Strain identifier

BacDive ID: 132477

Type strain: Yes

Species: Hamadaea flava

Strain history: CGMCC 4.7289 <-- W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM C0533.

NCBI tax ID(s): 1742688 (species)

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General

@ref: 24266

BacDive-ID: 132477

DSM-Number: 100517

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

description: Hamadaea flava DSM 100517 is an aerobe, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1742688
  • Matching level: species

strain history

@refhistory
24266<- W.-J. Li, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM C0533 <- C. Xiao
67770CGMCC 4.7289 <-- W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM C0533.

doi: 10.13145/bacdive132477.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Hamadaea
  • species: Hamadaea flava
  • full scientific name: Hamadaea flava Chu et al. 2016

@ref: 24266

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Hamadaea

species: Hamadaea flava

full scientific name: Hamadaea flava Chu et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 43674
  • gram stain: positive
  • motility: no

colony morphology

  • @ref: 43674
  • incubation period: 5 days
  • medium used: M5 medium

multimedia

  • @ref: 24266
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_100517.jpg
  • caption: Medium 987 28°
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24266ISP2 MEDIUM (DSMZ Medium 987)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium987.pdf
43674M5 mediumyescellulose 2.5 g, sodium pyruvate 2.0 g, L-proline 1g, KNO3 0.25 g, MgSO4 0.2 g, K2HPO4 0.2 g, CaCl2 0.5 g and H2O 1000 ml; pH 7.2, supplemented with nalidixic acid (25 mg/L) and nystatin (50 mg/L)
24266N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43674positivegrowth15-37
43674positiveoptimum28-30mesophilic
24266positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
43674positivegrowth6-8
43674positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43674
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43674NaClpositivegrowth0-3 %(w/v)
43674NaClpositiveoptimum0-1 %(w/v)

observation

@refobservation
43674Abundant globose bodies present
67770quinones: MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4367415971L-histidine-nitrogen source
4367417632nitrate-reduction
4367417108D-arabinose+carbon source
4367415824D-fructose+carbon source
4367412936D-galactose+carbon source
4367417634D-glucose+carbon source
4367416024D-mannose+carbon source
4367417306maltose+carbon source
4367416634raffinose+carbon source
4367433942ribose+carbon source
436745291gelatin+hydrolysis
4367428017starch+hydrolysis
4367453424tween 20+hydrolysis
4367453423tween 40+hydrolysis
4367453425tween 60+hydrolysis
4367453426tween 80+hydrolysis
4367417196L-asparagine+nitrogen source
4367429991L-aspartate+nitrogen source
4367417561L-cysteine+nitrogen source
4367416283L-cystine+nitrogen source
4367429985L-glutamate+nitrogen source
4367417191L-isoleucine+nitrogen source
4367418019L-lysine+nitrogen source
4367416643L-methionine+nitrogen source
4367417203L-proline+nitrogen source
4367417115L-serine+nitrogen source
4367416857L-threonine+nitrogen source
4367417895L-tyrosine+nitrogen source
4367416414L-valine+nitrogen source

enzymes

@refvalueactivityec
43674catalase+1.11.1.6
43674cytochrome oxidase+1.9.3.1
43674urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24266soilYunnan province, Shiling county, Impressive Toboco farmChinaCHNAsia
43674A soil sampleShiling county, Yunnan ProvinceChinaCHNAsia
67770Soil from Shiling CountyYunnan ProvinceChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_147271.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3745;97_4605;98_97482;99_147271&stattab=map
  • Last taxonomy: Hamadaea flava subclade
  • 16S sequence: KT946774
  • Sequence Identity:
  • Total samples: 1069
  • soil counts: 825
  • aquatic counts: 67
  • animal counts: 33
  • plant counts: 144

Safety information

risk assessment

  • @ref: 24266
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24266
  • description: Hamadaea flava strain YIM C0533 16S ribosomal RNA gene, partial sequence
  • accession: KT946774
  • length: 1520
  • database: ena
  • NCBI tax ID: 1742688

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hamadaea flava DSM 1005172852728668draftimg1742688
66792Hamadaea flava DSM 100517GCA_024172085contigncbi1742688

GC content

@refGC-contentmethod
4367469.4Thermal denaturation, fluorometry
2426669.4
6777069.4thermal denaturation, midpoint method (Tm)

External links

@ref: 24266

culture collection no.: DSM 100517, CGMCC 4.7289, CPCC 204160, KCTC 39591, YIM C0533, JCM 32491

straininfo link

  • @ref: 90810
  • straininfo: 400621

literature

  • topic: Phylogeny
  • Pubmed-ID: 26842996
  • title: Hamadaea flava sp. nov., isolated from a soil sample and emended description of the genus Hamadaea.
  • authors: Chu X, Li S, Chen W, Devi Asem M, Duan YQ, Nie GX, Hozzein WN, Zhi XY, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000949
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24266Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100517Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100517)
43674Xiao Chu, Shuai Li, Wei Chen, Mipeshwaree Devi Asem, Yan-Qing Duan, Guo-Xing Nie, Wael N. Hozzein, Xiao-Yang Zhi, Wen-Jun LiHamadaea flava sp. nov., isolated from a soil sample and emended description of the genus Hamadaea10.1099/ijsem.0.000949IJSEM 66: 1818-1822 201626842996
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/
90810Reimer, 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-ID400621.1