Name: Nocardioides flavus Y4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133240

Type strain:

Species: Nocardioides flavus

Strain Designation: Y4

Culture col. no.: CGMCC 1.12791, MCCC 1A09944, LMG 28100, JCM 19770

Strain history: G. Zhang Y4.

NCBI tax ID(s): 2058780 (species)

Section

Nocardioides flavus Y4 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from deep-sea sediment .

colony-forming
Gram-positive
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Propionibacteriales*
	Family	*Nocardioidaceae*
	Genus	*Nocardioides*
	Species	**Nocardioides flavus**
	Full Scientific Name (LPSN)	Nocardioides flavus Wang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25087]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25087]	Cell length	1.2-1.7 µm

[Ref.: #25087]	Cell width	0.5-0.6 µm

[Ref.: #25087]	Cell shape	rod-shaped

[Ref.: #25087]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.815

[Ref.: #25087]	Colony size	1.0-2.0 mm
[Ref.: #25087]	Colony color	yellow
[Ref.: #25087]	Colony shape	circular
[Ref.: #25087]	Incubation period	3 days
[Ref.: #25087]	Cultivation medium used	MZ2

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25087]

Culture medium

modified Zobell 2216E agar

[Ref.: #25087]

Culture medium growth

[Ref.: #25087]

Culture medium composition

expand / minimize

[Ref.: #25087]

Culture medium

MZ2

[Ref.: #25087]

Culture medium growth

		Temperature
[Ref.: #25087]	growth	4.0-40.0 °C
[Ref.: #25087]	optimum	35.0-37.0 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #25087]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25087]			optimum	7
[Ref.: #25087]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25087]

