Strain identifier

BacDive ID: 5624

Type strain: Yes

Species: Myroides phaeus

Strain Designation: MY15

Strain history: X.-H. Zhang and S. Yan MY15.

NCBI tax ID(s): 702745 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 16784

BacDive-ID: 5624

DSM-Number: 23313

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

description: Myroides phaeus MY15 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oral cavity of healthy people.

NCBI tax id

  • NCBI tax id: 702745
  • Matching level: species

strain history

@refhistory
16784<- X.-H. Zhang, Ocean Univ. China, Qingdao, P. R. China; MY15 <- S. Yan
67770X.-H. Zhang and S. Yan MY15.

doi: 10.13145/bacdive5624.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Myroides
  • species: Myroides phaeus
  • full scientific name: Myroides phaeus Yan et al. 2012

@ref: 16784

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Myroides

species: Myroides phaeus

full scientific name: Myroides phaeus Yan et al. 2012

strain designation: MY15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30087negative0.7-1.2 µm0.4-0.5 µmrod-shapedno
69480negative100

pigmentation

  • @ref: 30087
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16784
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16784positivegrowth28mesophilic
30087positivegrowth06-37
30087positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30087positivegrowth05-10alkaliphile
30087positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 30087
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30087no
69481no97
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
30087NaClpositivegrowth<6 %
30087NaClpositiveoptimum1 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3008730911sorbitol+carbon source
3008717992sucrose+carbon source
3008717632nitrate+reduction

enzymes

@refvalueactivityec
30087acid phosphatase+3.1.3.2
30087alkaline phosphatase+3.1.3.1
30087gelatinase+
30087urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16784oral cavity of healthy peopleQingdaoChinaCHNAsia
67770Human salivaChinaCHNAsia

isolation source categories

Cat1Cat2
#Host#Human
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_41066.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_195;96_674;97_13999;98_29905;99_41066&stattab=map
  • Last taxonomy: Myroides phaeus subclade
  • 16S sequence: GU253339
  • Sequence Identity:
  • Total samples: 3440
  • soil counts: 659
  • aquatic counts: 311
  • animal counts: 2353
  • plant counts: 117

Safety information

risk assessment

  • @ref: 16784
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16784
  • description: Myroides phaeus strain MY15 16S ribosomal RNA gene, partial sequence
  • accession: GU253339
  • length: 1481
  • database: ena
  • NCBI tax ID: 702745

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Myroides phaeus strain DSM 23313702745.3wgspatric702745
66792Myroides phaeus DSM 233132675903217draftimg702745
67770Myroides phaeus DSM 23313GCA_900099675scaffoldncbi702745

GC content

@refGC-contentmethod
1678434.3high performance liquid chromatography (HPLC)
3008734.3
6777034.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
gram-positiveno97.888yes
anaerobicno99.116no
halophileno86.086no
spore-formingno94.619yes
glucose-utilyes68.129no
thermophileno99.347yes
flagellatedno93.815yes
aerobicyes84.847yes
glucose-fermentno91.32no
motileno91.677yes

External links

@ref: 16784

culture collection no.: DSM 23313, LMG 25566, JCM 17139

straininfo link

  • @ref: 75107
  • straininfo: 406730

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21571938Myroides phaeus sp. nov., isolated from human saliva, and emended descriptions of the genus Myroides and the species Myroides profundi Zhang et al. 2009 and Myroides marinus Cho et al. 2011.Yan S, Zhao N, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.029215-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Humans, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Saliva/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Phylogeny25515411Myroides injenensis sp. nov., a new member isolated from human urine.Paek J, Shin JH, Shin Y, Park IS, Jin TE, Kook JK, Wie SH, Cho HG, Park SJ, Chang YHAntonie Van Leeuwenhoek10.1007/s10482-014-0317-y2014Bacterial Typing Techniques, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Flavobacteriaceae Infections/*microbiology, Humans, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Urine/*microbiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16784Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23313)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23313
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
30087Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2644428776041
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/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75107Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406730.1StrainInfo: A central database for resolving microbial strain identifiers