Nocardioides iriomotensis (DSM 25935, JCM 17985, KACC 14926)

Name: Nocardioides iriomotensis (DSM 25935, JCM 17985, KACC 14926)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11152

Type strain

Strain Designation IR27-S3

Culture col. no. DSM 25935 JCM 17985 KACC 14926 NBRC 105384 IR27-S3

NCBI tax ID(s) 715784

Special Collections DSMZ JCM Wink compendium

Links

Nocardioides iriomotensis IR27-S3 is a mesophilic prokaryote that was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402526

NBRC 105384,JCM 17985,DSM 25935

@ref 20215

Last LPSN update 2025-12-16 09:49:31

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides iriomotensis

Full scientific name Nocardioides iriomotensis Yamamura et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	97.9

Colony morphology

@ref	Colony color	Medium used
69327	Colorless	ISP 3
69327	Colorless	ISP 4
69327	Beige (1001)	ISP 2
69327	Beige (1001)	ISP 6
69327	Beige (1001)	ISP 7
69327	Ivory (1014)	suter with tyrosine
69327	Light ivory (1015)	ISP 5
69327	Light ivory (1015)	suter without tyrosine

Multicellular morphology

@ref	Complex name	Medium name
69327	Aerial mycelium	ISP 2
69327	Aerial mycelium	ISP 3
69327	Aerial mycelium	ISP 4
69327	Aerial mycelium	ISP 5
69327	Aerial mycelium	ISP 6
69327	Aerial mycelium	ISP 7
69327	Aerial mycelium	suter with tyrosine
69327	Aerial mycelium	suter without tyrosine

Pigmentation

@ref	Production	Color	Name
69327			melanin pigment
69327		Ochre brown (8001)	soluble pigment

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18127	RICH MEDIUM (DSMZ Medium 736)		Medium recipe at MediaDive	Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water
18127	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
18127	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	90.189
125439	obligate aerobe	99.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69327	NaCl	positive	growth	0-5 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69327	22599 ChEBI	arabinose	-	growth
69327	62968 ChEBI	cellulose	-	growth
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
69327	28757 ChEBI	fructose	+	growth
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
69327	17234 ChEBI	glucose	-	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69327	17268 ChEBI	inositol	-	growth
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69327	37684 ChEBI	mannose	+	growth
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
69327	16634 ChEBI	raffinose	-	growth
69327	26546 ChEBI	rhamnose	+	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69327	17992 ChEBI	sucrose	-	growth
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
69327	18222 ChEBI	xylose	-	growth

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	-	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	glycogen metabolism	100	5 of 5
66794	cardiolipin biosynthesis	100	7 of 7
66794	threonine metabolism	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	taurine degradation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	cellulose degradation	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	heme metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	metabolism of disaccharids	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	factor 420 biosynthesis	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	3-chlorocatechol degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	Entner Doudoroff pathway	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	alanine metabolism	79.31	23 of 29
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	tryptophan metabolism	76.32	29 of 38
66794	histidine metabolism	75.86	22 of 29
66794	acetate fermentation	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	non-pathway related	73.68	28 of 38
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	propanol degradation	71.43	5 of 7
66794	aclacinomycin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	phenol degradation	70	14 of 20
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	67.03	61 of 91
66794	acetoin degradation	66.67	2 of 3
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	IAA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	polyamine pathway	65.22	15 of 23
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cysteine metabolism	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	sulfate reduction	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	quinate degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	degradation of pentoses	50	14 of 28
66794	carnitine metabolism	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	resorcinol degradation	50	1 of 2
66794	androgen and estrogen metabolism	50	8 of 16
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonic acid metabolism	38.89	7 of 18
66794	vitamin B1 metabolism	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	methanogenesis from CO2	33.33	4 of 12
66794	sulfoquinovose degradation	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of sugar acids	32	8 of 25
66794	ascorbate metabolism	31.82	7 of 22
66794	vitamin B12 metabolism	29.41	10 of 34
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69327	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
69327	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
18127	soil	Okinawa, Iriomote Island	Japan	JPN	Asia
67770	Forest soil from Iriomote Island	Okinawa	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18127	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM416803v1 assembly for Nocardioides iriomotensis NBRC 105384	contig	GCA_004168035	715784.3	2866601643	715784	68.06

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18127	Nocardioides iriomotensis gene for 16S ribosomal RNA, partial sequence	AB544079	1463		715784

GC content

@ref	GC-content (mol%)	Method
18127	73.7
67770	73.7	high performance liquid chromatography (HPLC)
67770	72.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardioides iriomotensis NBRC 105384
NCBI: GCA_004168035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	79.30	no
125439	motility	BacteriaNetⓘ	no	55.30	no
125439	gram_stain	BacteriaNetⓘ	positive	97.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides iriomotensis strain NBRC 105384
PATRIC: 715784.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.88	no
125438	anaerobic	anaerobicⓘ	no	93.83	no
125438	spore-forming	spore-formingⓘ	no	51.50	no
125438	aerobic	aerobicⓘ	yes	90.19	no
125438	thermophilic	thermophileⓘ	no	93.50	no
125438	flagellated	motile2+ⓘ	no	77.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Investigation of dirigent like domains from bacterial genomes.	Bardin M, Rousselot-Pailley P, Tron T, Robert V.	BMC Bioinformatics	10.1186/s12859-022-04832-6	2022
Phylogeny	Nocardioides panacis sp. nov., isolated from soil of a ginseng field.	Park Y, Liu Q, Maeng S, Choi WJ, Chang Y, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.005400	2022
Phylogeny	Nocardioides guangzhouensis sp. nov., an actinobacterium isolated from soil.	Chen P, Fu Y, Cai Y, Lin Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.003726	2020
Phylogeny	Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan.	Amin A, Ahmed I, Habib N, Abbas S, Xiao M, Hozzein WN, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0711-8	2016
Phylogeny	Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil.	Yamamura H, Ohkubo SY, Nakagawa Y, Ishida Y, Hamada M, Otoguro M, Tamura T, Hayakawa M	Int J Syst Evol Microbiol	10.1099/ijs.0.025080-0	2010

References

#18127	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25935
#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 )
#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;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69327	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Nocardioides iriomotensis (DSM 25935, JCM 17985, KACC 14926)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004168035

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media