Mycobacterium phocaicum (DSM 45104, CCUG 50185, CIP 108542)

Name: Mycobacterium phocaicum (DSM 45104, CCUG 50185, CIP 108542)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8548

Type strain

Strain Designation N4

Culture col. no. DSM 45104 CCUG 50185 CIP 108542 JCM 15301 N4

NCBI tax ID(s) 319706

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- CCUG <- M. Drancourt, Timone, Marseille CIP <- 2004, M. Drancourt, La Timone Hosp., Marseille, France: strain N4 JCM <-- CCUG 50185 <-- M. Drancourt N4. CIP <- 2004, M. Drancourt, Timone Hosp., Marseille, France: strain N4

Links

Mycobacterium phocaicum N4 is a microaerophile, rod-shaped bacterium that was isolated from human bronchial aspirate.

rod-shaped microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 289775

CT2025-00088,CIP 108542,CCUG 50185,DSM 45104,JCM 15301

@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 phocaicum

Full scientific name Mycobacterium phocaicum Adékambi et al. 2006

Synonyms (1)

Mycolicibacterium phocaicum

Morphology

Cell morphology

@ref	Cell shape	Motility	Gram stain	Confidence
121803	rod-shaped
125439			positive	91.625

Colony morphology

58775

Incubation period2 days

Multimedia

@ref:	12346
multimedia content:	DSM_45104.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45104.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
12346	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
36341	MEDIUM 93 - for Mycobacterium avium subsp. sylvaticum		Distilled water make up to (900.000 ml);Glycerol (4.500 ml);Middlebrook7H10 agar (17.000 g);Middelbrook OADC enrichment (100.000 ml)
121803	CIP Medium 93	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
12346	positive	growth	37
36341	positive	growth	30
58775	positive	growth	37
67770	positive	growth	37
121803	positive	growth	22-37
121803	negative	growth	10
121803	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58775	microaerophile
121803	obligate aerobe
125439	obligate aerobe	99.075

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121803	606565 ChEBI	hippurate	+	hydrolysis
121803	17632 ChEBI	nitrate	+	reduction
121803	17632 ChEBI	nitrate	-	respiration
121803	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121803	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
121803	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
121803	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
121803	caseinase	-	3.4.21.50
121803	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121803	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121803	gamma-glutamyltransferase	-	2.3.2.2
121803	gelatinase	-
121803	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121803	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
121803	oxidase	-
121803	protease	-
68382	trypsin	-	3.4.21.4	from API zym
121803	tween esterase	+
121803	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
121803	-	+	+	+	+	+	-	-	-	-	+	+	-	+	-	+	-	-	-	-

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
121803	not determinedn.d.	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Airways
#Host Body Product	#Fluids	#Aspirate

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
12346	human bronchial aspirate	Homo sapiens	Marseille	France	FRA	Europe
58775	Human bronchial aspirate	Homo sapiens	Marseille	France	FRA	Europe
67770	Bronchial aspirate
121803	Bronchial aspiration		Marseille	France	FRA	Europe	1999

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12346	2	Risk group (German classification) According to TRBA 466
121803	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	ASM1073111v1 assembly for Mycolicibacterium phocaicum JCM 15301	complete	GCA_010731115	319706.13	8069322310	319706	98.5
67770	ASM567065v1 assembly for Mycolicibacterium phocaicum DSM 45104	contig	GCA_005670655	319706.12	8069316589	319706	63.25

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Mycobacterium phocaicum strain CCUG 50185 16S ribosomal RNA gene, partial sequence	DQ987741	530	319706
12346	Mycolicibacterium phocaicum strain CIP 108542 16S ribosomal RNA gene, partial sequence	AY859682	1482	319706
124043	Mycolicibacterium phocaicum strain CIP 108542 16S ribosomal RNA gene, partial sequence.	OR801629	1482	319706

GC content

@ref	GC-content (mol%)	Method
67770	64-66	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: ASM1073111v1 assembly for Mycolicibacterium phocaicum JCM 15301
BV-BRC: 319706.13

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.08	no
125439	gram_stain	BacteriaNetⓘ	positive	91.63	no
125439	motility	BacteriaNetⓘ	no	82.18	no
125439	spore_formation	BacteriaNetⓘ	no	76.09	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Mycolicibacterium phocaicum JCM 15301
NCBI: GCA_010731115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.98	no
125438	anaerobic	anaerobicⓘ	no	97.37	yes
125438	aerobic	aerobicⓘ	yes	87.90	no
125438	spore-forming	spore-formingⓘ	no	59.88	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA.	Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA.	BMC Evol Biol	10.1186/s12862-019-1447-7	2019
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 salfingeri sp. nov.: A novel nontuberculous mycobacteria isolated from a human wound infection.	Musser E, Smith C, Halse TA, Kohlerschmidt D, Rourke A, Fiero A, Musser KA, Escuyer V, Lapierre P.	Front Microbiol	10.3389/fmicb.2022.992610	2022
Phylogeny	rpoB gene sequence-based characterization of emerging non-tuberculous mycobacteria with descriptions of Mycobacterium bolletii sp. nov., Mycobacterium phocaicum sp. nov. and Mycobacterium aubagnense sp. nov.	Adekambi T, Berger P, Raoult D, Drancourt M	Int J Syst Evol Microbiol	10.1099/ijs.0.63969-0	2006

References

#12346	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45104
#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 )
#36341	; Curators of the CIP;
#58775	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 50185
#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 .
#121803	Collection of Institut Pasteur ; Curators of the CIP; CIP 108542
#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 phocaicum (DSM 45104, CCUG 50185, CIP 108542)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Enzymes

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_010731115

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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