Oxygen tolerance

aerobe

[Ref.: #25087]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.825

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25087]		NaCl		optimum	1	%
[Ref.: #25087]		NaCl		growth	0.0-10.0	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-8(H₄), MK-7(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25087]	(-)-quinic acid ChEBI	-	oxidation
[Ref.: #25087]	2,3-butanediol ChEBI	-	oxidation
[Ref.: #25087]	2-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #25087]	2-oxobutanoate ChEBI	-	oxidation
[Ref.: #25087]	2-oxoglutarate ChEBI	-	oxidation
[Ref.: #25087]	2-oxopentanoate ChEBI	-	oxidation
[Ref.: #25087]	3-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #25087]	4-hydroxy-L-proline ChEBI	-	oxidation
[Ref.: #25087]	4-hydroxybutyrate ChEBI	-	oxidation
[Ref.: #25087]	4-hydroxyphenylacetic acid ChEBI	-	oxidation
[Ref.: #25087]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	hydrolysis
[Ref.: #25087]	acetate ChEBI	+	oxidation
[Ref.: #25087]	adenosine ChEBI	+	oxidation
[Ref.: #25087]	adipate ChEBI	-	assimilation
[Ref.: #25087]	alpha-cyclodextrin ChEBI	-	oxidation
[Ref.: #25087]	alpha-D-glucose ChEBI	-	oxidation
[Ref.: #25087]	alpha-lactose ChEBI	-	oxidation
[Ref.: #25087]	ammonium ChEBI	+	nitrogen source
[Ref.: #25087]	amygdalin ChEBI	-	fermentation
[Ref.: #25087]	arabinose ChEBI	-	fermentation
[Ref.: #25087]	bromosuccinate ChEBI	-	oxidation
[Ref.: #25087]	carnitine ChEBI	-	oxidation
[Ref.: #25087]	casein	+	hydrolysis
[Ref.: #25087]	cellobiose ChEBI	-	oxidation
[Ref.: #25087]	cellulose ChEBI	-	hydrolysis
[Ref.: #25087]	cis-aconitate ChEBI	-	oxidation
[Ref.: #25087]	citrate ChEBI	-	oxidation
[Ref.: #25087]	citrate ChEBI	+	carbon source
[Ref.: #25087]	D-alanine ChEBI	-	oxidation
[Ref.: #25087]	D-arabitol ChEBI	-	oxidation
[Ref.: #25087]	D-fructose ChEBI	+	oxidation
[Ref.: #25087]	D-galactonic acid lactone ChEBI	-	oxidation
[Ref.: #25087]	D-galactose ChEBI	-	oxidation
[Ref.: #25087]	D-galacturonic acid ChEBI	-	oxidation
[Ref.: #25087]	D-glucarate ChEBI	-	oxidation
[Ref.: #25087]	D-gluconate ChEBI	-	oxidation
[Ref.: #25087]	D-glucosaminic acid ChEBI	-	oxidation
[Ref.: #25087]	D-glucose ChEBI	-	assimilation
[Ref.: #25087]	D-glucose 6-phosphate ChEBI	-	oxidation
[Ref.: #25087]	D-glucuronate ChEBI	-	oxidation
[Ref.: #25087]	D-malate ChEBI	+	oxidation
[Ref.: #25087]	D-mannitol ChEBI	-	assimilation
[Ref.: #25087]	D-mannitol ChEBI	-	oxidation
[Ref.: #25087]	D-mannose ChEBI	-	assimilation
[Ref.: #25087]	D-mannose ChEBI	+	oxidation
[Ref.: #25087]	D-psicose ChEBI	-	oxidation
[Ref.: #25087]	D-serine ChEBI	-	oxidation
[Ref.: #25087]	D-sorbitol ChEBI	-	oxidation
[Ref.: #25087]	decanoate ChEBI	-	assimilation
[Ref.: #25087]	dextrin ChEBI	-	oxidation
[Ref.: #25087]	erythritol ChEBI	-	oxidation
[Ref.: #25087]	esculin ChEBI	+	hydrolysis
[Ref.: #25087]	ethanolamine ChEBI	-	oxidation
[Ref.: #25087]	formate ChEBI	-	oxidation
[Ref.: #25087]	gamma-aminobutyric acid ChEBI	-	oxidation
[Ref.: #25087]	gelatin ChEBI	+	hydrolysis
[Ref.: #25087]	gentiobiose ChEBI	-	oxidation
[Ref.: #25087]	glucose ChEBI	-	fermentation
[Ref.: #25087]	glucose 1-phosphate ChEBI	-	oxidation
[Ref.: #25087]	glucuronamide ChEBI	-	oxidation
[Ref.: #25087]	glycerol ChEBI	-	oxidation
[Ref.: #25087]	glycerol 1-phosphate ChEBI	+	oxidation
[Ref.: #25087]	glycogen ChEBI	-	oxidation
[Ref.: #25087]	glycyl L-aspartic acid ChEBI	-	oxidation
[Ref.: #25087]	glycyl-l-glutamate ChEBI	-	oxidation
[Ref.: #25087]	inosine ChEBI	-	oxidation
[Ref.: #25087]	itaconate ChEBI	-	oxidation
[Ref.: #25087]	L-alaninamide ChEBI	-	oxidation
[Ref.: #25087]	L-alanine ChEBI	-	oxidation
[Ref.: #25087]	L-alanylglycine ChEBI	-	oxidation
[Ref.: #25087]	L-arabinose ChEBI	-	assimilation
[Ref.: #25087]	L-arabinose ChEBI	-	oxidation
[Ref.: #25087]	L-asparagine ChEBI	-	oxidation
[Ref.: #25087]	L-aspartate ChEBI	-	oxidation
[Ref.: #25087]	L-fucose ChEBI	-	oxidation
[Ref.: #25087]	L-glutamate ChEBI	-	oxidation
[Ref.: #25087]	L-histidine ChEBI	-	oxidation
[Ref.: #25087]	L-leucine ChEBI	-	oxidation
[Ref.: #25087]	L-ornithine ChEBI	-	oxidation
[Ref.: #25087]	L-phenylalanine ChEBI	-	oxidation
[Ref.: #25087]	L-proline ChEBI	-	oxidation
[Ref.: #25087]	L-pyroglutamic acid ChEBI	-	oxidation
[Ref.: #25087]	L-rhamnose ChEBI	-	oxidation
[Ref.: #25087]	L-serine ChEBI	-	oxidation
[Ref.: #25087]	L-threonine ChEBI	-	oxidation
[Ref.: #25087]	lactate ChEBI	-	oxidation
[Ref.: #25087]	lactulose ChEBI	-	oxidation
[Ref.: #25087]	malate ChEBI	-	assimilation
[Ref.: #25087]	malonate ChEBI	-	oxidation
[Ref.: #25087]	maltose ChEBI	-	assimilation
[Ref.: #25087]	maltose ChEBI	-	oxidation
[Ref.: #25087]	mannitol ChEBI	-	fermentation
[Ref.: #25087]	melibiose ChEBI	-	fermentation
[Ref.: #25087]	melibiose ChEBI	-	oxidation
[Ref.: #25087]	methyl beta-D-glucopyranoside ChEBI	-	oxidation
[Ref.: #25087]	methyl pyruvate ChEBI	-	oxidation
[Ref.: #25087]	monomethyl succinate ChEBI	-	oxidation
[Ref.: #25087]	myo-inositol ChEBI	-	fermentation
[Ref.: #25087]	myo-inositol ChEBI	-	oxidation
[Ref.: #25087]	N-acetylgalactosamine ChEBI	-	oxidation
[Ref.: #25087]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #25087]	N-acetylglucosamine ChEBI	-	oxidation
[Ref.: #25087]	nitrate ChEBI	+	reduction
[Ref.: #25087]	phenylacetate ChEBI	-	assimilation
[Ref.: #25087]	phenylethylamine ChEBI	-	oxidation
[Ref.: #25087]	potassium gluconate ChEBI	-	assimilation
[Ref.: #25087]	propionate ChEBI	-	oxidation
[Ref.: #25087]	putrescine ChEBI	-	oxidation
[Ref.: #25087]	raffinose ChEBI	-	oxidation
[Ref.: #25087]	rhamnose ChEBI	-	fermentation
[Ref.: #25087]	ribitol ChEBI	-	oxidation
[Ref.: #25087]	sebacic acid ChEBI	-	oxidation
[Ref.: #25087]	sodium citrate ChEBI	-	assimilation
[Ref.: #25087]	sorbitol ChEBI	-	fermentation
[Ref.: #25087]	starch ChEBI	-	hydrolysis
[Ref.: #25087]	succinamate ChEBI	-	oxidation
[Ref.: #25087]	succinate ChEBI	-	oxidation
[Ref.: #25087]	sucrose ChEBI	-	fermentation
[Ref.: #25087]	sucrose ChEBI	-	oxidation
[Ref.: #25087]	thymidine ChEBI	-	oxidation
[Ref.: #25087]	trehalose ChEBI	-	oxidation
[Ref.: #25087]	tryptophan ChEBI	-	energy source
[Ref.: #25087]	turanose ChEBI	-	oxidation
[Ref.: #25087]	tween 40 ChEBI	+	oxidation
[Ref.: #25087]	tween 80 ChEBI	+	oxidation
[Ref.: #25087]	uridine ChEBI	-	oxidation
[Ref.: #25087]	urocanic acid ChEBI	-	oxidation
[Ref.: #25087]	xylitol ChEBI	-	oxidation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #25087]	acetoin ChEBI	no
[Ref.: #25087]	hydrogen sulfide ChEBI	no
[Ref.: #25087]	indole ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test	Citrate test
[Ref.: #25087]	acetoin ChEBI	-
[Ref.: #25087]	citrate ChEBI				+
[Ref.: #25087]	glucose ChEBI		-
[Ref.: #25087]	indole ChEBI			-

	Enzyme	Enzyme activity	EC number
[Ref.: #25087]	acid phosphatase	+	3.1.3.2
[Ref.: #25087]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25087]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25087]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25087]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25087]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25087]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25087]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25087]	beta-galactosidase	+	3.2.1.23
[Ref.: #25087]	beta-glucosidase	+	3.2.1.21
[Ref.: #25087]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25087]	catalase	+	1.11.1.6
[Ref.: #25087]	cystine arylamidase	+	3.4.11.3
[Ref.: #25087]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25087]	esterase (C 4)	+
[Ref.: #25087]	esterase Lipase (C 8)	+
[Ref.: #25087]	gelatinase	+
[Ref.: #25087]	leucine arylamidase	+	3.4.11.1
[Ref.: #25087]	lipase (C 14)	-
[Ref.: #25087]	lysine decarboxylase	-	4.1.1.18
[Ref.: #25087]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25087]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25087]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #25087]	trypsin	+	3.4.21.4
[Ref.: #25087]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25087]	tryptophan decarboxylase	+	4.1.1.27
[Ref.: #25087]	urease	-	3.5.1.5
[Ref.: #25087]	valine arylamidase	+
	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.: #25087]	Sample type/isolated from	deep-sea sediment (depth of 7068 m)
[Ref.: #25087]	Geographic location (country and/or sea, region)	Western Pacific
[Ref.: #25087]	Geographic location	11.0000°/142.0000°
[Ref.: #25087]	Enrichment culture	isolation medium
[Ref.: #25087]	Enrichment culture composition	15.0 g agar and 1 litre natural seawater; pH 7.2 – 7.4
[Ref.: #25087]	Enrichment culture duration	21 days
[Ref.: #25087]	Enrichment culture temperature	28 ̊C

