Strain identifier

BacDive ID: 24207

Type strain: Yes

Species: Zhihengliuella flava

Strain Designation: H85-3

Strain history: <- M. Hamada, NBRC; NBRC 109021

NCBI tax ID(s): 1285193 (species)

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General

@ref: 21163

BacDive-ID: 24207

DSM-Number: 26152

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped

description: Zhihengliuella flava H85-3 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from marine beach sediment.

NCBI tax id

  • NCBI tax id: 1285193
  • Matching level: species

strain history

  • @ref: 21163
  • history: <- M. Hamada, NBRC; NBRC 109021

doi: 10.13145/bacdive24207.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Zhihengliuella
  • species: Zhihengliuella flava
  • full scientific name: Zhihengliuella flava Hamada et al. 2013

@ref: 21163

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Zhihengliuella

species: Zhihengliuella flava

full scientific name: Zhihengliuella flava Hamada et al. 2013

strain designation: H85-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31139positive1.5 µm0.45 µmrod-shapedno
69480positive100

pigmentation

  • @ref: 31139
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21163
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21163positivegrowth28mesophilic
31139positivegrowth10-37
31139positiveoptimum25mesophilic

culture pH

@refabilitytypepHPH range
31139positivegrowth6.0-11.0alkaliphile
31139positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31139
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
31139no
69481no99
69480no99.994

halophily

  • @ref: 31139
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 21163
  • murein short key: A11.35
  • type: A4alpha L-Lys-L-Ala-L-Glu

observation

  • @ref: 31139
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3113917057cellobiose+carbon source
3113928757fructose+carbon source
3113917234glucose+carbon source
3113917754glycerol+carbon source
3113917306maltose+carbon source
3113929864mannitol+carbon source
3113928053melibiose+carbon source
3113926546rhamnose+carbon source
3113917992sucrose+carbon source
311394853esculin+hydrolysis

enzymes

@refvalueactivityec
31139catalase+1.11.1.6
31139gelatinase+

Isolation, sampling and environmental information

isolation

  • @ref: 21163
  • sample type: marine beach sediment
  • geographic location: Chiba, Tokyo Bay, Tomiura Beach
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

taxonmaps

  • @ref: 69479
  • File name: preview.99_21271.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_158;97_13038;98_16043;99_21271&stattab=map
  • Last taxonomy: Zhihengliuella flava
  • 16S sequence: AB778260
  • Sequence Identity:
  • Total samples: 322
  • soil counts: 81
  • aquatic counts: 24
  • animal counts: 205
  • plant counts: 12

Safety information

risk assessment

  • @ref: 21163
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21163
  • description: Zhihengliuella flava gene for 16S ribosomal RNA, partial sequence
  • accession: AB778260
  • length: 1478
  • database: ena
  • NCBI tax ID: 1285193

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Zhihengliuella flava DSM 26152GCA_015751895contigncbi1285193
66792Zhihengliuella flava strain DSM 261521285193.3wgspatric1285193
66792Zhihengliuella flava DSM 261522880502868draftimg1285193

GC content

@refGC-contentmethod
2116370.3high performance liquid chromatography (HPLC)
3113970.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.08no
gram-positiveyes92.894yes
anaerobicno99.497no
aerobicyes94.36yes
halophileyes62.385no
spore-formingno90.468no
thermophileno98.077yes
glucose-utilyes89.95yes
flagellatedno95.735yes
glucose-fermentno82.955no

External links

@ref: 21163

culture collection no.: DSM 26152, NBRC 109021

straininfo link

  • @ref: 88153
  • straininfo: 400789

literature

  • topic: Phylogeny
  • Pubmed-ID: 23990654
  • title: Zhihengliuella flava sp. nov., an actinobacterium isolated from sea sediment, and emended description of the genus Zhihengliuella.
  • authors: Hamada M, Shibata C, Tamura T, Suzuki KI
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.053272-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21163Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26152Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26152)
31139Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172746728776041
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
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88153Reimer, 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-ID400789.1