Strain identifier

BacDive ID: 2827

Type strain: Yes

Species: Acetivibrio straminisolvens

Strain Designation: CSK1

Strain history: IAM 15070 <-- S. Kato CSK1.

NCBI tax ID(s): 1294263 (strain), 253314 (species)

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General

@ref: 6145

BacDive-ID: 2827

DSM-Number: 16021

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, filament-shaped, colony-forming

description: Acetivibrio straminisolvens CSK1 is an anaerobe, spore-forming, thermophilic bacterium that forms circular colonies and was isolated from a bacterial community constructed from composting processes.

NCBI tax id

NCBI tax idMatching level
253314species
1294263strain

strain history

@refhistory
6145<- S. Kato, University of Tokyo, Grad. School of Agricult. and Life Scs., Japan; CSK1 <- S. Kato {2002}
67770IAM 15070 <-- S. Kato CSK1.

doi: 10.13145/bacdive2827.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Acetivibrio
  • species: Acetivibrio straminisolvens
  • full scientific name: Acetivibrio straminisolvens (Kato et al. 2004) Tindall 2019

  • synonyms

    @refsynonym
    20215Clostridium straminisolvens
    20215Hungateiclostridium straminisolvens

@ref: 6145

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Acetivibrio

species: Acetivibrio straminisolvens

full scientific name: Acetivibrio straminisolvens (Kato et al. 2004) Tindall 2019

strain designation: CSK1

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilitygram stainconfidence
230773.0-8.0 µm0.5-1.0 µmfilament-shapedno
69480positive100

colony morphology

  • @ref: 23077
  • colony size: 1.0-2.0 mm
  • colony color: tan-yellow
  • colony shape: circular
  • medium used: cellobiose agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6145ACETIVIBRIO MEDIUM (DSMZ Medium 122)yeshttps://mediadive.dsmz.de/medium/122Name: ACETIVIBRIO MEDIUM (DSMZ Medium 122) Composition: Cellulose 10.0 g/l (optional) Na2-ß-glycerophosphate x 5 H2O 6.0 g/l K2HPO4 5.5 g/l Cellobiose 5.0 g/l Yeast extract 4.5 g/l MgCl2 x 6 H2O 2.6 g/l KH2PO4 1.43 g/l (NH4)2SO4 1.3 g/l L-Glutathione 0.25 g/l CaCl2 x 2 H2O 0.13 g/l FeSO4 x 7 H2O 0.0011 g/l Sodium resazurin 0.0005 g/l Distilled water
23077cellobiose agar mediumyes
23077medium 122yescontaining (per litre distilled water): (NH4)2SO4 , 1.3 g; MgCl2.6H2O, 2.6 g; KH2PO4 , 1.43 g; K2HPO4.3H2O, 7.2 g; CaCl2.6H2O, 0.13 g; FeSO4.7H2O, 1.1 mg; sodium b-glycerophosphate, 6.0 g; yeast extract, 4.5 g; filter paper, ball-milled cellulose or cellobiose, 10 g; glutathione (reduced), 0.25 g; and resazurin, 1 mg

culture temp

@refgrowthtypetemperaturerangeconfidence
6145positivegrowth50thermophilic
23077nogrowth<45.0thermophilic
23077nogrowth>65.0thermophilic
23077positiveoptimum50.0-55.0thermophilic
67770positivegrowth50thermophilic
69480thermophilic98.499

culture pH

@refabilitytypepHPH range
23077positiveoptimum7.5
23077positivegrowth6.0-8.5alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6145anaerobe
23077anaerobe
69480anaerobe100

spore formation

@refspore descriptiontype of sporespore formationconfidence
23077oval,subterminal,0.5-1.0 x 1.0-1.5 µmsporeyes
69480yes99.999

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
23077casein-degradation
23077nitrate-reduction17632
23077esculin+hydrolysis4853

metabolite production

  • @ref: 23077
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivity
23077lecithinase-
23077lipase-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperature
6145a bacterial community constructed from composting processesJapanJPNAsia
23077liquid mediumcontaining (per litre distilled water):yeast extract, 1 g; peptone, 5 g; CaCO3 , 2 g; NaCl, 5 g; dried rice straw, 10 g50.0
67770Straw-degrading bacterial community

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Environmental#Microbial community

taxonmaps

  • @ref: 69479
  • File name: preview.99_88047.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_196;96_2987;97_3672;98_60821;99_88047&stattab=map
  • Last taxonomy: Acetivibrio straminisolvens subclade
  • 16S sequence: AB125279
  • Sequence Identity:
  • Total samples: 195
  • soil counts: 88
  • aquatic counts: 41
  • animal counts: 35
  • plant counts: 31

Safety information

risk assessment

  • @ref: 6145
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6145
  • description: Clostridium straminisolvens gene for 16S rRNA, partial sequence
  • accession: AB125279
  • length: 1447
  • database: ena
  • NCBI tax ID: 253314

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium straminisolvens JCM 215311294263.3wgspatric1294263
66792Hungateiclostridium straminisolvens JCM 215312772190653draftimg1294263
67770Acetivibrio straminisolvens JCM 21531GCA_000521465contigncbi1294263

GC content

@refGC-contentmethod
614541.3
2307741.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes60no
motileno55.539yes
gram-positiveyes52.542no
anaerobicyes99.61yes
aerobicno98.761yes
halophileno96.264no
spore-formingyes95.639yes
thermophileyes99.082yes
glucose-utilyes82.44no
flagellatedno64.77no
glucose-fermentno50no

External links

@ref: 6145

culture collection no.: DSM 16021, IAM 15070, JCM 21531, NBRC 103399

straininfo link

  • @ref: 72351
  • straininfo: 134417

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545431Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community.Kato S, Haruta S, Cui ZJ, Ishii M, Yokota A, Igarashi YInt J Syst Evol Microbiol10.1099/ijs.0.63148-02004Anaerobiosis, Cellulose/*metabolism, Clostridium/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Movement, Oxygen/toxicity, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytology, TemperatureEnzymology
Phylogeny19542130Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge.Shiratori H, Sasaya K, Ohiwa H, Ikeno H, Ayame S, Kataoka N, Miya A, Beppu T, Ueda KInt J Syst Evol Microbiol10.1099/ijs.0.003483-02009Bacterial Typing Techniques, Base Composition, Cellobiose/*metabolism, Cellulose/*metabolism, Clostridium/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, *Hot Temperature, Methane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species SpecificityGenetics
Genetics24558248Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated from a Cellulose-Degrading Bacterial Community.Yuki M, Oshima K, Suda W, Sakamoto M, Kitamura K, Iida T, Hattori M, Ohkuma MGenome Announc10.1128/genomeA.00110-142014Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6145Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16021)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16021
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
23077Souichiro Kato,Shin Haruta,Zong Jun Cui,Masaharu Ishii,Akira Yokota,Yasuo Igarashi10.1099/ijs.0.63148-0Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial communityIJSEM 54: 2043-2047 200415545431
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)
72351Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134417.1StrainInfo: A central database for resolving microbial strain identifiers