbon source
[Ref.: #30447]	salicin ChEBI	+	carbon source
[Ref.: #30447]	sucrose ChEBI	+	carbon source
[Ref.: #30447]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30447]		catalase	+	1.11.1.6
[Ref.: #30447]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	degradation of pentoses	53.57	15 of 28
[Ref.: #66794]	oxidative phosphorylation	50.55	46 of 91
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	carotenoid biosynthesis	40.91	9 of 22
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #16184]	Sample type/isolated from	dairy environment
[Ref.: #16184]	Country	Germany
[Ref.: #16184]	Country ISO 3 Code	DEU
[Ref.: #16184]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

#Dairy product

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FN908502 (>99% sequence identity) for Sphingobacterium alimentarium subclade from Microbeatlas

Aquatic Samples	3015
Soil Samples	2932
Animal Samples	7572
Plant Samples	1008
Total Samples	14527

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

[Ref.: #16184]

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.: #16184]	Sphingobacterium alimentarium partial 16S rRNA gene, strain DSM 22362	FN908502	1492	ENA	797292 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobacterium alimentarium DSM 22362	GCA_004342685	contig	GenBank	797292 tax ID	*
[Ref.: #66792]	Sphingobacterium alimentarium strain DSM 22362	797292.3	wgs	PATRIC	797292 tax ID	*
[Ref.: #66792]	Sphingobacterium alimentarium DSM 22362	2791354870	draft	JGI IMG/M	797292 tax ID	*

[Ref.: #16184]	GC-content	39.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30447]	GC-content	39.3 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: Sphingobacterium alimentarium strain DSM 22362 PATRIC: 797292.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobacterium alimentarium strain DSM 22362 PATRIC: 797292.3
[Ref.: #69480]	motile	no	91.742	yes
[Ref.: #69480]	flagellated	no	96.845	yes
[Ref.: #69480]	gram-positive	no	97.8	yes
[Ref.: #69480]	anaerobic	no	98.866	yes
[Ref.: #69480]	halophile	no	92.833	no
[Ref.: #69480]	spore-forming	no	95.569	yes
[Ref.: #69480]	thermophile	no	99.432	yes
[Ref.: #69480]	glucose-util	yes	87.556	yes
[Ref.: #69480]	aerobic	yes	88.13	yes
[Ref.: #69480]	glucose-ferment	no	90.966	no

Availability in culture collections External links

[Ref.: #16184]

Culture collection no.

DSM 22362, LMG 25273, WCC 4521

[Ref.: #83295]

SI-ID 361451

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave.	Zhou XK, Huang Y, Li M, Zhang XF, Wei YQ, Cha QY, Zhang TK, Wang XJ, Liu JJ, Liu ZY, Qin SC, Mo MH	Int J Syst Evol Microbiol	10.1099/ijsem.0.004044	2020	*
Phylogeny	Sphingobacterium bovisgrunnientis sp. nov., isolated from yak milk.	Kaur M, Singh H, Sharma S, Mishra S, Tanuku NRS, Pinnaka AK	Int J Syst Evol Microbiol	10.1099/ijsem.0.002562	2018	*
Phylogeny	Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis.	Li GD, Chen X, Li QY, Xu FJ, Qiu SM, Jiang Y, Jiang CL	Antonie Van Leeuwenhoek	10.1007/s10482-015-0563-7	2015	*
Phylogeny	Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost.	Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.042481-0	2012	*
Phylogeny	Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment.	Schmidt VSJ, Wenning M, Scherer S	Int J Syst Evol Microbiol	10.1099/ijs.0.036327-0	2011	*

References

#16184

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22362

#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 )

#30447

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 #26782 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#83295

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-ID361451.1 )

#26782

IJSEM 1506 2012 ( DOI 10.1099/ijs.0.036327-0 , PubMed 21856986 )

* These data were automatically processed and therefore are not curated

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Sphingobacterium alimentarium strain DSM 22362

Sphingobacterium alimentarium strain DSM 22362

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