Mycobacterium crocinum (DSM 45433, ATCC BAA-1373, CIP 109269)

Name: Mycobacterium crocinum (DSM 45433, ATCC BAA-1373, CIP 109269)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8574

Type strain

Strain Designation czh-42

Culture col. no. DSM 45433 ATCC BAA-1373 CIP 109269 JCM 16369 czh-42

NCBI tax ID(s) 1305862 388459

Special Collections DSMZ JCM CIP Literature strains

History DSMZ <- CIP; CIP 109269 <- Q. X. Li, Honolulu, Hawai, USA; czh-42 JCM <-- CIP 109269 <-- Q. X. Li czh-42. CIP <- 2006, Q. X. Li, Honolulu, Hawaii, USA: strain czh-42

Links

Mycobacterium crocinum czh-42 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil.

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 360726

ATCC BAA-1373,CIP 109269,JCM 16369,DSM 45433

@ref 20215

Last LPSN update 2026-05-29 08:26:53

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium crocinum

Full scientific name Mycobacterium crocinum Hennessee et al. 2009

Synonyms (1)

Mycolicibacterium crocinum

BacDive ID	Other strains from **Mycobacterium crocinum** (2)	Type strain
136984	M. crocinum CIP 109266, ATCC BAA-1370
136985	M. crocinum CIP 109267, ATCC BAA-1371

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32638	positive	rod-shaped
118791
125439	positive		90.566

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16806	MIDDLEBROOK MEDIUM (DSMZ Medium 645)	Medium recipe at MediaDive	Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
37495	MEDIUM 55 - for Mycobacterium
118791	CIP Medium 55	Medium recipe at CIP
118791	CIP Medium 93	Medium recipe at CIP
118791	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
16806	positive	growth	37
32638	positive	growth	28-37
32638	positive	optimum	32.5
37495	positive	growth	30
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32638	aerobe
118791	obligate aerobe
125439	obligate aerobe	98.713

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32638	NaCl	positive	growth	<5.0 %

Observation

32638

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32638	30089 ChEBI	acetate	+	carbon source
32638	22599 ChEBI	arabinose	+	carbon source
32638	23652 ChEBI	dextrin	+	carbon source
32638	28757 ChEBI	fructose	+	carbon source
32638	24265 ChEBI	gluconate	+	carbon source
32638	17234 ChEBI	glucose	+	carbon source
32638	18403 ChEBI	L-arabitol	+	carbon source
32638	24996 ChEBI	lactate	+	carbon source
32638	29864 ChEBI	mannitol	+	carbon source
32638	37684 ChEBI	mannose	+	carbon source
32638	17632 ChEBI	nitrate	+	reduction
118791	17632 ChEBI	nitrate	+	reduction
118791	16301 ChEBI	nitrite	-	reduction
32638	17272 ChEBI	propionate	+	carbon source
32638	15361 ChEBI	pyruvate	+	carbon source
32638	33942 ChEBI	ribose	+	carbon source
32638	30031 ChEBI	succinate	+	carbon source
32638	27082 ChEBI	trehalose	+	carbon source
32638	53423 ChEBI	tween 40	+	carbon source
32638	53426 ChEBI	tween 80	+	carbon source
32638	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118791	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
32638	alkaline phosphatase	+	3.1.3.1
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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32638	catalase	+	1.11.1.6
118791	catalase	-	1.11.1.6
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
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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118791	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
118791	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
118791	-	+	+	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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
16806	soil	Hawai, Oahu	USA	USA	North America
67770	Non-contaminated soil from Wahiawa	HI	USA	USA	North America
118791	Environment, Soil	Oahu, Hawaii	United States of America	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16806	1	Risk group (German classification) According to TRBA 466
118791	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2237063v3 assembly for Mycolicibacterium crocinum JCM 16369	complete	GCA_022370635	388459.4		388459	97.56
66792	ASM2582243v1 assembly for Mycolicibacterium crocinum DSM 45433	scaffold	GCA_025822435	388459.5	8115304865	388459	66.21
66792	ASM131414v1 assembly for Mycolicibacterium crocinum JCM 16369	contig	GCA_001314145	1305862.4	2734481973	1305862	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
16806	Mycobacterium crocinum strain czh-42 16S ribosomal RNA gene, partial sequence	DQ534008	1398	388459
124043	Mycobacterium crocinum strain JCM 16369 16S ribosomal RNA gene, partial sequence.	MH169218	1484	388459
124043	Mycobacterium crocinum strain JCM 16369 16S ribosomal RNA gene, partial sequence.	MH169219	1486	388459

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2582243v1 assembly for Mycolicibacterium crocinum DSM 45433
NCBI: GCA_025822435

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.71	no
125439	gram_stain	BacteriaNetⓘ	positive	90.57	no
125439	motility	BacteriaNetⓘ	no	81.31	no
125439	spore_formation	BacteriaNetⓘ	no	78.07	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium crocinum JCM 16369
NCBI: GCA_022370635.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.43	no
125438	anaerobic	anaerobicⓘ	no	95.07	no
125438	aerobic	aerobicⓘ	yes	86.91	yes
125438	spore-forming	spore-formingⓘ	no	55.94	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	86.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera.	Gupta RS, Lo B, Son J.	Front Microbiol	10.3389/fmicb.2018.00067	2018
Phylogeny	Microbiological features and clinical relevance of new species of the genus Mycobacterium.	Tortoli E.	Clin Microbiol Rev	10.1128/cmr.00035-14	2014
	Complete Genome Sequences of 14 Nontuberculous Mycobacteria Type Strains.	Igarashi Y, Osugi A, Murase Y, Chikamatsu K, Shimomura Y, Hosoya M, Aono A, Morishige Y, Yamada H, Takaki A, Mitarai S.	Microbiol Resour Announc	10.1128/mra.01214-22	2023
	Description of Mycobacterium pinniadriaticum sp. nov., isolated from a noble pen shell (Pinna nobilis) population in Croatia.	Spicic S, Duvnjak S, Papic B, Reil I, Zrncic S, Mihaljevic Z, Naletilic S, Zupicic IG, Kompes G, Habrun B, Marekovic I, Zdelar-Tuk M.	Front Microbiol	10.3389/fmicb.2023.1289182	2023
Phylogeny	Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. nov.	Hennessee CT, Seo JS, Alvarez AM, Li QX	Int J Syst Evol Microbiol	10.1099/ijs.0.65827-0	2009

References

#16806	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45433
#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 )
#28849	IJSEM 378 2008 ( DOI 10.1099/ijs.0.65827-0 , PubMed 19196782 )
#32638	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 #28849
#37495	; Curators of the CIP;
#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;
#68382	Automatically annotated from API zym .
#118791	Collection of Institut Pasteur ; Curators of the CIP; CIP 109269
#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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Mycobacterium crocinum (DSM 45433, ATCC BAA-1373, CIP 109269)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_022370635

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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