Nocardia fusca (CIP 104513, IFO 14340, JCM 10427)

Name: Nocardia fusca (CIP 104513, IFO 14340, JCM 10427)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 136777

Type strain

Culture col. no. CIP 104513 IFO 14340 JCM 10427 BCRC 13734 NBRC 14340 2 more

NCBI tax ID(s) 1223549 941183

Special Collections DSMZ JCM CIP

History JCM <-- IFO 14340 <-- Z. Liu 1.128a. CIP <- 1995, IFO, "Nocardia fusca" <- IMAS

Links

Nocardia fusca CIP 104513 is an obligate aerobe, Gram-positive prokaryote of the family Not assigned to family.

Gram-positive obligate aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 62554

CIP 104513,IFO 14340,JCM 10427,CCRC 13734,NBRC 14340,BCRC 13734

@ref 36347

Phylum Not assigned to order

Class Not assigned to order

Order Not assigned to order

Family Not assigned to family

Genus Nocardia

Species Nocardia fusca

Type strain yes

Morphology

Cell morphology

@ref	Confidence	Gram stain
36347		positive
125438	90
125438	93.172	positive
125439	93.577	positive
125439	93.413

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
36347	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
36347	CIP Medium 3			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
36347	positive	growth	30
36347	positive	growth	30-37
36347	negative	growth	10
36347	negative	growth	45
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
36347	obligate aerobe
125439	obligate aerobe	96.645

Halophily

@ref	Salt	Growth	Tested relation	Concentration
36347	NaCl	positive	growth	0-6 %
36347	NaCl		growth	8 %
36347	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
36347	4853 ChEBI	esculin	+	hydrolysis
36347	606565 ChEBI	hippurate	-	hydrolysis
36347	17632 ChEBI	nitrate	+	reduction
36347	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
36347	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
36347	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
36347	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
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
68382	alpha-mannosidase	-	3.2.1.24	from API zym
36347	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
36347	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
36347	caseinase	-	3.4.21.50
36347	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
36347	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
36347	gelatinase	-
36347	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
36347	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
36347	ornithine decarboxylase	-	4.1.1.17
36347	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
36347	tween esterase	-
36347	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
36347	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	+	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
36347	not determinedn.d.	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	-	+	-	+	-	-	-	-	-	+	-	+

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
36347			China	CHN	Asia
67770	Soil	Beijing	China	CHN	Asia
36347	Environment, Soil		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB647161 (>99% sequence identity) for Nocardia from Microbeatlas

Aquatic Samples	469
Soil Samples	8278
Animal Samples	943
Plant Samples	1687
Total Samples	11377

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
36347	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM161842v1 assembly for Nocardia fusca NBRC 14340	contig	GCA_001618425	1223549.4	2681812988	1223549	56.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Nocardia fusca gene for 16S rRNA, partial sequence	AB647161	1457		941183

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM161842v1 assembly for Nocardia fusca NBRC 14340
BV-BRC: 1223549.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.65	no
125439	motility	BacteriaNetⓘ	no	93.41	no
125439	gram_stain	BacteriaNetⓘ	positive	93.58	no
125439	spore_formation	BacteriaNetⓘ	yes	74.14	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardia fusca NBRC 14340
PATRIC: 1223549.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.17	no
125438	anaerobic	anaerobicⓘ	no	96.62	no
125438	spore-forming	spore-formingⓘ	yes	59.96	no
125438	aerobic	aerobicⓘ	yes	88.88	yes
125438	thermophilic	thermophileⓘ	no	97.90	no
125438	flagellated	motile2+ⓘ	no	90.00	no

Literature

References

#36347	Collection of Institut Pasteur ; Curators of the CIP; CIP 104513
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#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 .
#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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