Mycobacterium confluentis (DSM 44017, ATCC 49920, CIP 105510)

Name: Mycobacterium confluentis (DSM 44017, ATCC 49920, CIP 105510)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8422

Type strain

Strain Designation 1389/90

Culture col. no. DSM 44017 ATCC 49920 CIP 105510 CCUG 37513 JCM 13671 2 more

NCBI tax ID(s) 28047

Special Collections DSMZ CCUG JCM CIP Wink compendium KCTC

Links

Mycobacterium confluentis 1389/90 is an aerobe, mesophilic, rod-shaped prokaryote that was isolated from human sputum.

rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 42754

CT2025-00070,ATCC 49920,DSM 44017,CCUG 37513,CIP 105510,JCM 13671,KCTC 19635

@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 confluentis

Full scientific name Mycobacterium confluentis Kirschner et al. 1992

Synonyms (1)

Mycolicibacterium confluentis

Morphology

Cell morphology

@ref	Cell shape	Motility
118724	rod-shaped
125439
125438

Colony morphology

@ref	Colony color	Incubation period	Medium used
19841	Pale yellow	10-14 days	5006
19841	Pale yellow	10-14 days	BUG
19841	Pale yellow	10-14 days	MB7H9
53707		2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
11459	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
11459	LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354)	Medium recipe at MediaDive	Name: LÖWENSTEIN-JENSEN MEDIUM (DSMZ Medium 354) Composition: Potato flour 18.6104 g/l L-Asparagin 2.23325 g/l KH2PO4 1.55087 g/l Mg-citrate 0.372208 g/l Malachite green 0.248139 g/l MgSO4 0.148883 g/l Glycerol Fresh egg mixture Distilled water
19841	BUG
19841	5006		Medium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
19841	MB7H9		Name: Middlebrook 7H9 (MB7H9) Broth Base Composition: Middelbrook 7H9 Broth Base 4.7 g/l Glycerol 2.0 g/l Casaminoacids 11.0 g/l Yeast extract 5.5 g/l Tween80 (20%) 2.5 g/l OADC-Enrichment 100 ml Agar 15.0 g/l Preparation: Dissolve in Milli-Q-H2O. Before Use add 10% OADC stock solution Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Maintenance and revitalization Organisms: Mycobacteria OADC stock solution old broth-name: OADC-Stock Composition: Bovine Serum Albumin, fraction V 5 % 1% Oleic Acid in 0.2N NaOH 5ml Glucose 2 % NaCl 0.85 % Comments: Melt 1% Oleic Acid in 65°C water bath. Dissolve all ingredients in 700ml of ddH2O. Adjust volume to 1L. Filter sterilize and store at 4°C. -To make 1% Oleic Acid in 0.2N NaOH: Dissolve 5g oleic acid (ampule) in 500ml 0.2N NaOH (300ml ddH2O + 20ml NaOH + adjust volume to 500ml). Heat solution to 55°C for oleic acid to melt. Store at -20°C in 50ml aliquots. There is no need to sterilize this. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: Mycobacteria
36364	MEDIUM 55 - for Mycobacterium
118724	CIP Medium 55	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
11459	positive	growth	37	mesophilic
19841	positive	optimum	37	mesophilic
36364	positive	growth	37	mesophilic
53707	positive	growth	22-37
67770	positive	growth	37	mesophilic
118724	positive	growth	25-37	mesophilic
118724	negative	growth	10
118724	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
53707	aerobe
118724	obligate aerobe
125439	obligate aerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
118724	606565 ChEBI	hippurate	-	hydrolysis
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
118724	17632 ChEBI	nitrate	+	reduction
118724	17632 ChEBI	nitrate	-	respiration
118724	16301 ChEBI	nitrite	-	reduction
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	+	hydrolysis	from API Coryne

