Strain identifier

BacDive ID: 8471

Type strain: Yes

Species: Mycobacterium porcinum

Strain Designation: E10241-1

Strain history: CIP <- 1999, ATCC <- M. Tsukamura: strain E10241-1 <- H. Nemoto

NCBI tax ID(s): 39693 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11617

BacDive-ID: 8471

DSM-Number: 44242

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, rod-shaped, human pathogen

description: Mycobacterium porcinum E10241-1 is an aerobe, mesophilic, rod-shaped human pathogen that was isolated from swine lymph node.

NCBI tax id

  • NCBI tax id: 39693
  • Matching level: species

strain history

@refhistory
11617<- A. F. Yassin <- ATCC <- M. Tsukamura, E 10241-1 <- H. Nemoto, Tachikawa 96
67770M. Tsukamura 19508 <-- H. Nemoto strain Tachikawa 96.
121943CIP <- 1999, ATCC <- M. Tsukamura: strain E10241-1 <- H. Nemoto

doi: 10.13145/bacdive8471.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Mycobacteriaceae
  • genus: Mycobacterium
  • species: Mycobacterium porcinum
  • full scientific name: Mycobacterium porcinum Tsukamura et al. 1983
  • synonyms

    • @ref: 20215
    • synonym: Mycolicibacterium porcinum

@ref: 11617

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium porcinum

full scientific name: Mycobacterium porcinum Tsukamura et al. 1983

strain designation: E10241-1

type strain: yes

Morphology

cell morphology

  • @ref: 121943
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19856Light ivory10-14 days5006
19856Light ivory10-14 daysMB7H10
19856Light ivory10-14 daysMB7H11
538012 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11617MYCOBACTERIUM MEDIUM (DSMZ Medium 219)yeshttps://mediadive.dsmz.de/medium/219Name: 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
11617MIDDLEBROOK MEDIUM (DSMZ Medium 645)yeshttps://mediadive.dsmz.de/medium/645Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water
19856MB7H10yesName: Middlebrook 7H10 (MB7H10) Broth Base Composition: amount in percent Middlebrook 7H10 Agar 1.9% Glycerol 0.5% OADC-Enrichment in ml (NL5633) 10ml Comments: Add broth base and glycerol to ddh2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: 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
19856MB7H11yesName: Middlebrook 7H11 (MB7H11) Broth Base Composition: Middlebrook 7H11 Agar 2% Glycerol 0.5% OADC-Enrichment 10ml Comments: Add broth base and glycerol to ddH2O. Adjust volumes. Autoclave. Cool to 42°C. Add OADC-Stock. Sterilisation: 20 minutes Temperature:121°C PH before: PH after: Biological details Culture type: suitable for: 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
198565006yesMedium: 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
36362MEDIUM 55 - for Mycobacteriumyes
121943CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
19856positiveoptimum37mesophilic
11617positivegrowth37mesophilic
36362positivegrowth37mesophilic
53801positivegrowth30-42
67770positivegrowth37mesophilic
121943positivegrowth22-37
121943nogrowth10psychrophilic
121943nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53801aerobe
121943obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
121943606565hippurate+hydrolysis
12194317632nitrate-reduction
12194316301nitrite-reduction
12194317632nitrate-respiration
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 121943
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 121943
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
121943oxidase-
121943beta-galactosidase-3.2.1.23
121943gelatinase-
121943amylase-
121943DNase-
121943caseinase-3.4.21.50
121943catalase+1.11.1.6
121943tween esterase-
121943gamma-glutamyltransferase-2.3.2.2
121943lecithinase-
121943lipase-
121943protease-
121943urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19856---+----+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19856-++-+----+-----+---
121943++++++++-++-+-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121943++-++-------------+------------+++---------------+++--------+------+----++++-++++--++-+-+-+++++-+--

Isolation, sampling and environmental information

isolation

@refsample type
11617swine lymph node
53801Swine lymph node,lymphadenitis
67770Swine lymphadenitis
121943Animal, Swine, lymph node

