Name: Sphingobium herbicidovorans MH
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14176

Type strain:

Species: Sphingobium herbicidovorans

Strain Designation: MH

Culture col. no.: DSM 11019, IFO 16415, LMG 18315, NBRC 16415, CCUG 56400, CIP 106705, ATCC 700291, KCTC 2939

Strain history: CIP <- 2000, LMG <- DSMZ <- H. Kohler <- F. Streichsbier, TU, Vienna, Flavobacterium sp.: strain MH

NCBI tax ID(s): 1219045 (strain), 76947 (species)

SI-ID 11836

LMG 18315, CIP 106705, IFO 16415, ATCC 700291, KCTC 2939, NBRC 16415, DSM 11019, CCUG 56400

Special Collections

Section

Sphingobium herbicidovorans MH is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

Gram-negative
motile
rod-shaped
aerobe
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingobium*
	Species	**Sphingobium herbicidovorans**
	Full Scientific Name (LPSN)	Sphingobium herbicidovorans (Zipper et al. 1997) Takeuchi et al. 2001

Synonym

Sphingomonas herbicidovorans

Information on morphological and physiological properties Morphology

[Ref.: #119881]	Gram stain	negative

[Ref.: #119881]	Cell shape	rod-shaped

[Ref.: #119881]	Motility	yes

[Ref.: #119881]	Pigment production	no
[Ref.: #119881]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4161]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #4161]

Culture medium growth

[Ref.: #4161]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4161]

Culture medium composition

expand / minimize

[Ref.: #4161]

Culture medium

MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)

[Ref.: #4161]

Culture medium growth

[Ref.: #4161]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4161]

Culture medium composition

expand / minimize

[Ref.: #40601]

Culture medium

MEDIUM 356 - for Sphingomonas herbicidovorans

[Ref.: #40601]

Culture medium growth

[Ref.: #40601]

Culture medium composition

expand / minimize

[Ref.: #119881]

Culture medium

CIP Medium 356

[Ref.: #119881]

Culture medium growth

[Ref.: #119881]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #4161]		growth	28 °C
[Ref.: #40601]		growth	30 °C
[Ref.: #60943]		growth	30 °C
[Ref.: #119881]		growth	25-37 °C
[Ref.: #119881]	no	growth	5 °C
[Ref.: #119881]	no	growth	10 °C
[Ref.: #119881]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60943]	Oxygen tolerance	aerobe
[Ref.: #119881]	Oxygen tolerance	obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #119881]	NaCl		growth	0-4	%
[Ref.: #119881]	NaCl	no	growth	6	%
[Ref.: #119881]	NaCl	no	growth	8	%
[Ref.: #119881]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #119881]	citrate ChEBI	-	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #119881]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #119881]	nitrate ChEBI	-	reduction
[Ref.: #119881]	nitrate ChEBI	-	respiration
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #119881]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #119881]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #119881]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #119881]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #119881]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #119881]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE, API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #119881]	caseinase	-	3.4.21.50
[Ref.: #119881]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #119881]	DNase	-
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #119881]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #119881]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #119881]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #119881]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #119881]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119881]	oxidase	+
[Ref.: #119881]	protease	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #119881]	tryptophan deaminase	-
[Ref.: #119881]	tween esterase	-
[Ref.: #119881]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #4161]	24850	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	+	-	-	+
[Ref.: #4161]	23188	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	+	-	-	+

API® Biotype100:

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

	API ID	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
[Ref.: #119881]	1781	not determinedn.d.	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #119881]	9737	-	+	-	-	-	+	+	+	+	-	+	+	-	-	-	+	+	-	-	-

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

[Ref.: #4161]	Sample type/isolated from	soil
[Ref.: #4161]	Geographic location (country and/or sea, region)	Vienna
[Ref.: #4161]	Country	Austria
[Ref.: #4161]	Country ISO 3 Code	AUT
[Ref.: #4161]	Continent	Europe

[Ref.: #60943]	Sample type/isolated from	Soil
[Ref.: #60943]	Country	Austria
[Ref.: #60943]	Country ISO 3 Code	AUT
[Ref.: #60943]	Continent	Europe

[Ref.: #119881]	Sample type/isolated from	Environment, Soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681063 (>99% sequence identity) for Sphingobium herbicidovorans from Microbeatlas

Aquatic Samples	58
Soil Samples	109
Animal Samples	107
Plant Samples	23
Total Samples	297

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

[Ref.: #4161]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119881]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Sphingobium herbicidovorans gene for 16S ribosomal RNA, partial sequence	AB022428	1438	GenBank ENA	76947 tax ID	*
[Ref.: #20218]	Sphingobium herbicidovorans gene for 16S rRNA, partial sequence, strain: NBRC 16415	AB681063	1412	GenBank ENA	76947 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium herbicidovorans NBRC 16415	2731957705	draft	JGI IMG/M	1219045 tax ID	*
[Ref.: #66792]	Sphingobium herbicidovorans MH	GCA_002080435	complete	GenBank ENA	76947 tax ID	*
[Ref.: #66792]	Sphingobium herbicidovorans NBRC 16415	GCA_000632125	contig	GenBank ENA	1219045 tax ID	*
[Ref.: #66792]	Sphingobium herbicidovorans NBRC 16415	1219045.4	wgs	PATRIC	1219045 tax ID	*
[Ref.: #66792]	Sphingobium herbicidovorans NBRC 16415	1219045.3	wgs	PATRIC	1219045 tax ID	*
[Ref.: #66792]	Sphingobium herbicidovorans NBRC 16415	2808606815	complete	JGI IMG/M	1219045 tax ID	*

Availability in culture collections External links

[Ref.: #4161]

Culture collection no.

DSM 11019, IFO 16415, LMG 18315, NBRC 16415, CCUG 56400, CIP 106705, ATCC 700291, KCTC 2939

[Ref.: #83339]

SI-ID 11836

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium pinisoli sp. nov., isolated from the rhizosphere soil of a Korean native pine tree.	Lee JC, Song JS, Whang KS	Antonie Van Leeuwenhoek	10.1007/s10482-018-01215-x	2018	*
Phylogeny	Sphingobium vermicomposti sp. nov., isolated from vermicompost.	Vaz-Moreira I, Faria C, Lopes AR, Svensson L, Falsen E, Moore ER, Ferreira AC, Nunes OC, Manaia CM	Int J Syst Evol Microbiol	10.1099/ijs.0.006163-0	2009	*
Phylogeny	Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov.	Prakash O, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.64080-0	2006	*

References

#4161

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11019

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#40601 ; Curators of the CIP;
#60943 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56400

#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 .

#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 .

#83339

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-ID11836.1 )

#119881 Collection of Institut Pasteur ; Curators of the CIP; CIP 106705
* These data were automatically processed and therefore are not curated

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