Strain identifier

BacDive ID: 132679

Type strain: Yes

Species: Acetivibrio saccincola

Strain Designation: GGR1

Strain history: <- D. Köck, TU Munich, Chair of Microbiology, Freising-Weihenstephan, Germany; GGR1 <- D. Köck; {2015}

NCBI tax ID(s): 1677857 (species)

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General

@ref: 24468

BacDive-ID: 132679

DSM-Number: 101079

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

description: Acetivibrio saccincola GGR1 is an anaerobe, spore-forming, thermophilic bacterium that forms circular colonies and was isolated from thermophilic lab scale biogas plant.

NCBI tax id

  • NCBI tax id: 1677857
  • Matching level: species

strain history

  • @ref: 24468
  • history: <- D. Köck, TU Munich, Chair of Microbiology, Freising-Weihenstephan, Germany; GGR1 <- D. Köck; {2015}

doi: 10.13145/bacdive132679.20230509.8.1

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 saccincola
  • full scientific name: Acetivibrio saccincola (Koeck et al. 2016) Tindall 2019

  • synonyms

    @refsynonym
    20215Herbivorax saccincola
    20215Hungateiclostridium saccincola

@ref: 24468

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Acetivibrio

species: Acetivibrio saccincola

full scientific name: Acetivibrio saccincola (Koeck et al. 2016) Tindall 2019

strain designation: GGR1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25017positive5.0-10.0 µm0.2 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 25017
  • colony size: 1.0-2.0 mm
  • colony color: dark yellow
  • colony shape: circular
  • medium used: GS2 agar plates

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
25017GS2 agar platesyes6g yeast extract, 2.9g K2HPO4, 2.1g urea, 1.5g KH2PO4, 2.9g trisodium citrate dihydrate, 1.0g cysteine hydrochloride monohydrate, 10 g MOPS, 0.1g MgCl2.6H2O, 0.015g CaCl2.2H2O, 0.125mg FeSO4 .7H2O and 0.01 % resazurin
24468CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255)yesName: CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255; with strain-specific modifications) Composition: Cellulose 9.98004 g/l Morpholinopropane sulfonic acid 9.98004 g/l Yeast extract 5.98802 g/l Cellobiose 4.99002 g/l Urea 1.99601 g/l L-Cysteine HCl x H2O 0.998004 g/l K2HPO4 x 3 H2O 0.998004 g/l KH2PO4 0.499002 g/l MgCl2 x 6 H2O 0.499002 g/l CaCl2 x 2 H2O 0.0499002 g/l FeSO4 x 7 H2O 0.0012475 g/l Sodium resazurin 0.000499002 g/l Distilled waterhttps://mediadive.dsmz.de/medium/255

culture temp

@refgrowthtypetemperaturerangeconfidence
25017positivegrowth45-65thermophilic
25017positiveoptimum60thermophilic
24468positivegrowth55thermophilic
69480thermophilic92.316

culture pH

@refabilitytypepHPH range
25017positivegrowth6.5-9.0alkaliphile
25017positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
25017anaerobe
69480anaerobe100

spore formation

@reftype of sporespore formationconfidence
25017endosporeyes
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
25017NaClpositivegrowth0-2.0 %(w/v)
25017NaCloptimum0.2 %(w/v)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
25017casein-hydrolysis
25017citrate-degradation16947
25017galactitol-fermentation16813
25017L-phenylalanine-other17295
25017lysine-other25094
25017ornithine-other18257
25017sulfate-reduction16189
25017tryptophan-energy source27897
25017urea-hydrolysis16199
25017arabinose-growth22599
25017cellobiose+carbon source17057
25017cellulose+carbon source62968
25017fructose-growth28757
25017galactose+carbon source28260
25017glucose+carbon source17234
25017lactose-growth17716
25017mannose-growth37684
25017sorbitol+carbon source30911
25017starch-growth28017
25017sucrose-growth17992
25017xylan+carbon source37166
25017xylose+carbon source18222

metabolite production

  • @ref: 25017
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 25017
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25017catalase-1.11.1.6
25017tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

  • @ref: 24468
  • sample type: thermophilic (55 °C) lab scale biogas plant
  • geographic location: Freising near Munich
  • country: Germany
  • origin.country: DEU
  • continent: Europe
  • latitude: 48.3996
  • longitude: 11.7297

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Industrial#Plant (Factory)
#Engineered#Laboratory
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_38629.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_196;96_18243;97_22512;98_28327;99_38629&stattab=map
  • Last taxonomy: Acetivibrio saccincola subclade
  • 16S sequence: LN868252
  • Sequence Identity:
  • Total samples: 7335
  • soil counts: 4138
  • aquatic counts: 988
  • animal counts: 1026
  • plant counts: 1183

Safety information

risk assessment

  • @ref: 24468
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
25017Clostridium sp. GGR1 partial 16S rRNA gene, isolate GGR1LN868252.11421nuccore1677857
24468Clostridium sp. GGR1 partial 16S rRNA gene, isolate GGR1LN8682521421ena1677857

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acetivibrio saccincola GGR1GCA_002844395completencbi1677857
66792Herbivorax saccincola strain GGR11677857.3completepatric1677857
66792Acetivibrio saccincola GGR12775506833completeimg1677857

GC content

@refGC-contentmethod
2501734.9genome sequence analysis
2446834.9sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes88no
flagellatedno81.434no
gram-positiveyes78.797yes
anaerobicyes99.622no
aerobicno97.787no
halophileno94.038no
spore-formingyes93.194yes
glucose-utilyes88.194yes
thermophileyes97.711no
motileyes54.065yes
glucose-fermentyes51.899no

External links

@ref: 24468

culture collection no.: DSM 101079, CECT 9155

straininfo link

  • @ref: 90987
  • straininfo: 396620

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27499077Herbivorax saccincola gen. nov., sp. nov., a cellulolytic, anaerobic, thermophilic bacterium isolated via in sacco enrichments from a lab-scale biogas reactor.Koeck DE, Mechelke M, Zverlov VV, Liebl W, Schwarz WHInt J Syst Evol Microbiol10.1099/ijsem.0.0013742016Bacterial Typing Techniques, Base Composition, Biofuels/*microbiology, Bioreactors/microbiology, Cellulose/metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Genetics29482868Characterization and high-quality draft genome sequence of Herbivorax saccincola A7, an anaerobic, alkaliphilic, thermophilic, cellulolytic, and xylanolytic bacterium.Aikawa S, Baramee S, Sermsathanaswadi J, Thianheng P, Tachaapaikoon C, Shikata A, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi ASyst Appl Microbiol10.1016/j.syapm.2018.01.0102018Animals, Bacterial Typing Techniques, Base Composition, Base Sequence, Cattle, Cellulose/*metabolism, *Clostridiales/classification/genetics/isolation & purification, Composting, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/microbiology, Genome, Bacterial/*genetics, Japan, Lignin/metabolism, Sequence Analysis, DNAMetabolism

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
24468Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101079Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101079)
25017D. E. M. Koeck, M.,Zverlov, V. V.,Liebl, W.,Schwarz, W. H.Herbivorax saccincola gen. nov., sp. nov., a cellulolytic, anaerobic, thermophilic bacterium isolated via in sacco enrichments from a lab-scale biogas reactor10.1099/ijsem.0.001374IJSEM 66: 4458-4463 201627499077
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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
90987Reimer, 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-ID396620.1