[Ref.: #67770]	Sample type/isolated from	Sediment from the Western Pacific
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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.: #25087]	Nocardioides sp. Y4 16S ribosomal RNA gene, partial sequence	KT962840	1475	GenBank	1537382 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nocardioides flavus Wang et al. 2016 CGMCC 1.12791	GCA_014653115	scaffold	GenBank	2058780 tax ID	*
[Ref.: #66792]	Nocardioides flavus Wang et al. 2016 strain CGMCC 1.12791	2058780.3	wgs	PATRIC	2058780 tax ID	*

[Ref.: #25087]

GC-content

70.4 mol%

high performance liquid chromatography (HPLC)

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: Nocardioides flavus Wang et al. 2016 CGMCC 1.12791 NCBI: GCA_014653115.1
[Ref.: #69481]	spore-forming	no	78	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nocardioides flavus Wang et al. 2016 CGMCC 1.12791 NCBI: GCA_014653115.1
[Ref.: #69480]	motile	no	96.961	no
[Ref.: #69480]	flagellated	no	98.797	no
[Ref.: #69480]	gram-positive	yes	92.783	yes
[Ref.: #69480]	anaerobic	no	98.483	yes
[Ref.: #69480]	aerobic	yes	91.733	yes
[Ref.: #69480]	halophile	no	90.979	no
[Ref.: #69480]	spore-forming	no	88.259	yes
[Ref.: #69480]	thermophile	no	96.703	yes
[Ref.: #69480]	glucose-util	yes	84.931	yes
[Ref.: #69480]	glucose-ferment	no	90.77	yes

Availability in culture collections External links

[Ref.: #25087]

Culture collection no.

CGMCC 1.12791, MCCC 1A09944, LMG 28100, JCM 19770

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides flavus sp. nov., isolated from marine sediment.	Wang S, Zhou Y, Zhang G	Int J Syst Evol Microbiol	10.1099/ijsem.0.001507	2016	*

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 )

#25087

S. Z. Wang, Y.,Zhang, G.: Nocardioides flavus sp. nov., isolated from marine sediment. IJSEM 66: 5275 - 5280 2016 ( DOI 10.1099/ijsem.0.001507 , PubMed 27654931 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

* These data were automatically processed and therefore are not curated

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Nocardioides flavus Wang et al. 2016 CGMCC 1.12791

Nocardioides flavus Wang et al. 2016 CGMCC 1.12791

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