Mycobacterium rutilum (DSM 45405, ATCC BAA-1375, CIP 109271)

Name: Mycobacterium rutilum (DSM 45405, ATCC BAA-1375, CIP 109271)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8577

Type strain

Strain Designation czh-117

Culture col. no. DSM 45405 ATCC BAA-1375 CIP 109271 JCM 16371 czh-117 1 more

NCBI tax ID(s) 1305864 370526

Special Collections DSMZ JCM CIP Literature strains

Links

Mycobacterium rutilum czh-117 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil.

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

Name and taxonomic classification

SI-ID 47851

ATCC BAA-1375,CIP 109271,JCM 16371,DSM 45405

@ref 20215

Last LPSN update 2025-12-16 09:48:52

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium rutilum

Full scientific name Mycobacterium rutilum Hennessee et al. 2009

Synonyms (1)

Mycolicibacterium rutilum

BacDive ID	Other strains from **Mycobacterium rutilum** (1)	Type strain
134704	M. rutilum CIP 109270, ATCC BAA-1374

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
32638	positive	rod-shaped
122323		rod-shaped
125438	positive		90.175
125439	positive		98.9

Multimedia

@ref:	16674
multimedia content:	DSM_45405.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45405.jpg
caption:	Medium 645 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16674	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
36355	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122323	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16674	positive	growth	28	mesophilic
32638	positive	growth	28-45
32638	positive	optimum	37	mesophilic
36355	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32638	aerobe
122323	obligate aerobe
125438	aerobe	90.123
125439	obligate aerobe	99.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32638	NaCl	positive	growth	2.5-5.0 %
32638	NaCl	positive	optimum	3.75 %

Observation

32638

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
32638	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
32638	29864 ChEBI	mannitol	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
122323	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
122323	16301 ChEBI	nitrite	-	reduction
32638	30911 ChEBI	sorbitol	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
32638	17151 ChEBI	xylitol	+	carbon source
32638	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
122323	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
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
32638	alpha-galactosidase	+	3.2.1.22
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32638	catalase	+	1.11.1.6
122323	catalase	+	1.11.1.6
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
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
122323	oxidase	+
32638	urease	+	3.5.1.5
122323	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE
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
122323	-	-	+	+	-	+	-	+	+	-	+	+	-	-	-	+	+	-	-	-
16674	-	-	+/-	+	-	+	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
16674	-	-	-	-	+	-	-	-	-	+	+/-	+	-	-	+	-	+/-	+/-	-	-	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	Isolation date
16674	soil	Oahu, Hawai	USA	USA	North America
67770	Soil from an urban park in Honolulu	HI	USA	USA	North America
122323	Environment, Soil	Oahu, Hawaii	United States of America	USA	North America	2004

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16674	1	Risk group (German classification) According to TRBA 466
122323	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	IMG-taxon 2636415969 annotated assembly for Mycolicibacterium rutilum DSM 45405	chromosome	GCA_900108565	370526.3	2636415969	370526	89.39
66792	ASM131418v1 assembly for Mycolicibacterium rutilum JCM 16371	contig	GCA_001314185	1305864.5	2734481975	1305864

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16674	Mycobacterium rutilum strain czh-117 16S ribosomal RNA gene, partial sequence	DQ370011	1418		370526

GC content

@ref	GC-content (mol%)	Method
67770	68.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycolicibacterium rutilum JCM 16371
NCBI: GCA_001314185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	66.10	no
125439	motility	BacteriaNetⓘ	no	88.20	no
125439	gram_stain	BacteriaNetⓘ	positive	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium rutilum strain DSM 45405
PATRIC: 370526.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.18	no
125438	anaerobic	anaerobicⓘ	no	97.57	no
125438	spore-forming	spore-formingⓘ	no	55.96	no
125438	aerobic	aerobicⓘ	yes	90.12	yes
125438	thermophilic	thermophileⓘ	no	97.50	no
125438	flagellated	motile2+ⓘ	no	87.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete Genome Sequence of Mycobacterium sp. Strain 3519A.	Bouam A, Levasseur A, Bonnet M, Borand L, Van Goethem C, Drancourt M, Godreuil S.	Genome Announc	10.1128/genomea.01565-17	2018
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
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

#16674	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45405
#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 )
#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 (see below)
#36355	; 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;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#122323	Collection of Institut Pasteur ; Curators of the CIP; CIP 109271
#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 rutilum (DSM 45405, ATCC BAA-1375, CIP 109271)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900108565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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