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Organ#Lymph node

taxonmaps

  • @ref: 69479
  • File name: preview.99_515.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_115;97_219;98_419;99_515&stattab=map
  • Last taxonomy: Mycolicibacterium
  • 16S sequence: AF480588
  • Sequence Identity:
  • Total samples: 496
  • soil counts: 45
  • aquatic counts: 64
  • animal counts: 50
  • plant counts: 337

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
11617yesyes2Risk group (German classification)
198562Risk group (German classification)
1219431Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium porcinum 16S ribosomal RNA gene, partial sequenceAF4805881456ena39693
20218Mycobacterium porcinum strain DSM 44242 16S ribosomal RNA gene, partial sequenceAF547958540ena39693
11617Mycolicibacterium porcinum strain CIP 105392 16S ribosomal RNA gene, partial sequenceAY4570771483ena39693

Genome sequences

  • @ref: 66792
  • description: Mycolicibacterium porcinum DSM 44242
  • accession: GCA_025823105
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 39693

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.791no
flagellatedno98.006no
gram-positiveyes90.599no
anaerobicno99.455yes
aerobicyes90.867yes
halophileno93.364no
spore-formingno83.976no
glucose-fermentno90.318no
thermophileno99.651yes
glucose-utilyes89.239no

External links

@ref: 11617

culture collection no.: DSM 44242, ATCC 33776, JCM 6378, CCUG 37674, CIP 105392, KCTC 9517

straininfo link

  • @ref: 77866
  • straininfo: 44973

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1883713Distribution of a novel mycolic acid in species of the genus Mycobacterium.Luquin M, Laneelle MA, Ausina V, Garcia Barcelo M, Belda F, Alonso C, Prats GInt J Syst Bacteriol10.1099/00207713-41-3-3901991Chromatography, Thin Layer, Mycobacterium/*analysis, Mycolic Acids/chemistry/*isolation & purificationPhylogeny
Phylogeny15583300Clinical and laboratory features of Mycobacterium porcinum.Wallace RJ Jr, Brown-Elliott BA, Wilson RW, Mann L, Hall L, Zhang Y, Jost KC Jr, Brown JM, Kabani A, Schinsky MF, Steigerwalt AG, Crist CJ, Roberts GD, Blacklock Z, Tsukamura M, Silcox V, Turenne CJ Clin Microbiol10.1128/JCM.42.12.5689-5697.20042004Animals, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/genetics, *Bacterial Typing Techniques, Base Sequence, Chaperonin 60, Chaperonins/genetics, DNA, Ribosomal/analysis, Humans, Microbial Sensitivity Tests, Molecular Sequence Data, Mycobacterium/*classification/drug effects/genetics/pathogenicity, Mycobacterium Infections/microbiology/physiopathology, Mycobacterium fortuitum/classification/drug effects/genetics/pathogenicity, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Swine/*microbiologyPathogenicity
Pathogenicity19086435[Microbiological properties of M. porcinum isolated from a patient with impairments in IL-12/IFN-gamma pathway].Kazumi Y, Maeda S, Udagawa T, Sugawara I, Kamiya HKekkaku2008Animals, Anti-Bacterial Agents/pharmacology, Base Sequence, Drug Resistance, Bacterial, Genes, Bacterial/genetics, Genetic Predisposition to Disease/genetics, Guinea Pigs, Humans, *Interferon-gamma, *Interleukin-12, Male, *Mutation, Mycobacterium fortuitum/drug effects/genetics/*isolation & purification/pathogenicity, Receptors, Interferon/*genetics, Signal Transduction/*genetics/physiology, Young AdultEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11617Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44242)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44242
19856Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44242.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
36362Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17406
53801Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37674)https://www.ccug.se/strain?id=37674
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
77866Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44973.1StrainInfo: A central database for resolving microbial strain identifiers
121943Curators of the CIPCollection of Institut Pasteur (CIP 105392)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105392