Nocardia mikamii (DSM 45174, JCM 15508, 188-03)

Name: Nocardia mikamii (DSM 45174, JCM 15508, 188-03)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10826

Type strain

Strain Designation 188-03, W8061

Culture col. no. DSM 45174 JCM 15508 188-03 W8061 NBRC 108933

NCBI tax ID(s) 1223548 508464

Special Collections DSMZ JCM Wink compendium Literature strains

History <- J. M. Brown; W8061 <- Al State Health Dept. USA J. M. Brown W8061 <-- Alabama State Health Dept., AL, USA <-- St. Vincent Hosp., Birmingham, AL, USA.

Links

Nocardia mikamii 188-03 is an aerobe, spore-forming, mesophilic prokaryote that builds an aerial mycelium and was isolated from human sputum.

spore-forming Gram-positive rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 402087

JCM 15508,NBRC 108933,DSM 45174

@ref 20215

Last LPSN update 2026-02-09 11:20:21

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Nocardia

Species Nocardia mikamii

Full scientific name Nocardia mikamii Jannat-Khah et al. 2010

BacDive ID	Other strains from **Nocardia mikamii** (1)	Type strain
161666	N. mikamii JCM 15866, IFM 0177

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
29546	positive	rod-shaped
125438			90
125438	positive		91.596
125439	positive		97.4

Colony morphology

@ref	Colony color	Medium used
69376	Deep orange (2011)	ISP 2
69376	Daffodil yellow (1007)	suter with tyrosine
69376	Daffodil yellow (1007)	suter without tyrosine
69376	Pastel orange (2003)	ISP 3
69376	Pastel yellow (1034)	ISP 5
69376	Pastel yellow (1034)	ISP 6
69376	Salmon orange (2012)	ISP 7
69376	Yellow orange (2000)	ISP 4

Multicellular morphology

@ref	Complex name	Complex color	Medium name
69376	Aerial mycelium	Cream (9001)	ISP 2
69376	Aerial mycelium	Pure white (9010)	ISP 3
69376	Aerial mycelium		ISP 4
69376	Aerial mycelium	Pure white (9010)	ISP 5
69376	Aerial mycelium	Cream (9001)	ISP 6
69376	Aerial mycelium	Pure white (9010)	ISP 7
69376	Aerial mycelium	Light ivory (1015)	suter with tyrosine
69376	Aerial mycelium	Light ivory (1015)	suter without tyrosine

Pigmentation

@ref	Color	Name
29546
69376		melanin pigment
69376	Beige red (3012)	soluble pigment

Multimedia

@ref:	15611
multimedia content:	DSM_45174.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45174.jpg
caption:	Medium 535 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

@ref:	69376
multimedia content:	DSM_45174_image3.jpeg
multimedia.multimedia content:	DSM_45174_image3.jpeg
caption:	Plates (BHI, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69376
multimedia content:	DSM_45174_image4.jpeg
multimedia.multimedia content:	DSM_45174_image4.jpeg
caption:	Plates (BHI, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15611	BHI MEDIUM (DSMZ Medium 215)		Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
15611	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)		Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15611	positive	growth	28	mesophilic
29546	positive	growth	25-45
29546	positive	optimum	35	mesophilic
67770	positive	growth	35	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29546	aerobe
125439	obligate aerobe	99.7

Spore formation

29546

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69376	NaCl	positive	growth	0-2.5 %

Observation

@ref	Observation
29546	aggregates in chains
67770	quinones: MK-8(H₄, ω-cycl)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69376	22599 ChEBI	arabinose	-	growth
69376	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
29546	28757 ChEBI	fructose	+	carbon source
69376	28757 ChEBI	fructose	-	growth
29546	28260 ChEBI	galactose	+	carbon source
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
29546	17234 ChEBI	glucose	+	carbon source
69376	17234 ChEBI	glucose	+	growth
29546	17754 ChEBI	glycerol	+	carbon source
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69376	17268 ChEBI	inositol	-	growth
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69376	37684 ChEBI	mannose	-	growth
29546	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
69376	16634 ChEBI	raffinose	-	growth
69376	26546 ChEBI	rhamnose	-	growth
29546	17814 ChEBI	salicin	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69376	17992 ChEBI	sucrose	-	growth
29546	27082 ChEBI	trehalose	+	carbon source
69376	18222 ChEBI	xylose	-	growth

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	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
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	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
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	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
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
68382	valine arylamidase	+		from API zym

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
69376	-	-	+	+	-	-	-	-	-	+/-	-	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
69376	not determinedn.d.	+/-	+/-	+	+/-	+	+	+/-	-	-	+	+/-	-	+/-	-	+/-	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Fluids	#Sputum

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15611	human sputum	Birmingham, AL	USA	USA	North America
67770	Sputum	AL	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence EU484388 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples	606
Soil Samples	2461
Animal Samples	719
Plant Samples	386
Total Samples	4172

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15611	2	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	ASM161350v1 assembly for Nocardia mikamii NBRC 108933	contig	GCA_001613505	1223548.4	2731957757	1223548	70.16

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
15611	Nocardia mikamii NBRC 108933 strain W8061 16S ribosomal RNA gene, partial sequence	EU484388	1477	1223548
124043	Nocardia sp. W8988 16S ribosomal RNA gene, partial sequence.	EU484389	1439	508464
124043	Nocardia sp. W8988 16S ribosomal RNA gene, partial sequence.	EU484390	1439	508464
124043	Nocardia sp. W8988 16S ribosomal RNA gene, partial sequence.	EU484391	1439	508464

GC content

@ref	GC-content (mol%)	Method
15611	68.3	high performance liquid chromatography (HPLC)
29546	68.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nocardia mikamii NBRC 108933
NCBI: GCA_001613505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.70	no
125439	gram_stain	BacteriaNetⓘ	positive	97.40	no
125439	motility	BacteriaNetⓘ	no	84.10	no
125439	spore_formation	BacteriaNetⓘ	yes	72.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia mikamii NBRC 108933
PATRIC: 1223548.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.60	yes
125438	anaerobic	anaerobicⓘ	no	97.14	yes
125438	spore-forming	spore-formingⓘ	yes	65.38	yes
125438	aerobic	aerobicⓘ	yes	89.70	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	90.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardia shinanonensis sp. nov., isolated from a patient with endophthalmitis.	Matsumoto T, Negishi T, Hamada M, Komaki H, Gonoi T, Yaguchi T	Int J Syst Evol Microbiol	10.1099/ijsem.0.001197	2016
Phylogeny	Nocardia mikamii sp. nov., isolated from human pulmonary infections in the USA.	Jannat-Khah D, Kroppenstedt RM, Klenk HP, Sproer C, Schumann P, Lasker BA, Steigerwalt AG, Hinrikson HP, Brown JM	Int J Syst Evol Microbiol	10.1099/ijs.0.015594-0	2009

References

#15611	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45174
#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 )
#25942	IJSEM 2272 2010 ( DOI 10.1099/ijs.0.015594-0 , PubMed 19915112 )
#29546	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 #25942
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69376	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Nocardia mikamii (DSM 45174, JCM 15508, 188-03)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001613505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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