Sphingomonas phyllosphaerae (DSM 17258, CECT 5832, LMG 21958)

Name: Sphingomonas phyllosphaerae (DSM 17258, CECT 5832, LMG 21958)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14241

Type strain

Strain Designation FA2

Culture col. no. DSM 17258 CECT 5832 LMG 21958 FA2 CIP 108674

NCBI tax ID(s) 257003

Special Collections DSMZ Literature strains CIP

History DSMZ <- E. Velázquez, Univers. Salamanca <-A. Abril, Córdoba, Argentinia CIP <- 2005, CECT <- 2003, E. Velasquez, Salamanca Univ., Salamanca, Spain: strain FA2

Links

Sphingomonas phyllosphaerae FA2 is an aerobe, Gram-negative, motile bacterium that was isolated from phyllosphere of Acacia caven.

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

Name and taxonomic classification

SI-ID 99921

LMG 21958,CECT 5832,CIP 108674,DSM 17258

@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 phyllosphaerae

Full scientific name Sphingomonas phyllosphaerae Rivas et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31233	negative	1.7 µm	0.7 µm	rod-shaped
125438	negative				96.833
121816	negative			rod-shaped

Pigmentation

31233

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6859	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39770	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
121816	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6859	positive	growth	28
39770	positive	growth	25
121816	positive	growth	10-37
121816	negative	growth	5
121816	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31233	aerobe
121816	obligate aerobe
125439	obligate aerobe	99.238

Spore formation

@ref	Spore formation	Confidence
31233
125439		97.448
125438		90.064

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121816	NaCl	positive	growth	0-2 %
121816	NaCl		growth	4 %
121816	NaCl		growth	6 %
121816	NaCl		growth	8 %
121816	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31233	17128 ChEBI	adipate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
31233	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31233	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
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
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
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
31233	4853 ChEBI	esculin	+	hydrolysis
121816	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31233	28757 ChEBI	fructose	+	carbon source
31233	33984 ChEBI	fucose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
31233	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
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
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	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
31233	17716 ChEBI	lactose	+	carbon source
31233	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
31233	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
31233	506227 ChEBI	N-acetylglucosamine	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
121816	17632 ChEBI	nitrate	-	reduction
121816	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121816	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
31233	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
31233	17992 ChEBI	sucrose	+	carbon source
31233	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
31233	18222 ChEBI	xylose	+	carbon source

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121816	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121816	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121816	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
121816	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	+	3.2.1.23	from API zym
121816	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	+	3.2.1.31	from API zym
121816	caseinase	-	3.4.21.50
31233	catalase	+	1.11.1.6
121816	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
31233	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
121816	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121816	gelatinase	+
68369	gelatinase	-		from API 20NE
121816	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121816	lipase	-
68382	lipase (C 14)	-		from API zym
121816	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
121816	ornithine decarboxylase	-	4.1.1.17
121816	oxidase	-
121816	protease	-
68382	trypsin	-	3.4.21.4	from API zym
121816	tryptophan deaminase	-
121816	tween esterase	-
121816	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

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
121816	-	+	+	+	-	+	+	+	-	-	+	+	+	+	+	+	+	+	+	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6859	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	-	-	+	+	-	-

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
121816	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
121816	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	-	+	+	+	+	-	+	+	+	+	+	+	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	+	-	-	-	+	+	+	-	+	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent	Geographic location
6859	phyllosphere of Acacia caven	Acacia caven	Argentina	ARG	Middle and South America
121816	Environment, Phyllosphere, acacia caven		Argentina	ARG	Middle and South America	Central part

Taxonmaps

69479

Global distribution of 16S sequence AY453855 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	128
Soil Samples	153
Animal Samples	324
Plant Samples	272
Total Samples	877

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6859	1	Risk group (German classification) According to TRBA 466
121816	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
66792	ASM42764v1 assembly for Sphingomonas phyllosphaerae FA2	scaffold	GCA_000427645	1090319.3	2516493027	1090319	78.24

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6859	Sphingomonas phyllosphaerae 16S ribosomal RNA gene, complete sequence	AY453855	1481		257003

GC content

6859

GC-content (mol%)61

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM42764v1 assembly for Sphingomonas phyllosphaerae FA2
BV-BRC: 1090319.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.24	no
125439	gram_stain	BacteriaNetⓘ	negative	85.68	no
125439	motility	BacteriaNetⓘ	yes	50.70	no
125439	spore_formation	BacteriaNetⓘ	no	97.45	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas phyllosphaerae FA2 FA2
NCBI: GCA_000427645.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.83	yes
125438	anaerobic	anaerobicⓘ	no	97.10	yes
125438	aerobic	aerobicⓘ	yes	86.86	yes
125438	spore-forming	spore-formingⓘ	no	90.06	yes
125438	thermophilic	thermophileⓘ	no	98.08	yes
125438	flagellated	motile2+ⓘ	yes	67.80	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina.	Rivas R, Abril A, Trujillo ME, Velazquez E	Int J Syst Evol Microbiol	10.1099/ijs.0.63102-0	2004

References

#6859	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17258
#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 )
#27558	IJSEM 2147 2004 ( DOI 10.1099/ijs.0.63102-0 , PubMed 15545449 )
#31233	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 #27558
#39770	; Curators of the CIP;
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#121816	Collection of Institut Pasteur ; Curators of the CIP; CIP 108674
#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 )

Content

About us

Sphingomonas phyllosphaerae (DSM 17258, CECT 5832, LMG 21958)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000427645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media