Mycobacterium hodleri (DSM 44183, CCUG 38151, CIP 104909)

Name: Mycobacterium hodleri (DSM 44183, CCUG 38151, CIP 104909)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8454

Type strain

Strain Designation EMI 2

Culture col. no. DSM 44183 CCUG 38151 CIP 104909 EMI 2 LMG 19253 1 more

NCBI tax ID(s) 1305625 49897

Special Collections DSMZ CCUG JCM CIP

Links

Mycobacterium hodleri EMI 2 is an aerobe, mesophilic, rod-shaped prokaryote that was isolated from fluoranthene and benzapyren contaminated soil.

rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 13219

LMG 19253,CIP 104909,DSM 44183,CT2025-00080,CCUG 38151,JCM 12141

@ref 20215

Last LPSN update 2025-12-16 09:48:50

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium hodleri

Full scientific name Mycobacterium hodleri Kleespies et al. 1996

Synonyms (1)

Mycolicibacterium hodleri

Morphology

Cell morphology

@ref	Cell shape	Motility
119927	rod-shaped
125438
125439

Colony morphology

54103

Incubation period4 days

Multimedia

@ref:	11581
multimedia content:	DSM_44183.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_44183.jpg
caption:	Medium 645 37°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11581	PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250)	Medium recipe at MediaDive	Name: PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250) Composition: Agar 20.0 g/l Proteose peptone no. 3 5.0 g/l Meat extract 3.0 g/l Glycerol Distilled water
11581	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
36386	MEDIUM 55 - for Mycobacterium
119927	CIP Medium 55	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11581	positive	growth	37	mesophilic
36386	positive	growth	25	mesophilic
54103	positive	growth	30	mesophilic
67770	positive	growth	28	mesophilic
119927	positive	growth	10-30
119927	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
54103	aerobe
119927	obligate aerobe
125439	obligate aerobe

Observation

67770

Observationquinones: MK-9(H₂), MK-8(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119927	606565 ChEBI	hippurate	+	hydrolysis
119927	17632 ChEBI	nitrate	-	reduction
119927	17632 ChEBI	nitrate	-	respiration
119927	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119927	35581 ChEBI	indole

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
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
119927	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
119927	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
119927	caseinase	-	3.4.21.50
119927	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
119927	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119927	gamma-glutamyltransferase	-	2.3.2.2
119927	gelatinase	-
119927	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119927	lipase	-
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
119927	oxidase	-
119927	protease	-
68382	trypsin	-	3.4.21.4	from API zym
119927	tween esterase	+
119927	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
119927	-	+	+	+	+	+	+	+	-	-	+	+	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Contamination
#Environmental	#Terrestrial

Isolation

@ref	Sample type
11581	fluoranthene and benzapyren contaminated soil
54103	Contaminant of fluoranthrene and benzapyrin
67770	Soil contaminated with fluoranthene and benzopyrene
119927	Fluoranthene and benzapyrin contaminated

Taxonmaps

69479

Global distribution of 16S sequence X93184 (>99% sequence identity) for Mycolicibacterium from Microbeatlas

Aquatic Samples	579
Soil Samples	1352
Animal Samples	443
Plant Samples	395
Total Samples	2769

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11581	1	Risk group (German classification) According to TRBA 466
119927	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	ASM2582224v1 assembly for Mycolicibacterium hodleri DSM 44183	scaffold	GCA_025822245	49897.8	8047375681	49897	61.62
66792	ASM131380v1 assembly for Mycolicibacterium hodleri JCM 12141	contig	GCA_001313805	1305625.4	2681813036	1305625

Genome browser: GCA_025822245

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Mycobacterium hodleri strain CIP 104909 16S ribosomal RNA gene, partial sequence	AF547936	540	49897
20218	Mycolicibacterium hodleri strain DSM 44183 16S-23S ribosomal RNA intergenic spacer, complete sequence	KC010494	456	49897
20218	M.hodleri 16S rRNA gene	X93184	1459	49897
124043	Mycobacterium hodleri strain JCM 12141 16S ribosomal RNA gene, partial sequence.	MH169217	1483	49897
124043	Mycobacterium hodleri strain JCM 12141 16S ribosomal RNA gene, partial sequence.	MH169216	1483	49897

GC content

@ref	GC-content (mol%)	Method
11581	73	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycolicibacterium hodleri DSM 44183
NCBI: GCA_025822245

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	60.80	no
125439	motility	BacteriaNetⓘ	no	80.70	no
125439	gram_stain	BacteriaNetⓘ	positive	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacterium hodleri JCM 12141
PATRIC: 1305625.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	78.62	no
125438	anaerobic	anaerobicⓘ	no	86.62	yes
125438	spore-forming	spore-formingⓘ	no	78.57	no
125438	aerobic	aerobicⓘ	yes	82.70	yes
125438	thermophilic	thermophileⓘ	no	94.57	yes
125438	flagellated	motile2+ⓘ	no	95.75	no

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
Genetics	Characterization of Mycobacterium antarcticum sp. nov., a psychrotolerant member of the genus Mycobacterium isolated from Antarctic soil.	Shimada S, Aoki K, Shiozawa A, Nakai R, Fujiwara N, Komori K, Kudoh S, Imura S, Ishii Y, Tateda K.	Sci Rep	10.1038/s41598-025-16147-6	2025
Phylogeny	Mycobacterium sediminis sp. nov. and Mycobacterium arabiense sp. nov., two rapidly growing members of the genus Mycobacterium.	Zhang DF, Chen X, Zhang XM, Zhi XY, Yao JC, Jiang Y, Xiong Z, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.050567-0	2013
Phylogeny	Mycobacterium hodleri sp. nov., a new member of the fast-growing mycobacteria capable of degrading polycyclic aromatic hydrocarbons.	Kleespies M, Kroppenstedt RM, Rainey FA, Webb LE, Stackebrandt E	Int J Syst Bacteriol	10.1099/00207713-46-3-683	1996

References

#11581	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44183
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#36386	; Curators of the CIP;
#54103	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38151
#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 .
#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 .
#119927	Collection of Institut Pasteur ; Curators of the CIP; CIP 104909
#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 hodleri (DSM 44183, CCUG 38151, CIP 104909)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_025822245

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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