Name: Williamsia sterculiae DSM 45741
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24667

Type strain:

Species: Williamsia sterculiae

Culture col. no.: DSM 45741, CPCC 203464, KCTC 29118, JCM 31496

Strain history: <- Yu-Qin Zhang, Institute of Medicinal Biotechnology, China

NCBI tax ID(s): 1344003 (species)

SI-ID 403462

DSM 45741

Section

Williamsia sterculiae DSM 45741 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface-sterilized stems of medicinal plant.

Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Gordoniaceae*
	Genus	*Williamsia*
	Species	**Williamsia sterculiae**
	Full Scientific Name (LPSN)	Williamsia sterculiae Fang et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31120]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #31120]	Cell length	1.35 µm

[Ref.: #31120]	Cell width	0.65 µm

[Ref.: #31120]	Cell shape	rod-shaped

[Ref.: #31120]	Motility	no

[Ref.: #31120]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20909]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #20909]

Culture medium growth

[Ref.: #20909]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20909]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20909]	growth	28 °C
[Ref.: #31120]	growth	10-37 °C
[Ref.: #31120]	optimum	28 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	28 °C

[Ref.: #20909]	Temperature range	mesophilic
[Ref.: #31120]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31120]			optimum	7
[Ref.: #31120]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31120]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31120]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31120]		NaCl		growth	0-3	%
[Ref.: #31120]		NaCl		optimum	0.5	%

[Ref.: #67770]	Observation	quinones: MK-8(H₂)
[Ref.: #67771]	Observation	quinones: MK-8 (H2)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31120]	acetate ChEBI	+	carbon source
[Ref.: #31120]	alanine ChEBI	+	carbon source
[Ref.: #31120]	aspartate ChEBI	+	carbon source
[Ref.: #31120]	citrate ChEBI	+	carbon source
[Ref.: #31120]	gluconate ChEBI	+	carbon source
[Ref.: #31120]	glucose ChEBI	+	carbon source
[Ref.: #31120]	glucuronamide ChEBI	+	carbon source
[Ref.: #31120]	glutamate ChEBI	+	carbon source
[Ref.: #31120]	L-arabitol ChEBI	+	carbon source
[Ref.: #31120]	lactate ChEBI	+	carbon source
[Ref.: #31120]	malate ChEBI	+	carbon source
[Ref.: #31120]	mannitol ChEBI	+	carbon source
[Ref.: #31120]	myo-inositol ChEBI	+	carbon source
[Ref.: #31120]	nitrate ChEBI	+	reduction
[Ref.: #31120]	propionate ChEBI	+	carbon source
[Ref.: #31120]	quinate ChEBI	+	carbon source
[Ref.: #31120]	rhamnose ChEBI	+	carbon source
[Ref.: #31120]	serine ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #31120]	acid phosphatase	+	3.1.3.2
[Ref.: #31120]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31120]	catalase	+	1.11.1.6
[Ref.: #31120]	gelatinase	+
[Ref.: #31120]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	IAA biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	87.5	7 of 8
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		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.: #67771]	Sample type/isolated from	surface-sterilized stems of medicinal plant
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #20909]	Sample type/isolated from	surface-sterilized stem of the medicinal plant Sterculiae lychnophorae
[Ref.: #20909]	Host species	Sterculiae lychnophorae
[Ref.: #20909]	Geographic location (country and/or sea, region)	Yunnan
[Ref.: #20909]	Country	China
[Ref.: #20909]	Country ISO 3 Code	CHN
[Ref.: #20909]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Stem of a medicinal plant, Sterculiae lychnophora Hance
[Ref.: #67770]	Host species	Sterculiae lychnophora
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yunnan medical plant plantation
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Stem (Branch)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC550143 (>99% sequence identity) for Williamsia sterculiae subclade from Microbeatlas

Aquatic Samples	168
Soil Samples	187
Animal Samples	326
Plant Samples	19
Total Samples	700

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

[Ref.: #20909]

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.: #20909]	Williamsia sterculiae strain CPCC 203464 16S ribosomal RNA gene, partial sequence	KC550143	1512	ENA	1344003 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Williamsia sterculiae CPCC 203464	GCA_900156495	scaffold	GenBank	1344003 tax ID
[Ref.: #66792]	Williamsia sterculiae strain CPCC 203464	1344003.3	wgs	PATRIC	1344003 tax ID	*
[Ref.: #66792]	Williamsia sterculiae CPCC 203464.	2681812929	draft	JGI IMG/M	1344003 tax ID	*

[Ref.: #20909]	GC-content	65.4 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31120]	GC-content	65.4 mol%
[Ref.: #67770]	GC-content	67.2 mol%	genome sequence analysis

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: Williamsia sterculiae CPCC 203464 NCBI: GCA_900156495.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Williamsia sterculiae strain CPCC 203464 PATRIC: 1344003.3
[Ref.: #69480]	motile	no	94.959	yes
[Ref.: #69480]	gram-positive	yes	91.079	yes
[Ref.: #69480]	anaerobic	no	99.613	yes
[Ref.: #69480]	halophile	no	91.967	yes
[Ref.: #69480]	spore-forming	no	83.594	yes
[Ref.: #69480]	thermophile	no	99.321	yes
[Ref.: #69480]	glucose-util	yes	89.261	yes
[Ref.: #69480]	aerobic	yes	90.074	yes
[Ref.: #69480]	flagellated	no	98.719	yes
[Ref.: #69480]	glucose-ferment	no	90.174	no

Availability in culture collections External links

[Ref.: #20909]

Culture collection no.

DSM 45741, CPCC 203464, KCTC 29118, JCM 31496

[Ref.: #88506]

SI-ID 403462

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant.	Fang XM, Su J, Wang H, Wei YZ, Zhang T, Zhao LL, Liu HY, Ma BP, Klenk HP, Zhang YQ, Yu LY	Int J Syst Evol Microbiol	10.1099/ijs.0.052688-0	2013	*

References

#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 )

#20909

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45741

#31120

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 #27449 (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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#88506

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-ID403462.1 )

#27449

IJSEM 4158 2013 ( DOI 10.1099/ijs.0.052688-0 , PubMed 23771621 )

* These data were automatically processed and therefore are not curated

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Williamsia sterculiae CPCC 203464

Williamsia sterculiae strain CPCC 203464

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