Strain identifier

BacDive ID: 134234

Type strain: No

Species: Tsukamurella pulmonis

Strain Designation: K362

Strain history: DSM 44990 <-- P. J. McCarthy K362 <-- J. Olson.

NCBI tax ID(s): 47312 (species)

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General

@ref: 32031

BacDive-ID: 134234

DSM-Number: 44990

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped

description: Tsukamurella pulmonis K362 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from deep marine sponge.

NCBI tax id

  • NCBI tax id: 47312
  • Matching level: species

strain history

  • @ref: 67770
  • history: DSM 44990 <-- P. J. McCarthy K362 <-- J. Olson.

doi: 10.13145/bacdive134234.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Tsukamurellaceae
  • genus: Tsukamurella
  • species: Tsukamurella pulmonis
  • full scientific name: Tsukamurella pulmonis Yassin et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Tsukamurella spongiae

@ref: 32031

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Mycobacteriales

family: Tsukamurellaceae

genus: Tsukamurella

species: Tsukamurella pulmonis

strain designation: K362

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32031positive3.5 µm1 µmrod-shapedno
125438no93
125438positive91.309
125439positive99.4

Culture and growth conditions

culture temp

@refgrowthtypetemperature
32031positivegrowth25-45
32031positiveoptimum31
61582positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
32031aerobe
61582aerobe
125438aerobe90.336
125439obligate aerobe95.4

spore formation

  • @ref: 32031
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32031NaClpositivegrowth0.0-4.0 %
32031NaClpositiveoptimum0.5 %

observation

  • @ref: 32031
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3203122599arabinose+carbon source
3203118403L-arabitol+carbon source
3203117057cellobiose+carbon source
3203128757fructose+carbon source
3203128260galactose+carbon source
3203117234glucose+carbon source
3203129864mannitol+carbon source
3203137684mannose+carbon source
3203128053melibiose+carbon source
3203126546rhamnose+carbon source
3203133942ribose+carbon source
3203117814salicin+carbon source
3203130911sorbitol+carbon source
3203117992sucrose+carbon source
3203127082trehalose+carbon source
3203118222xylose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
32031deep marine sponge
61582Deep-water marine hexactinellid spongeof the coast Antilles CuraçaoNetherlandsNLDMiddle and South America
67770Deep-water marine hexactinellid sponge with associated zoanthidscoast of CuraçaoNetherlands AntillesNLDNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Porifera (Sponges)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3845.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1974;97_2373;98_2929;99_3845&stattab=map
  • Last taxonomy: Tsukamurella
  • 16S sequence: KF410344
  • Sequence Identity:
  • Total samples: 12359
  • soil counts: 3431
  • aquatic counts: 2978
  • animal counts: 5160
  • plant counts: 790

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
32031Tsukamurella spongiae strain K362 16S ribosomal RNA gene, partial sequenceAY7142391480nuccore47312
67770Tsukamurella spongiae strain DSM 44990 16S ribosomal RNA gene, partial sequenceKF4103441480nuccore47312

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tsukamurella pulmonis strain DSM 4499047312.11wgspatric47312
66792Tsukamurella pulmonis DSM 449902700989556draftimg47312
67770Tsukamurella pulmonis DSM 44990GCA_001575215contigncbi47312

GC content

@refGC-contentmethod
3203174.6
6777071.1genome sequence analysis
6777071genome sequence analysis
6777074.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.309yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.754yes
125438spore-formingspore-formingAbility to form endo- or exosporesno55.507no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.336yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97no
125438motile2+flagellatedAbility to perform flagellated movementno93yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes50
125439BacteriaNetmotilityAbility to perform movementno81.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.4

External links

@ref: 32031

culture collection no.: CCUG 58061, JCM 14882, DSM 44990, NRRL B-24467, JCM 18308, IFM 10862

straininfo link

  • @ref: 91828
  • straininfo: 297472

literature

  • topic: Phylogeny
  • Pubmed-ID: 17625179
  • title: Tsukamurella spongiae sp. nov., a novel actinomycete isolated from a deep-water marine sponge.
  • authors: Olson JB, Harmody DK, Bej AK, McCarthy PJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64837-0
  • year: 2007
  • mesh: Actinobacteria/chemistry/*classification/genetics/*isolation & purification, Animals, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Mycolic Acids/analysis, Netherlands Antilles, Nucleic Acid Hybridization, Phylogeny, Porifera/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Genetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
32031Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172828228776041
61582Curators of the CCUGhttps://www.ccug.se/strain?id=58061Culture Collection University of Gothenburg (CCUG) (CCUG 58061)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91828Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID297472.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG