Sphingomonas yabuuchiae (DSM 14562, GTC 868, JCM 11416)

Name: Sphingomonas yabuuchiae (DSM 14562, GTC 868, JCM 11416)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14232

Type strain

Strain Designation A1-18

Culture col. no. DSM 14562 GTC 868 JCM 11416 CCUG 52398 A1-18 1 more

NCBI tax ID(s) 172044

Special Collections DSMZ CCUG JCM CIP Literature strains

History DSMZ <- T. Ezaki, Gifu; GTC 868 JCM <-- T. Ezaki A1-18. CIP <- 2004, JCM <- 2001, T. Ezaki: strain A1-18

Links

Sphingomonas yabuuchiae A1-18 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from air in Russian space station Mir.

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

Name and taxonomic classification

SI-ID 131536

JCM 11416,DSM 14562,CIP 108439,CCUG 52398,BCRC 17618,CCRC 17618

@ref 20215

Last LPSN update 2026-05-29 08:28:14

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas yabuuchiae

Full scientific name Sphingomonas yabuuchiae Li et al. 2004

BacDive ID	Other strains from **Sphingomonas yabuuchiae** (1)	Type strain
153198	S. yabuuchiae CCUG 48701

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30014	negative	2.5 µm	0.5 µm	rod-shaped
125439	negative				93.226
125438	negative				95.639
124006	negative			rod-shaped

Colony morphology

59538

Incubation period2 days

Pigmentation

30014

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5385	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
5385	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
37292	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
124006	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5385	positive	growth	30
30014	positive	optimum	30
37292	positive	growth	30
59538	positive	growth	30-37
67770	positive	growth	30
124006	positive	growth	25-41
124006	negative	growth	5
124006	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30014	aerobe
59538	aerobe
124006	obligate aerobe
125439	obligate aerobe	98.479

Spore formation

@ref	Spore formation	Confidence
125439		98.43

Halophily

@ref	Salt	Growth	Tested relation	Concentration
124006	NaCl	positive	growth	0-4 %
124006	NaCl		growth	6 %
124006	NaCl		growth	8 %
124006	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
30014	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
30014	17057 ChEBI	cellobiose	+	carbon source
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
124006	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
30014	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
30014	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
30014	24265 ChEBI	gluconate	+	carbon source
30014	17234 ChEBI	glucose	+	carbon source
30014	17754 ChEBI	glycerol	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
30014	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
30014	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
30014	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
30014	28053 ChEBI	melibiose	+	carbon source
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
30014	506227 ChEBI	N-acetylglucosamine	+	carbon source
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
124006	17632 ChEBI	nitrate	-	reduction
124006	17632 ChEBI	nitrate	-	respiration
124006	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
30014	16634 ChEBI	raffinose	+	carbon source
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
30014	17992 ChEBI	sucrose	+	carbon source
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
30014	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
30014	53426 ChEBI	tween 80	+	carbon source
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
124006	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
124006	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
124006	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
124006	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
124006	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	+	3.2.1.31	from API zym
124006	caseinase	-	3.4.21.50
30014	catalase	+	1.11.1.6
124006	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
124006	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
124006	gelatinase	-
124006	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
124006	lipase	-
68382	lipase (C 14)	-		from API zym
124006	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
124006	ornithine decarboxylase	-	4.1.1.17
124006	oxidase	-
124006	protease	-
68382	trypsin	+	3.4.21.4	from API zym
124006	tryptophan deaminase	+
124006	tween esterase	-
124006	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	glycogen metabolism	100	5 of 5
66794	quinate degradation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	ketogluconate metabolism	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glutamate and glutamine metabolism	75	21 of 28
66794	biotin biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	d-xylose degradation	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	citric acid cycle	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	70.21	66 of 94
66794	propionate fermentation	70	7 of 10
66794	octane oxidation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	tyrosine metabolism	64.29	9 of 14
66794	vitamin B6 metabolism	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoleucine metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	pyrimidine metabolism	60	27 of 45
66794	glycolysis	58.82	10 of 17
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	arginine metabolism	54.17	13 of 24
66794	degradation of pentoses	53.57	15 of 28
66794	tryptophan metabolism	52.63	20 of 38
66794	CDP-diacylglycerol biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	histidine metabolism	48.28	14 of 29
66794	lysine metabolism	47.62	20 of 42
66794	ascorbate metabolism	45.45	10 of 22
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	vitamin B12 metabolism	41.18	14 of 34
66794	carotenoid biosynthesis	40.91	9 of 22
66794	O-antigen biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	sulfate reduction	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	oxidative phosphorylation	34.07	31 of 91
66794	enterobactin biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	urea cycle	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	arachidonic acid metabolism	27.78	5 of 18
66794	degradation of hexoses	27.78	5 of 18
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	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	sulfopterin metabolism	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
124006	-	+	+	+	-	+	+	-	+	-	+	+	+	+	+	+	+	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
124006	not determinedn.d.	-	-	-	+	-	+	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	-	+	-	+	+	+	+	+	+	-	-	+	-	-	-	+	+/-	-	-	+/-	+/-	-	-	+/-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
124006	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	+	+	-	+	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	+	+	+	-	+	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Air	#Indoor Air

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Geographic location
5385	air in Russian space station Mir	Space			space station Mir
59538	Air sample	Space			Russian space station,Mir
67770	Air sample from the Russian space station Mir
124006	Environment, Air sample from Russian space Station Mir	Russian Federation	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence AB071955 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	176
Soil Samples	20
Animal Samples	228
Plant Samples	17
Total Samples	441

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5385	1	Risk group (German classification) According to TRBA 466
124006	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4266106v1 assembly for Sphingomonas yabuuchiae JCM 11416	contig	GCA_042661065			172044	74.49
66792	ASM1419959v1 assembly for Sphingomonas yabuuchiae DSM 14562	scaffold	GCA_014199595	172044.4	2828620820	172044	67.11
124043	ASM4242950v1 assembly for Sphingomonas yabuuchiae JCM 11416	contig	GCA_042429505			172044	63.81
66792	ASM1705245v1 assembly for Sphingomonas yabuuchiae DSM 14562	contig	GCA_017052455	172044.5	8004127661	172044	52.17
124043	ASM3953598v1 assembly for Sphingomonas yabuuchiae JCM 11416	contig	GCA_039535985			172044	2.75

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30014	Sphingomonas yabuuchiae gene for 16S rRNA, partial sequence	AB071955	1454		172044

GC content

@ref	GC-content (mol%)	Method
30014	66.1
67770	66.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4266106v1 assembly for Sphingomonas yabuuchiae JCM 11416
NCBI: GCA_042661065

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.48	no
125439	gram_stain	BacteriaNetⓘ	negative	93.23	no
125439	motility	BacteriaNetⓘ	yes	52.48	no
125439	spore_formation	BacteriaNetⓘ	no	98.43	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas yabuuchiae DSM 14562
NCBI: GCA_014199595.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.64	no
125438	anaerobic	anaerobicⓘ	no	94.57	no
125438	aerobic	aerobicⓘ	yes	87.13	yes
125438	spore-forming	spore-formingⓘ	no	86.85	no
125438	thermophilic	thermophileⓘ	no	98.16	yes
125438	flagellated	motile2+ⓘ	yes	64.45	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas aquatica sp. nov., isolated from tap water.	Choi GM, Jo JH, Kang MS, Kim MS, Lee SY, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.001682	2017
Phylogeny	Sphingomonas aeria sp. nov. from indoor air of a pharmaceutical environment.	Park HK, Han JH, Kim TS, Joung Y, Cho SH, Kwon SW, Kim SB	Antonie Van Leeuwenhoek	10.1007/s10482-014-0302-5	2014
Phylogeny	Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir.	Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H, Huang X, Kobayashi K, Ezaki T	Int J Syst Evol Microbiol	10.1099/ijs.0.02829-0	2004

References

#5385	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14562
#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 )
#26378	IJSEM 819 2004 ( DOI 10.1099/ijs.0.02829-0 , PubMed 15143030 )
#30014	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 #26378
#37292	; Curators of the CIP;
#59538	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52398
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#124006	Collection of Institut Pasteur ; Curators of the CIP; CIP 108439
#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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Sphingomonas yabuuchiae (DSM 14562, GTC 868, JCM 11416)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Pathway annotation

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

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Genome sequences

Genome browser: GCA_042661065

16S sequences

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