Sphingobacterium alimentarium (DSM 22362, LMG 25273, WCC 4521)

Name: Sphingobacterium alimentarium (DSM 22362, LMG 25273, WCC 4521)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14130

Type strain

Culture col. no. DSM 22362 LMG 25273 WCC 4521

NCBI tax ID(s) 797292

Special Collections DSMZ Literature strains

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

Links

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

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 361451

LMG 25273,DSM 22362,DSM 22632

@ref 20215

Last LPSN update 2025-12-16 09:50:16

Domain Pseudomonadati

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Sphingobacterium

Species Sphingobacterium alimentarium

Full scientific name Sphingobacterium alimentarium Schmidt et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30447	negative	1.75 µm	0.8 µm	rod-shaped
125438	negative				98
125439	negative				99.5

Pigmentation

30447

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16184	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)	Range
16184	positive	growth	28	mesophilic
30447	positive	growth	10-41

Culture pH

@ref	Ability	Type	PH	PH range
30447	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30447	aerobe
125439	obligate aerobe	94.8

Spore formation

@ref	Spore formation	Confidence
30447
125439		98.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30447	NaCl	positive	growth	0-3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30447	17057 ChEBI	cellobiose	+	carbon source
30447	4853 ChEBI	esculin	+	hydrolysis
30447	28757 ChEBI	fructose	+	carbon source
30447	17234 ChEBI	glucose	+	carbon source
30447	28087 ChEBI	glycogen	+	carbon source
30447	17716 ChEBI	lactose	+	carbon source
30447	17306 ChEBI	maltose	+	carbon source
30447	37684 ChEBI	mannose	+	carbon source
30447	28053 ChEBI	melibiose	+	carbon source
30447	506227 ChEBI	N-acetylglucosamine	+	carbon source
30447	16634 ChEBI	raffinose	+	carbon source
30447	17814 ChEBI	salicin	+	carbon source
30447	17992 ChEBI	sucrose	+	carbon source
30447	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30447	catalase	+	1.11.1.6
30447	cytochrome oxidase	+	1.9.3.1

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Dairy product

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
16184	dairy environment	Germany	DEU	Europe

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16184	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	ASM434268v1 assembly for Sphingobacterium alimentarium DSM 22362	contig	GCA_004342685	797292.3	2791354870	797292	50.99

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16184	Sphingobacterium alimentarium partial 16S rRNA gene, strain DSM 22362	FN908502	1492		797292

GC content

@ref	GC-content (mol%)	Method
16184	39.3	high performance liquid chromatography (HPLC)
30447	39.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobacterium alimentarium DSM 22362
NCBI: GCA_004342685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.10	no
125439	motility	BacteriaNetⓘ	no	69.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobacterium alimentarium strain DSM 22362
PATRIC: 797292.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	96.79	yes
125438	aerobic	aerobicⓘ	yes	79.84	no
125438	spore-forming	spore-formingⓘ	no	87.84	yes
125438	thermophilic	thermophileⓘ	no	96.98	yes
125438	flagellated	motile2+ⓘ	no	88.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Prevalence of diversified antibiotic resistant bacteria within sanitation related facilities of human populated workplaces in Abbottabad.	Ali J, Awan MOU, Akca G, Zeb I, Amin BA, Ahmad R, Shah MM, Nazir R.	PLoS One	10.1371/journal.pone.0233325	2020
Phylogeny	An isolated cellulolytic Escherichia coli from bovine rumen produces ethanol and hydrogen from corn straw.	Pang J, Liu ZY, Hao M, Zhang YF, Qi QS.	Biotechnol Biofuels	10.1186/s13068-017-0852-7	2017
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 )
#26782	IJSEM 1506 2012 ( DOI 10.1099/ijs.0.036327-0 , PubMed 21856986 )
#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
#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 .
#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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Sphingobacterium alimentarium (DSM 22362, LMG 25273, WCC 4521)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004342685

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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