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BacDive ID 134234
Type strain
Strain Designation K362
Culture col. no. CCUG 58061 JCM 14882 DSM 44990 NRRL B-24467 K362 IFM 10862 JCM 18308 2 more
NCBI tax ID(s) 47312
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 32031

BacDive-ID: 134234

DSM-Number: 44990

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

description: Tsukamurella pulmonis K362 is an aerobe, Gram-positive, rod-shaped prokaryote 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/bacdive134234.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/bacillati
  • keyword: phylum/actinomycetota
  • 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

Genome sequences

  • @ref: 67770
  • description: ASM157521v1 assembly for Tsukamurella pulmonis DSM 44990
  • assembly level: contig
  • INSDC accession: GCA_001575215
  • BV-BRC accession: 47312.11
  • IMG accession: 2700989556
  • NCBI tax ID: 47312
  • score: 69.35

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
124043Tsukamurella pulmonis strain DSM 44990 16S ribosomal RNA gene, partial sequence.KX9245251221nuccore47312

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

Literature

@ref: 32031

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

straininfo link

  • @ref: 126262
  • straininfo: 297472

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625179Tsukamurella spongiae sp. nov., a novel actinomycete isolated from a deep-water marine sponge.Olson JB, Harmody DK, Bej AK, McCarthy PJInt J Syst Evol Microbiol10.1099/ijs.0.64837-02007Actinobacteria/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 AcidGenetics
Genetics27493643Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era.Teng JL, Tang Y, Huang Y, Guo FB, Wei W, Chen JH, Wong SS, Lau SK, Woo PC.Front Microbiol10.3389/fmicb.2016.011372016Species, Genomics, reclassification, Phylogenomic, TsukamurellaPhylogeny
28442613Reply to Perez del Molino Bernal and Agüero Balbin, "seqA1 Is a Useful Target for Identification of Tsukamurella pulmonis".Teng JLL, Tang Y, Lau SKP, Woo PCY.J Clin Microbiol10.1128/jcm.00238-172017Actinomycetales, Actinomycetales Infections
Enzymology29739926MALDI-TOF MS for identification of Tsukamurella species: Tsukamurella tyrosinosolvens as the predominant species associated with ocular infections.Teng JLL, Tang Y, Wong SSY, Fong JYH, Zhao Z, Wong CP, Chen JHK, Ngan AHY, Wu AKL, Fung KSC, Que TL, Lau SKP, Woo PCY.Emerg Microbes Infect10.1038/s41426-018-0083-42018isolation & purification, microbiology, microbiology, methods, methodsPhylogeny
Genetics30186281Genome-Based Taxonomic Classification of the Phylum Actinobacteria.Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.Front Microbiol10.3389/fmicb.2018.020072018Morphology, Chemotaxonomy, G+C content, Genome size, Phylogenetic systematics, Phylogenomics, Genome Blast Distance PhylogenyPhylogeny

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)
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/
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
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
126262A. 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. ReimerStrainInfo—the central database for linked microbial strain identifiers10.1093/database/baaf059

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