Name: Ornithinimicrobium flavum DSM 26802
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158266

Type strain:

Species: Ornithinimicrobium flavum

Culture col. no.: DSM 26802, KCTC 29164, NBRC 109452, CPCC 203535

Strain history: <- Y.-Q. Zhang, Chinese Acad. Med. Sciences & Peking Union Medical College; CPCC 203535 <- X.-M. Fang

NCBI tax ID(s): 1288636 (species)

SI-ID 404408

DSM 26802

Section

Ornithinimicrobium flavum DSM 26802 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from leaf of a medicinal plant, Paris polyphylla var. yunnanensis .

colony-forming
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	*Micrococcales*
	Family	*Ornithinimicrobiaceae*
	Genus	*Ornithinimicrobium*
	Species	**Ornithinimicrobium flavum**
	Full Scientific Name (LPSN)	Ornithinimicrobium flavum Fang et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65277]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #65277]	Cell length	0.8-1.7 µm
[Ref.: #65277]	Cell length	0.6-1 µm

[Ref.: #65277]	Cell width	0.6-1 µm

[Ref.: #65277]	Cell shape	rod-shaped
[Ref.: #65277]	Cell shape	coccus-shaped

[Ref.: #65277]	Motility	no

[Ref.: #65277]	Colony color	yellow
[Ref.: #65277]	Colony shape	circular
[Ref.: #65277]	Cultivation medium used	nutrient agar

Information on culture and growth conditions Culture and growth conditions

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Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

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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

GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)

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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

Nutrient agar (NA)

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Culture medium growth

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #64925]			growth	28 °C
[Ref.: #65277]			growth	28-30 °C

[Ref.: #64925]	Temperature range	mesophilic
[Ref.: #65277]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65277]			growth	6-7

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #65277]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.976

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65277]		NaCl		growth	0-5	%(w/v)
[Ref.: #65277]		NaCl		optimum	0-1	%(w/v)

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Observation

not acid-fast

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65277]	2-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #65277]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #65277]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #65277]	acetate ChEBI	+	carbon source
[Ref.: #65277]	acetoacetate ChEBI	+	carbon source
[Ref.: #65277]	bromosuccinate ChEBI	-	carbon source
[Ref.: #65277]	cellobiose ChEBI	-	carbon source
[Ref.: #65277]	D-arabitol ChEBI	-	carbon source
[Ref.: #65277]	D-aspartate ChEBI	-	carbon source
[Ref.: #65277]	D-fructose 6-phosphate ChEBI	+	carbon source
[Ref.: #65277]	D-fucose ChEBI	-	carbon source
[Ref.: #65277]	D-glucuronate ChEBI	+	carbon source
[Ref.: #65277]	D-malate ChEBI	-	carbon source
[Ref.: #65277]	D-mannitol ChEBI	-	carbon source
[Ref.: #65277]	D-mannose ChEBI	-	carbon source
[Ref.: #65277]	D-saccharate ChEBI	-	carbon source
[Ref.: #65277]	D-serine ChEBI	-	carbon source
[Ref.: #65277]	D-sorbitol ChEBI	-	carbon source
[Ref.: #65277]	dextrin ChEBI	+	carbon source
[Ref.: #65277]	formate ChEBI	+	carbon source
[Ref.: #65277]	gelatin ChEBI	-	hydrolysis
[Ref.: #65277]	gentiobiose ChEBI	-	carbon source
[Ref.: #65277]	glucose ChEBI	-	fermentation
[Ref.: #65277]	glucuronamide ChEBI	+	carbon source
[Ref.: #65277]	glycerol ChEBI	-	carbon source
[Ref.: #65277]	glycine-proline ChEBI	-	carbon source
[Ref.: #65277]	inosine ChEBI	-	carbon source
[Ref.: #65277]	L-arginine ChEBI	-	carbon source
[Ref.: #65277]	L-histidine ChEBI	-	carbon source
[Ref.: #65277]	L-pyroglutamic acid ChEBI	-	carbon source
[Ref.: #65277]	L-rhamnose ChEBI	-	carbon source
[Ref.: #65277]	L-serine ChEBI	-	carbon source
[Ref.: #65277]	L-tyrosine ChEBI	-	hydrolysis
[Ref.: #65277]	lactose ChEBI	-	carbon source
[Ref.: #65277]	maltose ChEBI	-	carbon source
[Ref.: #65277]	melibiose ChEBI	-	carbon source
[Ref.: #65277]	methyl beta-D-glucopyranoside ChEBI	-	carbon source
[Ref.: #65277]	methyl pyruvate ChEBI	-	carbon source
[Ref.: #65277]	milk	+	assimilation
[Ref.: #65277]	myo-inositol ChEBI	-	carbon source
[Ref.: #65277]	N-acetyl-beta-D-mannosamine ChEBI	-	carbon source
[Ref.: #65277]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #65277]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #65277]	n-acetylneuraminate ChEBI	-	carbon source
[Ref.: #65277]	nitrate ChEBI	+	reduction
[Ref.: #65277]	pectin ChEBI	+	carbon source
[Ref.: #65277]	quinate ChEBI	-	carbon source
[Ref.: #65277]	raffinose ChEBI	-	carbon source
[Ref.: #65277]	salicin ChEBI	-	carbon source
[Ref.: #65277]	stachyose ChEBI	-	carbon source
[Ref.: #65277]	starch ChEBI	+	hydrolysis
[Ref.: #65277]	sucrose ChEBI	-	carbon source
[Ref.: #65277]	trehalose ChEBI	-	carbon source
[Ref.: #65277]	turanose ChEBI	-	carbon source
[Ref.: #65277]	tween 40 ChEBI	+	carbon source
[Ref.: #65277]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #65277]	acetoin ChEBI	no
[Ref.: #65277]	hydrogen sulfide ChEBI	no
[Ref.: #65277]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #65277]		acetoin ChEBI	-
[Ref.: #65277]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #65277]	acid phosphatase	+	3.1.3.2
[Ref.: #65277]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65277]	alpha-glucosidase	+	3.2.1.20
[Ref.: #65277]	catalase	+	1.11.1.6
[Ref.: #65277]	cystine arylamidase	+	3.4.11.3
[Ref.: #65277]	cytochrome oxidase	-	1.9.3.1
[Ref.: #65277]	esterase	+
[Ref.: #65277]	esterase Lipase (C 8)	+
[Ref.: #65277]	leucine arylamidase	+	3.4.11.1
[Ref.: #65277]	lipase (C 14)	+
[Ref.: #65277]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65277]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65277]

