Name: Kocuria flava HO-9041
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7662

Type strain:

Species: Kocuria flava

Strain Designation: HO-9041

Culture col. no.: DSM 22142, CCTCC AB 206106, KCTC 19306, JCM 15621, NBRC 107626

Strain history: <- X Luo, CCTCC, China

NCBI tax ID(s): 446860 (species)

SI-ID 400794

DSM 22142

Section

Kocuria flava HO-9041 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from air.

coccus-shaped
Gram-positive
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	*Micrococcaceae*
	Genus	*Kocuria*
	Species	**Kocuria flava**
	Full Scientific Name (LPSN)	Kocuria flava Zhou et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32328]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #32328]	Cell shape	coccus-shaped

[Ref.: #32328]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.725

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16161]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #16161]

Culture medium growth

[Ref.: #16161]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16161]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16161]	growth	28 °C
[Ref.: #32328]	growth	28-45 °C
[Ref.: #67770]	growth	35 °C
[Ref.: #67771]	growth	35 °C

[Ref.: #16161]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32328]			growth	07-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32328]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32328]		NaCl		growth	0-10	%

[Ref.: #67770]	Observation	quinones: MK-8(H₂), MK-9(H₂), MK-7(H₂)
[Ref.: #67771]	Observation	quinones: MK-8(H2), MK-9(H2)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32328]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #32328]	arabinose ChEBI	+	carbon source
[Ref.: #32328]	gluconate ChEBI	+	carbon source
[Ref.: #32328]	lactose ChEBI	+	carbon source
[Ref.: #32328]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #32328]	nitrate ChEBI	+	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32328]		catalase	+	1.11.1.6
[Ref.: #32328]		urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	myo-inositol biosynthesis	100	10 of 10
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ketogluconate metabolism	100	8 of 8
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	citric acid cycle	92.86	13 of 14
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	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]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	allantoin degradation	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	oxidative phosphorylation	64.84	59 of 91
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	ubiquinone biosynthesis	28.57	2 of 7
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #16161]	Sample type/isolated from	air
[Ref.: #16161]	Geographic location (country and/or sea, region)	Xinjiang
[Ref.: #16161]	Country	China
[Ref.: #16161]	Country ISO 3 Code	CHN
[Ref.: #16161]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Air
[Ref.: #67770]	Geographic location (country and/or sea, region)	Xinjiang
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From air
[Ref.: #67771]	Geographic location (country and/or sea, region)	Xinjiang
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Air

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF602041 (>99% sequence identity) for Kocuria flava subclade from Microbeatlas

Aquatic Samples	840
Soil Samples	1734
Animal Samples	2511
Plant Samples	897
Total Samples	5982

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

[Ref.: #16161]

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.: #16161]	Kocuria flava strain HO-9041 16S ribosomal RNA gene, partial sequence	EF602041	1443	ENA	446860 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]	Kocuria flava HO-9041	2721755800	complete	JGI IMG/M	446860 tax ID	*
[Ref.: #66792]	Kocuria flava NBRC 107626	GCA_007992135	contig	GenBank	446860 tax ID	*
[Ref.: #66792]	Kocuria flava strain HO-9041	446860.3	complete	PATRIC	446860 tax ID	*
[Ref.: #66792]	Kocuria flava strain HO-9041	446860.5	plasmid	PATRIC	446860 tax ID	*
[Ref.: #66792]	Kocuria flava strain HO-9041	446860.6	plasmid	PATRIC	446860 tax ID	*
[Ref.: #66792]	Kocuria flava strain HO-9041	446860.4	plasmid	PATRIC	446860 tax ID	*

[Ref.: #16161]	GC-content	71.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32328]	GC-content	71 mol%
[Ref.: #67770]	GC-content	71 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	73.9 mol%	genome sequence analysis
[Ref.: #67771]	GC-content	71.0 mol%

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: Kocuria flava HO-9041 NCBI: GCA_001482365.1
[Ref.: #69481]	spore-forming	yes	52	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Kocuria flava HO-9041 NCBI: GCA_001482365.1
[Ref.: #69480]	flagellated	no	97.23	yes
[Ref.: #69480]	gram-positive	yes	93.597	yes
[Ref.: #69480]	anaerobic	no	99.55	no
[Ref.: #69480]	aerobic	yes	93.13	no
[Ref.: #69480]	halophile	yes	59.044	no
[Ref.: #69480]	spore-forming	no	90.856	no
[Ref.: #69480]	glucose-util	yes	87.629	no
[Ref.: #69480]	motile	no	91.026	no
[Ref.: #69480]	thermophile	no	97.72	yes
[Ref.: #69480]	glucose-ferment	no	82.68	no

Availability in culture collections External links

[Ref.: #16161]

Culture collection no.

DSM 22142, CCTCC AB 206106, KCTC 19306, JCM 15621, NBRC 107626

[Ref.: #77106]

SI-ID 400794

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics Provides Insights Into the Marine Adaptation in Sponge-Derived Kocuriaflava S43.	Sun W, Liu C, Zhang F, Zhao M, Li Z	Front Microbiol	10.3389/fmicb.2018.01257	2018	*
Phylogeny	Kocuria oceani sp. nov., isolated from a deep-sea hydrothermal plume.	Zhang L, Xi L, Ruan J, Huang Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001599	2017	*
Genetics	Complete genome sequence of Kocuria flava strain HO-9041, a heavy metal removal bacterium from Xinjiang.	Zhou M, Zhang Y, Li X, Wang Z, Tang J, Mu Y, Fang C, Chen X, Dai J	J Biotechnol	10.1016/j.jbiotec.2016.01.004	2016	*
Phylogeny	Kocuria dechangensis sp. nov., an actinobacterium isolated from saline and alkaline soils.	Wang K, Zhang L, Liu Y, Pan Y, Meng L, Xu T, Zhang C, Liu H, Hong S, Huang H, Jiang J	Int J Syst Evol Microbiol	10.1099/ijs.0.000372	2015	*
Phylogeny	Kocuria flava sp. nov. and Kocuria turfanensis sp. nov., airborne actinobacteria isolated from Xinjiang, China.	Zhou G, Luo X, Tang Y, Zhang L, Yang Q, Qiu Y, Fang C	Int J Syst Evol Microbiol	10.1099/ijs.0.65323-0	2008	*

References

#16161

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22142

#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 )

#32328

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 #28562 (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 )

#77106

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-ID400794.1 )

#28562

IJSEM 1304 2008 ( DOI 10.1099/ijs.0.65323-0 , PubMed 18523169 )

* These data were automatically processed and therefore are not curated

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