Strain identifier

BacDive ID: 11264

Type strain: Yes

Species: Murinocardiopsis flavida

Strain Designation: 14-Be-013

Strain history: CIP <- 2010, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 14-Be-013

NCBI tax ID(s): 645275 (species)

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General

@ref: 16152

BacDive-ID: 11264

DSM-Number: 45312

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

description: Murinocardiopsis flavida 14-Be-013 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from wall paper of an outer house wall colonized with moulds.

NCBI tax id

  • NCBI tax id: 645275
  • Matching level: species

strain history

@refhistory
16152<- P. Kämpfer, Univ. Giessen, Germany; 14-Be-013 <- C. Trautmann, Berlin
67770CCM 7612 <-- P. Kämpfer 14-Be-013.
119375CIP <- 2010, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 14-Be-013

doi: 10.13145/bacdive11264.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Murinocardiopsis
  • species: Murinocardiopsis flavida
  • full scientific name: Murinocardiopsis flavida Kämpfer et al. 2010

@ref: 16152

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Murinocardiopsis

species: Murinocardiopsis flavida

full scientific name: Murinocardiopsis flavida Kämpfer et al. 2010 emend. Nouioui et al. 2018

strain designation: 14-Be-013

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29567positive
119375positiverod-shapedno
125439positive99.9
125439no93.2
125438no93.5
125438positive90.663

colony morphology

  • @ref: 61309
  • incubation period: 3-7 days

pigmentation

  • @ref: 29567
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16152GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
16152GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
37577MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
16152TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
16152BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
119375CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperature
16152positivegrowth28
37577positivegrowth30
61309positivegrowth30
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29567aerobe
61309aerobe
119375obligate aerobe
125439obligate aerobe99.5

spore formation

@refspore formationconfidence
29567no
125439yes94.5

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4), MK-11(H4), MK-12(H2), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29567370543-hydroxybutyrate+carbon source
2956730089acetate+carbon source
2956715963ribitol+carbon source
2956722599arabinose+carbon source
2956717057cellobiose+carbon source
2956728757fructose+carbon source
2956728260galactose+carbon source
2956717234glucose+carbon source
2956724996lactate+carbon source
2956725115malate+carbon source
2956717306maltose+carbon source
2956729864mannitol+carbon source
2956737684mannose+carbon source
2956717268myo-inositol+carbon source
29567506227N-acetylglucosamine+carbon source
2956726271proline+carbon source
2956715361pyruvate+carbon source
2956726546rhamnose+carbon source
2956733942ribose+carbon source
2956717814salicin+carbon source
2956727082trehalose+carbon source
2956718222xylose+carbon source
11937517632nitrate+reduction
11937516301nitrite-reduction

metabolite production

  • @ref: 119375
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
119375oxidase+
119375catalase+1.11.1.6
119375urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119375-----+-------+-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16152wall paper of an outer house wall colonized with mouldsBerlinGermanyDEUEurope
61309Indoor walls colonized with moldsBerlinGermanyDEUEurope
67770Wallpaper of an outer house wall and colonized with mouldsBerlinGermanyDEUEurope
119375Wallpaper materialBerlinGermanyDEUEurope2006

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#House
#Engineered#Industrial#Engineered product
#Host#Fungi

taxonmaps

  • @ref: 69479
  • File name: preview.99_47000.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_21368;97_26664;98_33924;99_47000&stattab=map
  • Last taxonomy: Murinocardiopsis flavida subclade
  • 16S sequence: FN393755
  • Sequence Identity:
  • Total samples: 227
  • soil counts: 82
  • aquatic counts: 8
  • animal counts: 118
  • plant counts: 19

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
161521Risk group (German classification)
1193751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16152
  • description: Murinocardiopsis flavida partial 16S rRNA gene, strain 14-Be-013
  • accession: FN393755
  • length: 1418
  • database: nuccore
  • NCBI tax ID: 645275

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Murinocardiopsis flavida strain DSM 45312645275.3wgspatric645275
66792Murinocardiopsis flavida DSM 453122728369519draftimg645275
67770Murinocardiopsis flavida DSM 45312GCA_003014485scaffoldncbi645275

GC content

  • @ref: 67770
  • GC-content: 72.4
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.663yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.564yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.011yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes79.159no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.03yes
125438motile2+flagellatedAbility to perform flagellated movementno93.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes94.5
125439BacteriaNetmotilityAbility to perform movementno93.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.5

External links

@ref: 16152

culture collection no.: DSM 45312, CCM 7612, CCUG 57390, JCM 17973, CIP 110198

straininfo link

  • @ref: 80497
  • straininfo: 370399

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19734281Murinocardiopsis flavida gen. nov., sp. nov., an actinomycete isolated from indoor walls.Kampfer P, Schafer J, Lodders N, Martin KInt J Syst Evol Microbiol10.1099/ijs.0.015990-02009Actinobacteria/*classification/genetics/*isolation & purification/metabolism, Construction Materials/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny21216917Spinactinospora alkalitolerans gen. nov., sp. nov., an actinomycete isolated from marine sediment.Chang X, Liu W, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.027383-02011Actinobacteria/*classification/genetics/*isolation & purification/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, Seawater/*microbiology, Sodium Chloride/metabolismMetabolism
Phylogeny35085063Spiractinospora alimapuensis gen. nov., sp. nov., isolated from marine sediment of Valparaiso Bay (Chile) and proposal for reclassification of two species of the genus Nocardiopsis.Claverias FP, Serna-Cardona N, Cumsille A, Zamora-Leiva L, Riesco R, Couve E, Trujillo ME, Camara BInt J Syst Evol Microbiol10.1099/ijsem.0.0052072022Bacterial Typing Techniques, Base Composition, Bays, Chile, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, *Nocardiopsis/classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16152Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45312)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45312
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
29567Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2596228776041
37577Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8031
61309Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57390)https://www.ccug.se/strain?id=57390
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
80497Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370399.1StrainInfo: A central database for resolving microbial strain identifiers
119375Curators of the CIPCollection of Institut Pasteur (CIP 110198)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110198
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1