Strain identifier

BacDive ID: 6246

Type strain: Yes

Species: Intrasporangium chromatireducens

Strain Designation: Q5-1

Strain history: <- H Liu, Huzhong Agriculture Univ., China

NCBI tax ID(s): 1386088 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 18112

BacDive-ID: 6246

DSM-Number: 25801

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

description: Intrasporangium chromatireducens Q5-1 is an aerobe, Gram-positive bacterium that was isolated from subsurface soil of manganese mine.

NCBI tax id

  • NCBI tax id: 1386088
  • Matching level: species

strain history

@refhistory
18112<- KCTC; KCTC 19811
67770CGMCC 1.10750 <-- H. Liu et al. Q5-1.
67771<- H Liu, Huzhong Agriculture Univ., China

doi: 10.13145/bacdive6246.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Intrasporangium
  • species: Intrasporangium chromatireducens
  • full scientific name: Intrasporangium chromatireducens Liu et al. 2012

@ref: 18112

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Intrasporangium

species: Intrasporangium chromatireducens

full scientific name: Intrasporangium chromatireducens Liu et al. 2012

strain designation: Q5-1

type strain: yes

Morphology

cell morphology

@refgram staincell widthmotility
30193positive0.3-0.5 µmno
67771positive

pigmentation

  • @ref: 30193
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18112TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18112GYM 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

culture temp

@refgrowthtypetemperature
18112positivegrowth28
30193positivegrowth10-45
30193positiveoptimum37
67770positivegrowth37
67771positivegrowth37

culture pH

@refabilitytypepHPH range
30193positivegrowth05-10alkaliphile
30193positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30193aerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
30193NaClpositivegrowth0-4 %
30193NaClpositiveoptimum1 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30193168082-dehydro-D-gluconate+carbon source
30193370543-hydroxybutyrate+carbon source
3019330089acetate+carbon source
3019317128adipate+carbon source
3019316449alanine+carbon source
3019324265gluconate+carbon source
3019317234glucose+carbon source
3019327570histidine+carbon source
3019324996lactate+carbon source
3019325115malate+carbon source
3019317306maltose+carbon source
3019329864mannitol+carbon source
3019337684mannose+carbon source
3019333942ribose+carbon source
3019331011valerate+carbon source
301934853esculin+hydrolysis
3019317632nitrate+reduction

enzymes

@refvalueactivityec
30193catalase+1.11.1.6
30193urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18112subsurface soil of manganese mineHunan ProvinceChinaCHNAsia
67770Subsurface soil of a manganese mineHunan Province, central-south ChinaChinaCHNAsia
67771From chromium-manganese mineHunanChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5336.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2582;97_3164;98_3976;99_5336&stattab=map
  • Last taxonomy: Intrasporangium chromatireducens subclade
  • 16S sequence: FJ487951
  • Sequence Identity:
  • Total samples: 383
  • soil counts: 233
  • aquatic counts: 25
  • animal counts: 98
  • plant counts: 27

Safety information

risk assessment

  • @ref: 18112
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18112
  • description: Intrasporangium chromatireducens Q5-1 16S ribosomal RNA gene, partial sequence
  • accession: FJ487951
  • length: 1449
  • database: nuccore
  • NCBI tax ID: 584657

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Intrasporangium chromatireducens Q5-1584657.9wgspatric584657
66792Intrasporangium chromatireducens Q5-12588253842draftimg584657
67770Intrasporangium chromatireducens Q5-1GCA_000576575contigncbi584657

GC content

@refGC-contentmethod
1811271.5
6777071.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.167no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.354yes
69480spore-formingspore-formingAbility to form endo- or exosporesno55.739no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.275yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.033yes
69480flagellatedmotile2+Ability to perform flagellated movementno87yes

External links

@ref: 18112

culture collection no.: DSM 25801, CCTCC Aa 2010019, CGMCC 1.10750, KCTC 19811, NRRL B-59521, JCM 18316

straininfo link

  • @ref: 75724
  • straininfo: 397273

literature

  • topic: Phylogeny
  • Pubmed-ID: 21441371
  • title: Intrasporangium chromatireducens sp. nov., a chromate-reducing actinobacterium isolated from manganese mining soil, and emended description of the genus Intrasporangium.
  • authors: Liu H, Wang H, Wang G
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.030528-0
  • year: 2011
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, China, Chromates/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Lipids/analysis, *Manganese, *Mining, Molecular Sequence Data, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18112Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25801)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25801
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
30193Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2653928776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
75724Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397273.1StrainInfo: A central database for resolving microbial strain identifiers