Fatty acid	Percentage
C16:0 iso	33.7
C15:0 iso	25.5
C15:0 anteiso	11.2
C14:0 iso	7.6
C15:0	4.1
C17:0 iso	2.3
C17:0 anteiso	2.1
C16:0	1.7

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

[Ref.: #64925]	Sample type/isolated from	leaf of a medicinal plant, Paris polyphylla var. yunnanensis (Franch.)
[Ref.: #64925]	Geographic location (country and/or sea, region)	Yunnan Province, Xishuangbanna
[Ref.: #64925]	Country	China
[Ref.: #64925]	Country ISO 3 Code	CHN
[Ref.: #64925]	Continent	Asia

[Ref.: #65277]	Sample type/isolated from	surface-sterilized leaf of a medicinal plant, P. polyphylla var. yunnanensis (Franch.)
[Ref.: #65277]	Geographic location (country and/or sea, region)	Xishuangbanna in Yunnan province
[Ref.: #65277]	Country	China
[Ref.: #65277]	Country ISO 3 Code	CHN
[Ref.: #65277]	Continent	Asia
[Ref.: #65277]	Enrichment culture	nutreint agar
[Ref.: #65277]	Enrichment culture composition	with 0.2% starch
[Ref.: #65277]	Enrichment culture duration	7 days
[Ref.: #65277]	Enrichment culture temperature	28 ̊C
[Ref.: #65277]	Isolation/enrichment procedure	isolated on isolation medium plate containing starch 2 g, K2HPO4 0.5 g, MgSO4 0.5 g, KNO3 1 g, NaCl 0.4 g, FeSO4 x 7H2O 0.01 g and agar 15 g per litre (pH 7.2). The purified isolate was cultured on nutrient agar with 0.2 % starch at 28°C for 7 days.
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC550155 (>99% sequence identity) for Ornithinimicrobium flavum subclade from Microbeatlas

Aquatic Samples	226
Soil Samples	234
Animal Samples	1394
Plant Samples	72
Total Samples	1926

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

[Ref.: #64925]

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.: #64925]	Ornithinimicrobium flavum 16S ribosomal RNA gene, partial sequence	KC550155	1515	ENA	1288636 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ornithinimicrobium flavum CPCC 203535	GCA_004526345	complete	GenBank	1288636 tax ID	*
[Ref.: #66792]	Ornithinimicrobium flavum strain CPCC 203535	1288636.3	complete	PATRIC	1288636 tax ID	*
[Ref.: #66792]	Ornithinimicrobium flavum CPCC 203535	2836947475	complete	JGI IMG/M	1288636 tax ID	*

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GC-content

71.4 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 GenomeNet Sporulation v. 1 based on: Ornithinimicrobium flavum CPCC 203535 NCBI: GCA_004526345.1
[Ref.: #69481]	spore-forming	no	80	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ornithinimicrobium flavum CPCC 203535 NCBI: GCA_004526345.1
[Ref.: #69480]	motile	no	94.771	yes
[Ref.: #69480]	flagellated	no	98.928	no
[Ref.: #69480]	gram-positive	yes	87.542	no
[Ref.: #69480]	anaerobic	no	99.277	yes
[Ref.: #69480]	aerobic	yes	91.063	yes
[Ref.: #69480]	halophile	no	83.822	yes
[Ref.: #69480]	spore-forming	no	93.882	yes
[Ref.: #69480]	glucose-util	yes	91.038	no
[Ref.: #69480]	thermophile	no	98.135	yes
[Ref.: #69480]	glucose-ferment	no	89.893	yes

Availability in culture collections External links

[Ref.: #64925]

Culture collection no.

DSM 26802, KCTC 29164, NBRC 109452, CPCC 203535

[Ref.: #111084]

SI-ID 404408

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ornithinimicrobium pratense sp. nov., isolated from meadow soil.	Guo Q, Wang B, Zhou Z, Ke X, Zhang L, Chen M, Lin M, Wang W, Zhang W, Li X	Int J Syst Evol Microbiol	10.1099/ijsem.0.004557	2020	*
Phylogeny	Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla.	Fang XM, Yan D, Bai JL, Su J, Liu HY, Ma BP, Zhang YQ, Yu LY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002328	2017	*

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 )

#64925

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26802

#65277

Xiao-Mei Fang, Dong Yan, Jing-Lin Bai, Jing Su, Hong-Yu Liu, Bai-Ping Ma, Yu-Qin Zhang, Li-Yan Yu: Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla. IJSEM 67: 4541 - 4545 2017 ( DOI 10.1099/ijsem.0.002328 , PubMed 28945533 )

#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) .

#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 )

#111084

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-ID404408.1 )

* These data were automatically processed and therefore are not curated

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Ornithinimicrobium flavum CPCC 203535

Ornithinimicrobium flavum CPCC 203535

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