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118724	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118724	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118724	beta-galactosidase	-	3.2.1.23
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
118724	caseinase	-	3.4.21.50
118724	catalase	+	1.11.1.6
68379	catalase	+	1.11.1.6	from API Coryne
68382	cystine arylamidase	-	3.4.11.3	from API zym
118724	DNase	-
68382	esterase lipase (C 8)	+		from API zym
118724	gamma-glutamyltransferase	-	2.3.2.2
118724	gelatinase	-
68379	gelatinase	-		from API Coryne
118724	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118724	lipase	-
68382	lipase (C 14)	-		from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
118724	oxidase	-
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
118724	tryptophan deaminase	-
118724	tween esterase	-
118724	urease	+	3.5.1.5
68379	urease	+	3.5.1.5	from API Coryne

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
19841	+	+	-	-	-	+	+	-	+	+	-	not determinedn.d.	-	-	-	+	+	-	-	-	not determinedn.d.
53707	+	+	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	+

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
19841	not determinedn.d.	+	+	+	-	+	+	-	+	-	+	-	-	-	+	+	+	+	-	-
53707	-	-	-	+	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-
118724	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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
118724	not determinedn.d.	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Human
#Host Body Product	#Fluids

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
11459	human sputum	Koblenz	Germany	DEU	Europe
53707	Human sputum
67770	Sputum from a healthy male
118724	Human, Sputum

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
11459	1	Risk group (German classification) According to TRBA 466
19841	1	Risk group (German classification) According to TRBA 466
118724	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	ASM1072989v1 assembly for Mycolicibacterium confluentis JCM 13671	complete	GCA_010729895	28047.9	8110674579	28047	98.98
66792	ASM2582284v1 assembly for Mycolicibacterium confluentis DSM 44017	scaffold	GCA_025822845	28047.11	8115871502	28047	68.84
67770	ASM210210v1 assembly for Mycolicibacterium confluentis DSM 44017	contig	GCA_002102105	28047.3	2865351897	28047	67.88

Genome browser: GCA_010729895

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Mycobacterium confluentis strain CIP 105510 16S ribosomal RNA gene, partial sequence	AF547913	544	28047
20218	Mycobacterium confluentis 16S rRNA gene, type strain DSM 44017T	AJ634379	1504	28047
67770	M.confluentis gene for 16S rRNA	X63608	1335	28047

GC content

@ref	GC-content (mol%)	Method
67770	67.5	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycolicibacterium confluentis JCM 13671
NCBI: GCA_010729895

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	54.00	no
125439	motility	BacteriaNetⓘ	no	79.10	no
125439	gram_stain	BacteriaNetⓘ	positive	90.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacterium confluentis JCM 13671
NCBI: GCA_010729895.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.73	no
125438	anaerobic	anaerobicⓘ	no	95.76	yes
125438	aerobic	aerobicⓘ	yes	88.50	yes
125438	spore-forming	spore-formingⓘ	no	61.61	no
125438	thermophilic	thermophileⓘ	no	96.90	yes
125438	flagellated	motile2+ⓘ	no	92.50	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
	Genomics Insights into Mycolicibacterium Hassiacum Causing Infection in a Cat with Pyogranulomatous Dermatitis and Panniculitis.	Smedile D, Iurescia M, Carfora V, Cocumelli C, Palmerini T, Diaconu EL, Congiu I, Donati V, Stravino F, Sorbara L, Romano E, Caprioli A, Battisti A.	Pathogens	10.3390/pathogens13090785	2024
Phylogeny	Rapid identification of mycobacterial whole cells in solid and liquid culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry.	Lotz A, Ferroni A, Beretti JL, Dauphin B, Carbonnelle E, Guet-Revillet H, Veziris N, Heym B, Jarlier V, Gaillard JL, Pierre-Audigier C, Frapy E, Berche P, Nassif X, Bille E.	J Clin Microbiol	10.1128/jcm.01397-10	2010
Phylogeny	Mycobacterium confluentis sp. nov.	Kirschner P, Teske A, Schroder KH, Kroppenstedt RM, Wolters J, Bottger EC	Int J Syst Bacteriol	10.1099/00207713-42-2-257	1992

References

#11459	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 44017
#19841	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#36364	; Curators of the CIP;
#53707	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 37513
#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;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#118724	Collection of Institut Pasteur ; Curators of the CIP; CIP 105510
#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 confluentis (DSM 44017, ATCC 49920, CIP 105510)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Enzymes

API coryne

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_010729895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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