Name: Ornithinimicrobium pekingense LW6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6280

Type strain:

Species: Ornithinimicrobium pekingense

Strain Designation: LW6

Culture col. no.: DSM 21552, CGMCC 1.5362, JCM 14001

Strain history: S.-J. Liu LW6.

NCBI tax ID(s): 1122622 (strain), 384677 (species)

Section

Ornithinimicrobium pekingense LW6 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from activated sludge, wastewater treatment bioreactor.

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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Ornithinimicrobiaceae*
	Genus	*Ornithinimicrobium*
	Species	**Ornithinimicrobium pekingense**
	Full Scientific Name (LPSN)	Ornithinimicrobium pekingense Liu et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32268]	Gram stain	positive
[Ref.: #32268]	Cell length	1.3 µm
[Ref.: #32268]	Cell width	0.65 µm
[Ref.: #32268]	Cell shape	rod-shaped
[Ref.: #32268]	Motility	no

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

[Ref.: #32268]

Pigment production

yes

Multimedia content

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Caption:

Medium 535 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

BHI MEDIUM (DSMZ Medium 215)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15791]	growth	28 °C
[Ref.: #32268]	growth	26-38 °C
[Ref.: #32268]	optimum	35 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #15791]	Temperature range	mesophilic
[Ref.: #32268]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32268]			optimum	8
[Ref.: #32268]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32268]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.98

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32268]		NaCl		growth	7	%

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Observation

quinones: MK-8(H₄), MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32268]	acetate ChEBI	+	carbon source
[Ref.: #32268]	cellobiose ChEBI	+	carbon source
[Ref.: #32268]	citrate ChEBI	+	carbon source
[Ref.: #32268]	fructose ChEBI	+	carbon source
[Ref.: #32268]	galactose ChEBI	+	carbon source
[Ref.: #32268]	L-arabitol ChEBI	+	carbon source
[Ref.: #32268]	nitrate ChEBI	+	reduction
[Ref.: #32268]	raffinose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32268]		catalase	+	1.11.1.6
[Ref.: #32268]		gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	metabolism of disaccharids	81.82	9 of 11
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin E metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	peptidoglycan biosynthesis	66.67	10 of 15
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[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]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #15791]	Sample type/isolated from	activated sludge, wastewater treatment bioreactor
[Ref.: #15791]	Geographic location (country and/or sea, region)	Peking
[Ref.: #15791]	Country	China
[Ref.: #15791]	Country ISO 3 Code	CHN
[Ref.: #15791]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Activated sludge of a bioreactor treating wastewater
[Ref.: #67770]	Geographic location (country and/or sea, region)	Beijing
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Wastewater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ512860 (>99% sequence identity) for Ornithinimicrobium from Microbeatlas

Aquatic Samples	205
Soil Samples	222
Animal Samples	798
Plant Samples	83
Total Samples	1308

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

[Ref.: #15791]

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.: #15791]	Ornithinimicrobium pekingense strain LW6 16S ribosomal RNA gene, partial sequence	DQ512860	1396	ENA	1122622 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Ornithinimicrobium pekingense DSM 21552 DSM 21552	GCA_000421185	scaffold	GenBank	1122622 tax ID
[Ref.: #66792]	Ornithinimicrobium pekingense CGMCC 1.5362	GCA_014644955	scaffold	GenBank	384677 tax ID	*
[Ref.: #66792]	Ornithinimicrobium pekingense DSM 21552	1122622.9	wgs	PATRIC	1122622 tax ID	*
[Ref.: #66792]	Ornithinimicrobium pekingense strain CGMCC 1.5362	384677.7	wgs	PATRIC	384677 tax ID	*
[Ref.: #66792]	Ornithinimicrobium pekingense DSM 21552	2524614884	draft	JGI IMG/M	1122622 tax ID	*

[Ref.: #15791]	GC-content	69 mol%
[Ref.: #67770]	GC-content	72.9 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	69 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ornithinimicrobium pekingense DSM 21552 DSM 21552 NCBI: GCA_000421185.1
[Ref.: #69480]	anaerobic	no	93.548	yes
[Ref.: #69480]	spore-forming	no	99.98	no
[Ref.: #69480]	gram-positive	yes	100	no
[Ref.: #69480]	thermophile	no	97.79	yes
[Ref.: #69480]	motile	no	89.018	yes

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ornithinimicrobium pekingense DSM 21552 DSM 21552 NCBI: GCA_000421185.1
[Ref.: #69481]	spore-forming	no	87	no

Availability in culture collections External links

[Ref.: #15791]

Culture collection no.

DSM 21552, CGMCC 1.5362, JCM 14001

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ornithinimicrobium cerasi sp. nov., isolated from the fruit of Cerasus pseudocerasus and emended description of the genus Ornithinimicrobium.	Fang XM, Du HJ, Bai JL, He WN, Li J, Wang H, Su J, Liu HY, Zhang YQ, Yu LY	Int J Syst Evol Microbiol	10.1099/ijsem.0.003957	2020	*
Phylogeny	Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva.	Ramaprasad EVV, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijsem.0.000624	2015	*
Phylogeny	Ornithinimicrobium pekingense sp. nov., isolated from activated sludge.	Liu XY, Wang BJ, Jiang CY, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65229-0	2008	*

References

#15791

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21552

#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 )

#32268

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 #28509 (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;

#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 )

#28509

IJSEM 116 2008 ( DOI 10.1099/ijs.0.65229-0 , PubMed 18175694 )

* These data were automatically processed and therefore are not curated

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Ornithinimicrobium pekingense DSM 21552 DSM 21552

Ornithinimicrobium pekingense DSM 21552 DSM 21552

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