Strain identifier

BacDive ID: 2853

Type strain: Yes

Species: Acetivibrio clariflavus

Strain Designation: EBR-02E-0045

Strain history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; EBR 45 <- H. Shiratori {2004}

NCBI tax ID(s): 720554 (strain), 288965 (species)

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General

@ref: 8129

BacDive-ID: 2853

DSM-Number: 19732

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, chemoorganotroph, spore-forming, thermophilic, Gram-variable, rod-shaped, colony-forming

description: Acetivibrio clariflavus EBR-02E-0045 is an anaerobe, chemoorganotroph, spore-forming bacterium that forms circular colonies and was isolated from methanogenic sludge of a cellulose-degrading bioreactor.

NCBI tax id

NCBI tax idMatching level
288965species
720554strain

strain history

  • @ref: 8129
  • history: <- K. Ueda, Nihon Univ., College of Bioresource Sci., Fujisawa, Japan; EBR 45 <- H. Shiratori {2004}

doi: 10.13145/bacdive2853.20230509.8.1

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 clariflavus
  • full scientific name: Acetivibrio clariflavus (Shiratori et al. 2009) Tindall 2019

  • synonyms

    @refsynonym
    20215Clostridium clariflavum
    20215Hungateiclostridium clariflavum

@ref: 8129

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Acetivibrio

species: Acetivibrio clariflavus

full scientific name: Acetivibrio clariflavus (Shiratori et al. 2009) Tindall 2019

strain designation: EBR-02E-0045

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
29002variable3.5 µm0.45 µmrod-shapedno
25435variable2-5 µm0.4-0.5 µmrod-shapednoperitrichous
69480positive100

colony morphology

  • @ref: 25435
  • colony size: 1-2 mm
  • colony color: bright yellow
  • colony shape: circular
  • medium used: Solid agar containing cellulose or cellobiose as a carbon source

pigmentation

  • @ref: 29002
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8129RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520)yeshttps://mediadive.dsmz.de/medium/520Name: RUMINOCLOSTRIDIUM CELLULOLYTICUM (CM3) MEDIUM (DSMZ Medium 520) Composition: Cellulose 9.97009 g/l (optional) Cellobiose 5.98205 g/l K2HPO4 x 3 H2O 2.89133 g/l Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l KH2PO4 1.49551 g/l (NH4)2SO4 1.29611 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.199402 g/l CaCl2 x 2 H2O 0.0747757 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l FeSO4 x 7 H2O 0.00124626 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water
25435Solid agar containing cellulose or cellobiose as a carbon sourceyes

culture temp

@refgrowthtypetemperaturerange
8129positivegrowth55thermophilic
29002positivegrowth45-65thermophilic
29002positiveoptimum57.5thermophilic
25435positiveoptimum55-60thermophilic
25435positivegrowth45-65thermophilic

culture pH

@refabilitytypepH
29002positivegrowth6.0-8.0
29002positiveoptimum7.5
25435positivegrowth6-8
25435positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8129anaerobe
29002anaerobe
25435anaerobe
69480anaerobe100

nutrition type

  • @ref: 25435
  • type: chemoorganotroph

spore formation

@refspore formationspore descriptiontype of sporeconfidence
29002yes
25435yesoval and subterminalspore
69480yes100

halophily

@refsaltgrowthtested relationconcentration
29002NaClpositivegrowth0-0.7 %
29002NaClpositiveoptimum0.4 %
25435NaClpositivegrowth0-0.7 %(w/v)
25435NaClpositiveoptimum0.4 %(w/v)

observation

  • @ref: 25435
  • observation: non-motile, although retarded peritrichious flagella are present

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2900217057cellobiose+carbon source
290024853esculin+hydrolysis
2543515963ribitol-assimilation
2543527613amygdalin-assimilation
2543522599arabinose-assimilation
25435casein-hydrolysis
2543517057cellobiose+carbon source
2543517057cellobiose+energy source
2543562968cellulose+carbon source
2543562968cellulose+energy source
2543516813galactitol-assimilation
2543517113erythritol-assimilation
254354853esculin+hydrolysis
2543528757fructose-assimilation
2543528260galactose-assimilation
254355291gelatin-hydrolysis
2543517234glucose-assimilation
2543517754glycerol-assimilation
2543528087glycogen-assimilation
2543517268myo-inositol-assimilation
2543515443inulin-assimilation
2543517716lactose-assimilation
2543517306maltose-assimilation
2543529864mannitol-assimilation
2543537684mannose-assimilation
254356731melezitose-assimilation
2543528053melibiose-assimilation
2543517632nitrate-reduction
2543516634raffinose-assimilation
2543526546rhamnose-assimilation
2543533942ribose-assimilation
2543517814salicin-assimilation
2543530911sorbitol-assimilation
2543527922sorbose-assimilation
2543528017starch-hydrolysis
2543517992sucrose-assimilation
2543516189sulfate-reduction
2543527082trehalose-assimilation
2543517151xylitol-assimilation
2543518222xylose-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
2543530089acetateyes
2543516526carbon dioxideyes
2543518276dihydrogenyes
2543524996DL-lactateyes
2543516236ethanolyes
2543515740formateyes
2543535581indoleno

enzymes

@refvalueactivityec
25435lecithinase-
25435lipase-
25435catalase1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 8129
  • sample type: methanogenic sludge of a cellulose-degrading bioreactor
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation
#Engineered#Bioreactor
#Environmental#Terrestrial#Mud (Sludge)
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1387.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_196;96_802;97_936;98_1096;99_1387&stattab=map
  • Last taxonomy: Acetivibrio clariflavus subclade
  • 16S sequence: AB186359
  • Sequence Identity:
  • Total samples: 1684
  • soil counts: 734
  • aquatic counts: 312
  • animal counts: 288
  • plant counts: 350

