Strain identifier

BacDive ID: 132395

Type strain: Yes

Species: Agathobacter ruminis

Strain Designation: JK 623

Strain history: <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; JK 623 <- J. Kopecny

NCBI tax ID(s): 1712665 (species)

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General

@ref: 24184

BacDive-ID: 132395

DSM-Number: 29029

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, Gram-negative, motile, rod-shaped, colony-forming

description: Agathobacter ruminis JK 623 is an obligate anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from rumen fluid of sheep.

NCBI tax id

  • NCBI tax id: 1712665
  • Matching level: species

strain history

  • @ref: 24184
  • history: <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; JK 623 <- J. Kopecny

doi: 10.13145/bacdive132395.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Agathobacter
  • species: Agathobacter ruminis
  • full scientific name: Agathobacter ruminis Rosero et al. 2016

@ref: 24184

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Agathobacter

species: Agathobacter ruminis

full scientific name: Agathobacter ruminis Rosero et al. 2016

strain designation: JK 623

type strain: yes

Morphology

cell morphology

  • @ref: 43769
  • gram stain: negative
  • cell length: 1.5-2.1 µm
  • cell width: 0.3-0.4 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 43769
  • colony size: 3-4 mm
  • colony color: White
  • colony shape: circular
  • incubation period: 2 days
  • medium used: M10 agar medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43769M10 agar mediumyes
24184PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
43769positivegrowth25-45
43769positiveoptimum35-39mesophilic
24184positivegrowth37mesophilic

culture pH

@refabilitytypepH
43769positivegrowth6-8
43769positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43769
  • oxygen tolerance: obligate anaerobe

spore formation

  • @ref: 43769
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4376915963ribitol-builds acid from
4376917108D-arabinose-builds acid from
4376918333D-arabitol-builds acid from
4376928847D-fucose-builds acid from
4376962318D-lyxose-builds acid from
4376916899D-mannitol-builds acid from
4376916024D-mannose-builds acid from
4376916988D-ribose-builds acid from
4376917924D-sorbitol-builds acid from
4376916443D-tagatose-builds acid from
4376916813galactitol-builds acid from
4376917113erythritol-builds acid from
4376915978glycerol 3-phosphate-builds acid from
4376918403L-arabitol-builds acid from
4376918287L-fucose-builds acid from
4376917266L-sorbose-builds acid from
4376965328L-xylose-builds acid from
4376917716lactose-builds acid from
437696731melezitose-builds acid from
4376928053melibiose-builds acid from
4376943943methyl alpha-D-mannoside-builds acid from
4376937657methyl D-glucoside-builds acid from
4376917268myo-inositol-builds acid from
43769506227N-acetylglucosamine-builds acid from
4376932032potassium gluconate-builds acid from
4376916634raffinose-builds acid from
4376917814salicin-builds acid from
4376932528turanose-builds acid from
4376917151xylitol-builds acid from
4376927613amygdalin+builds acid from
4376918305arbutin+builds acid from
4376917057cellobiose+builds acid from
4376915824D-fructose+builds acid from
4376917634D-glucose+builds acid from
4376928066gentiobiose+builds acid from
4376928087glycogen+builds acid from
4376915443inulin+builds acid from
4376930849L-arabinose+builds acid from
43769maltose hydrate+builds acid from
4376926546rhamnose+builds acid from
4376917992sucrose+builds acid from
437694853esculin+hydrolysis
437695291gelatin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
43769urease-3.5.1.5
43769catalase-1.11.1.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24184--++-++/-+---------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24184rumen fluid of sheepCentral BohemiaCzech RepublicCZEEurope
43769The rumen fluid of sheep grazing in a semi-natural meadowBohemiaCzech RepublicCZEEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Meadow
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body Product#Fluids#Rumen fluid
#Host Body-Site#Organ#Rumen

taxonmaps

  • @ref: 69479
  • File name: preview.99_29178.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_5741;97_17525;98_21769;99_29178&stattab=map
  • Last taxonomy: Agathobacter ruminis subclade
  • 16S sequence: KT229569
  • Sequence Identity:
  • Total samples: 8137
  • soil counts: 67
  • aquatic counts: 43
  • animal counts: 7857
  • plant counts: 170

Safety information

risk assessment

  • @ref: 24184
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24184
  • description: Agathobacter ruminis strain JK623 16S ribosomal RNA gene, partial sequence
  • accession: KT229569
  • length: 1434
  • database: ena
  • NCBI tax ID: 1712665

Genome sequences

  • @ref: 66792
  • description: Agathobacter ruminis DSM 29029
  • accession: GCA_028539255
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1712665

GC content

  • @ref: 24184
  • GC-content: 41.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes85.415yes
flagellatedno56.698no
gram-positiveyes57.109yes
anaerobicyes99.556no
aerobicno99.168yes
halophileno89.501no
spore-formingyes59.122no
glucose-fermentyes71.098no
thermophileno91.816yes
glucose-utilyes87.102no

External links

@ref: 24184

culture collection no.: DSM 29029, LMG 28559

straininfo link

  • @ref: 90737
  • straininfo: 396458

literature

  • topic: Phylogeny
  • Pubmed-ID: 26619944
  • title: Reclassification of Eubacterium rectale (Hauduroy et al. 1937) Prevot 1938 in a new genus Agathobacter gen. nov. as Agathobacter rectalis comb. nov., and description of Agathobacter ruminis sp. nov., isolated from the rumen contents of sheep and cows.
  • authors: Rosero JA, Killer J, Sechovcova H, Mrazek J, Benada O, Fliegerova K, Havlik J, Kopecny J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000788
  • year: 2015

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
24184Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29029Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29029)
43769Jaime A. Rosero, Jirí Killer, Hana Sechovcova, Jakub Mrázek, Oldrich Benada, Katerina Fliegerová, Jaroslav Havlí´k, Jan KopecnýReclassification of Eubacterium rectale (Hauduroy et al. 1937) Prévot 1938 in a new genus Agathobacter gen. nov. as Agathobacter rectalis comb. nov., and description of Agathobacter ruminis sp. nov., isolated from the rumen contents of sheep and cows10.1099/ijsem.0.000788IJSEM 66: 768-773 201626619944
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
68380Automatically annotated from API rID32A
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/
90737Reimer, 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-ID396458.1