Strain identifier

BacDive ID: 8544

Type strain: Yes

Species: Mycobacterium pseudoshottsii

Strain Designation: L15

Strain history: CIP <- 2007, M. Rhodes, Virginia Inst. of Marine, Virginia, USA: strain L15

NCBI tax ID(s): 1136880 (strain), 265949 (species)

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General

@ref: 12350

BacDive-ID: 8544

DSM-Number: 45108

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, ovoid-shaped, animal pathogen

description: Mycobacterium pseudoshottsii L15 is an obligate aerobe, mesophilic, ovoid-shaped animal pathogen that was isolated from granulomatous lesions in splenic tissue from a striped bass.

NCBI tax id

NCBI tax idMatching level
1136880strain
265949species

strain history

@refhistory
12350<- NCTC
378352007, M. Rhodes, Virginia Inst. of Marine, Virginia, USA: strain L15
67770NCTC 13318 <-- M. W. Rhodes et al. L15.
122001CIP <- 2007, M. Rhodes, Virginia Inst. of Marine, Virginia, USA: strain L15

doi: 10.13145/bacdive8544.20230509.8.1

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 pseudoshottsii
  • full scientific name: Mycobacterium pseudoshottsii Rhodes et al. 2005

@ref: 12350

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Mycobacteriaceae

genus: Mycobacterium

species: Mycobacterium pseudoshottsii

full scientific name: Mycobacterium pseudoshottsii Rhodes et al. 2005 emend. Nouioui et al. 2018

strain designation: L15

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilityconfidencegram stain
313370.9 µm0.5 µmovoid-shaped
69480no96.626
69480100positive
122001rod-shapedno

pigmentation

  • @ref: 31337
  • production: yes

multimedia

  • @ref: 12350
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45108.jpg
  • caption: Medium 645 25°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12350MIDDLEBROOK 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
37835MEDIUM 55 - for Mycobacteriumyes
122001CIP Medium 93yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=93
122001CIP Medium 55yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55

culture temp

@refgrowthtypetemperaturerange
12350positivegrowth25mesophilic
31337positivegrowth23-37
31337positiveoptimum24psychrophilic
37835positivegrowth25mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122001
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
31337no
69480no99.849

halophily

  • @ref: 31337
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3133753426tween 80+carbon source
12200117632nitrate-reduction
12200116301nitrite-reduction

metabolite production

  • @ref: 122001
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31337acid phosphatase+3.1.3.2
31337catalase+1.11.1.6
31337urease+3.5.1.5
122001oxidase-
122001catalase+1.11.1.6
122001urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122001-++++++++-++--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
12350granulomatous lesions in splenic tissue from a striped bass(Morone saxatilis)
67770Granulomatous lesions in splenic tissue from a striped bass (Morone saxatilis)Morone saxatilisChesapeake BayUSAUSANorth America
122001Granulomatous splenix lesion in striped bass, Morone saxatilisChesapeake bayUnited States of AmericaUSANorth America2002

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body-Site#Other#Wound
#Host Body-Site#Organ#Spleen

taxonmaps

  • @ref: 69479
  • File name: preview.99_691.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_691&stattab=map
  • Last taxonomy: Mycobacterium
  • 16S sequence: AY570988
  • Sequence Identity:
  • Total samples: 2597
  • soil counts: 1494
  • aquatic counts: 660
  • animal counts: 250
  • plant counts: 193

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
12350yes1Risk group (German classification)
1220011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Mycobacterium pseudoshottsii partial 16S rRNA gene, type strain NCTC 13318TAM884320565ena1136880
20218Mycobacterium pseudoshottsii strain NCTC 13318 16S ribosomal RNA gene, partial sequenceDQ987742543ena1136880
12350Mycobacterium pseudoshottsii 16S ribosomal RNA gene, partial sequenceAY5709881453ena1136880
67770Mycobacterium pseudoshottsii gene for 16S ribosomal RNA, partial sequence, strain: JCM 15466AB5487131475ena1136880

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Mycobacterium pseudoshottsii JCM 15466GCA_003584745completencbi1136880
66792Mycobacterium pseudoshottsii JCM 154661136880.4completepatric1136880
66792Mycobacterium pseudoshottsii L151136880.3wgspatric1136880
66792Mycobacterium pseudoshottsii JCM 154662909077730completeimg1136880
67770Mycobacterium pseudoshottsii JCM 15466GCA_001515365scaffoldncbi1136880
66792Mycobacterium pseudoshottsii DSM 45108GCA_025821505contigncbi265949

GC content

  • @ref: 67770
  • GC-content: 65.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno79no
motileno95.414no
flagellatedno98.678no
gram-positiveyes85.452no
anaerobicno98.267no
aerobicyes86.268no
halophileno80.502no
spore-formingno88.242yes
thermophileno96.612yes
glucose-utilyes70.965no
glucose-fermentno92.499no

External links

@ref: 12350

culture collection no.: DSM 45108, ATCC BAA 883, NCTC 13318, JCM 15466, CIP 109775

straininfo link

  • @ref: 77929
  • straininfo: 131085

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879246Mycobacterium pseudoshottsii sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay striped bass (Morone saxatilis).Rhodes MW, Kator H, McNabb A, Deshayes C, Reyrat JM, Brown-Elliott BA, Wallace R, Trott KA, Parker JM, Lifland B, Osterhout G, Kaattari I, Reece K, Vogelbein W, Ottinger CAInt J Syst Evol Microbiol10.1099/ijs.0.63343-02005Animals, Anti-Bacterial Agents/pharmacology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Bass/*microbiology, Chaperonin 60, Chaperonins/genetics, DNA Transposable Elements, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Molecular Sequence Data, Mycobacterium/*classification/*isolation & purification/physiology, Mycolic Acids/analysis/isolation & purification, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, VirginiaEnzymology
Genetics26868383Draft Genome Sequence of the Fish Pathogen Mycobacterium pseudoshottsii Strain JCM15466, a Species Closely Related to M. marinum.Hikima J, Sakai M, Aoki T, Takeyama H, Hawke J, Mori K, Tashiro K, Kuhara SGenome Announc10.1128/genomeA.01630-152016
29192083Complete Chromosome Sequence of a Mycolactone-Producing Mycobacterium, Mycobacterium pseudoshottsii.Yoshida M, Miyamoto Y, Ogura Y, Hayashi T, Hoshino YGenome Announc10.1128/genomeA.01363-172017

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12350Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45108)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45108
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
31337Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127651
37835Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7555
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/
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
77929Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131085.1StrainInfo: A central database for resolving microbial strain identifiers
122001Curators of the CIPCollection of Institut Pasteur (CIP 109775)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109775