Mycobacterium vicinigordonae (DSM 105979, CMCC 93559, 24)

Name: Mycobacterium vicinigordonae (DSM 105979, CMCC 93559, 24)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 160319

Type strain

Strain Designation 24

Culture col. no. DSM 105979 CMCC 93559 24

NCBI tax ID(s) 1719132

Special Collections DSMZ

History <- J. Luo, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and thoracic tumor research institute, National Clinical Laboratory on tuberculosis; 24 <- G. Liu, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and thoracic tumor research institute, National Clinical Laboratory on tuberculosis; 24

Links

Mycobacterium vicinigordonae 24 is a bacterium that was isolated from sputum from a pulmonary infection patient.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402327

DSM 105979

@ref 20215

Last LPSN update 2026-02-09 11:38:52

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Mycobacteriaceae

Genus Mycobacterium

Species Mycobacterium vicinigordonae

Full scientific name Mycobacterium vicinigordonae Liu et al. 2021

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	positive	90.2

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
67222	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
67222	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
67222	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
67222	MYCOBACTERIUM MEDIUM (DSMZ Medium 219)	Medium recipe at MediaDive	Name: MYCOBACTERIUM MEDIUM (DSMZ Medium 219) Composition: Agar 20.0 g/l Na2HPO4 x 12 H2O 2.5 g/l Yeast extract 2.0 g/l Proteose peptone no. 3 2.0 g/l Casein peptone 2.0 g/l Sodium citrate 1.5 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.6 g/l Tween 0.5 g/l Glycerol Distilled water
67222	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

Culture temp

@ref	Growth	Type	Temperature (°C)
67222	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

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

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
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
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
68379	beta-galactosidase	-	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68369	gelatinase	-		from API 20NE
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

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
67222	-	-	+/-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

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
67222	-	-	+/-	+	-	+	-	+/-	-	-	+	+/-	-	-	-	-	-	-	-	-
67222	-	-	+/-	+	-	+/-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-

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
67222	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+/-	-	-	not determinedn.d.

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67222	sputum from a pulmonary infection patient	Guangdong Province, Luoding City (22° 45' 14.19'' N, 111° 34' 39.26'' E)	China	CHN	Asia	22.7539	111.578 22.7539/111.578

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1346642v1 assembly for Mycobacterium vicinigordonae 24	complete	GCA_013466425	1778.48	2990140032	1719132	96.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67222	Mycobacterium vicinigordonae 16S ribosomal RNA gene, partial sequence	KT763328	1393		1719132

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Mycobacterium vicinigordonae 24
NCBI: GCA_013466425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	66.30	no
125439	motility	BacteriaNetⓘ	no	82.00	no
125439	gram_stain	BacteriaNetⓘ	positive	90.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycobacterium vicinigordonae 24
NCBI: GCA_013466425.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.98	no
125438	anaerobic	anaerobicⓘ	no	94.87	no
125438	aerobic	aerobicⓘ	yes	73.40	no
125438	spore-forming	spore-formingⓘ	no	64.84	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	87.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Mycobacterium vicinigordonae sp. nov., a slow-growing scotochromogenic species isolated from sputum.	Liu G, Yu X, Luo J, Hu Y, Dong L, Jiang G, Huo F, Wang F, Liang Q, Huang H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004796	2021

References

#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 )
#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) .
#67222	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105979
#68369	Automatically annotated from API 20NE .
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#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 vicinigordonae (DSM 105979, CMCC 93559, 24)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API coryne

API zym

API 20NE

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_013466425

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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