Safety information

risk assessment

  • @ref: 8129
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8129
  • description: Clostridium clariflavum gene for 16S rRNA
  • accession: AB186359
  • length: 1560
  • database: ena
  • NCBI tax ID: 720554

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acetivibrio clariflavus DSM 19732GCA_000237085completencbi720554
66792Clostridium clariflavum DSM 19732720554.3completepatric720554
66792Hungateiclostridium clariflavum EBR 45, DSM 197322507262051completeimg720554

GC content

@refGC-contentmethod
812936.9high performance liquid chromatography (HPLC)
2900236.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes83no
motileyes53.062yes
flagellatedno66.023no
gram-positiveno68.872yes
anaerobicyes99.998yes
aerobicno98.592yes
halophileno98.217yes
spore-formingyes95.979yes
thermophileyes98.22yes
glucose-utilyes80.492yes
glucose-fermentyes53.814no

External links

@ref: 8129

culture collection no.: DSM 19732, NBRC 101661, EBR 45

straininfo link

  • @ref: 72377
  • straininfo: 308309

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Genetics22675603Complete Genome Sequence of Clostridium clariflavum DSM 19732.Izquierdo JA, Goodwin L, Davenport KW, Teshima H, Bruce D, Detter C, Tapia R, Han S, Land M, Hauser L, Jeffries CD, Han J, Pitluck S, Nolan M, Chen A, Huntemann M, Mavromatis K, Mikhailova N, Liolios K, Woyke T, Lynd LRStand Genomic Sci10.4056/sigs.25357322012
Metabolism23265814Exploration of the key microbes involved in the cellulolytic activity of a microbial consortium by serial dilution.Zhang Q, Tian M, Tang L, Li H, Li W, Zhang J, Zhang H, Mao ZBioresour Technol10.1016/j.biortech.2012.11.0972012Base Sequence, Biological Oxygen Demand Analysis, Clostridium/genetics/*metabolism, Cluster Analysis, Computational Biology, DNA Primers/genetics, Denaturing Gradient Gel Electrophoresis, Fermentation, Lignin/*metabolism, Manihot/*chemistry/metabolism, Molecular Sequence Data, Paenibacillus/genetics/*metabolism, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
25426163Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellum to utilize hemicellulose and unpretreated plant material.Izquierdo JA, Pattathil S, Guseva A, Hahn MG, Lynd LRBiotechnol Biofuels10.1186/s13068-014-0136-42014
Metabolism26521249Integration of bacterial expansin-like proteins into cellulosome promotes the cellulose degradation.Chen C, Cui Z, Song X, Liu YJ, Cui Q, Feng YAppl Microbiol Biotechnol10.1007/s00253-015-7071-62015Bacillus subtilis/*enzymology/genetics, Bacterial Proteins/*metabolism, Biotransformation, Cellulose/*metabolism, Cellulosomes/*metabolism, Clostridium/*enzymology/genetics, HydrolysisEnzymology
Enzymology27155425Exploration of the key functional proteins from an efficient cellulolytic microbial consortium using dilution-to-extinction approach.Zhang Q, Li H, Zhu X, Lai F, Zhai Z, Wang YJ Environ Sci (China)10.1016/j.jes.2015.09.0032015Bacterial Proteins/*genetics, Cellulose/*metabolism, Electrophoresis, Polyacrylamide Gel, *Microbial ConsortiaMetabolism
Phylogeny30136170Comparative Biochemical Analysis of Cellulosomes Isolated from Clostridium clariflavum DSM 19732 and Clostridium thermocellum ATCC 27405 Grown on Plant Biomass.Shinoda S, Kurosaki M, Kokuzawa T, Hirano K, Takano H, Ueda K, Haruki M, Hirano NAppl Biochem Biotechnol10.1007/s12010-018-2864-62018*Biomass, Cell Proliferation, Cellulosomes/*metabolism, Clostridium thermocellum/*cytology, Oryza/*chemistryMetabolism
Enzymology30903213Highly thermostable GH51 alpha-arabinofuranosidase from Hungateiclostridium clariflavum DSM 19732.Geng A, Wu J, Xie R, Wang H, Wu Y, Li X, Chang F, Sun JAppl Microbiol Biotechnol10.1007/s00253-019-09753-82019Arabinose/*metabolism, Bacterial Proteins/*chemistry/genetics/metabolism, Clostridiales/chemistry/*enzymology/genetics, Enzyme Stability, Glycoside Hydrolases/*chemistry/genetics/metabolism, Hot Temperature, Hydrogen-Ion Concentration, Kinetics, Substrate Specificity, Xylans/metabolismMetabolism
Metabolism33215261A novel bacterial GH30 xylobiohydrolase from Hungateiclostridium clariflavum.Suchova K, Puchart V, Biely PAppl Microbiol Biotechnol10.1007/s00253-020-11023-x2020Acremonium, Clostridiales, *Endo-1,4-beta Xylanases/genetics/metabolism, Oligosaccharides, Substrate Specificity, *Xylans

Reference

@idauthorscataloguedoi/urltitlepubmedID_cross_referencejournal
8129Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19732)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19732
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
2543510.1099/ijs.0.003483-019542130
29002Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125435
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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)
72377Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308309.1StrainInfo: A central database for resolving microbial strain identifiers