Strain identifier

BacDive ID: 132588

Type strain: Yes

Species: Ruthenibacterium lactatiformans

Strain Designation: 585-1

Strain history: <- V. Shcherbakova, Russian Academy of Sciences, Inst. of Biochem. and Physiology, Moscow, Russia; 585-1 <- B.A. Efimov, Russian Natl. Res. Med. Univ., Moscow

NCBI tax ID(s): 1550024 (species)

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General

@ref: 24377

BacDive-ID: 132588

DSM-Number: 100348

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

description: Ruthenibacterium lactatiformans 585-1 is an obligate anaerobe, chemoorganoheterotroph, mesophilic bacterium that forms circular colonies and was isolated from faeces of healthy men.

NCBI tax id

  • NCBI tax id: 1550024
  • Matching level: species

strain history

  • @ref: 24377
  • history: <- V. Shcherbakova, Russian Academy of Sciences, Inst. of Biochem. and Physiology, Moscow, Russia; 585-1 <- B.A. Efimov, Russian Natl. Res. Med. Univ., Moscow

doi: 10.13145/bacdive132588.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Ruthenibacterium
  • species: Ruthenibacterium lactatiformans
  • full scientific name: Ruthenibacterium lactatiformans Shkoporov et al. 2016

@ref: 24377

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Ruthenibacterium

species: Ruthenibacterium lactatiformans

full scientific name: Ruthenibacterium lactatiformans Shkoporov et al. 2016

strain designation: 585-1

type strain: yes

Morphology

cell morphology

  • @ref: 43087
  • gram stain: negative
  • cell length: 1.3-1.9 µm
  • cell width: 0.3-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43087
  • type of hemolysis: gamma
  • colony size: 0.15-0.4 mm
  • colony color: colourless
  • colony shape: circular
  • incubation period: 3-4 days
  • medium used: EG blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43087EG blood agaryes
43087MRS brothyes
24377PYG 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
24377RUMEN BACTERIA MEDIUM (DSMZ Medium 330)yeshttps://mediadive.dsmz.de/medium/330Name: RUMEN BACTERIA MEDIUM (DSMZ Medium 330) Composition: Na2CO3 4.0 g/l Trypticase peptone 2.0 g/l D-Glucose 0.5 g/l Yeast extract 0.5 g/l Maltose 0.5 g/l Cellobiose 0.5 g/l Starch 0.5 g/l Glycerol 0.5 g/l NaCl 0.456 g/l K2HPO4 0.3 g/l L-Cysteine HCl x H2O 0.25 g/l Na2S x 9 H2O 0.25 g/l (NH4)2SO4 0.228 g/l KH2PO4 0.228 g/l MgSO4 x 7 H2O 0.095 g/l CaCl2 x 2 H2O 0.0608 g/l Hemin 0.001 g/l Sodium resazurin 0.0005 g/l NaOH None Distilled water

culture temp

@refgrowthtypetemperaturerange
43087positiveoptimum37mesophilic
24377positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43087
  • oxygen tolerance: obligate anaerobe

nutrition type

  • @ref: 43087
  • type: chemoorganoheterotroph

spore formation

  • @ref: 43087
  • type of spore: spore
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
430874853esculin+hydrolysis
4308728017starch+hydrolysis
430875291gelatin-degradation
4308717634D-glucose+builds acid from
4308712936D-galactose+builds acid from
4308717306maltose+builds acid from
4308717814salicin+builds acid from
4308762345L-rhamnose+builds acid from
4308730849L-arabinose-builds acid from
4308715963ribitol-builds acid from
4308717716lactose-builds acid from
4308716899D-mannitol-builds acid from
4308716634raffinose-builds acid from
4308727082trehalose-builds acid from
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
430872637amikacinyesyes
430872676amoxicillinyesyes
4308728971ampicillinyesyes
430872955azithromycinyesyes
430873542cephalothinyesyes
430873745clindamycinyesyes
4308763598levofloxacinyesyes
4308763607linezolidyesyes
4308718208penicillin gyesyes
4308728001vancomycinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
4308735581indoleno
4308716004(R)-lactateyes
4308730031succinateyes
6838035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
43087catalase-1.11.1.6
43087urease-3.5.1.5
43087alpha-glucosidase+3.2.1.20
43087beta-glucosidase+3.2.1.21
43087N-acetyl-beta-glucosaminidase+3.2.1.52
43087beta-glucuronidase+3.2.1.31
43087alpha-arabinosidase-3.2.1.55
43087alpha-fucosidase-3.2.1.51
43087alpha-galactosidase+3.2.1.22
43087beta-galactosidase+3.2.1.23
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
68380beta-glucosidase+3.2.1.21
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
24377--++-++----------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
24377faeces of healthy menMoscowRussiaRUSEurope
43087stool sample of a 31-year-old healthy Russian maleRussiaRUS

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_3903.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_286;96_1997;97_2400;98_2967;99_3903&stattab=map
  • Last taxonomy: Ruthenibacterium lactatiformans subclade
  • 16S sequence: KM098109
  • Sequence Identity:
  • Total samples: 305547
  • soil counts: 1989
  • aquatic counts: 6411
  • animal counts: 296291
  • plant counts: 856

Safety information

risk assessment

  • @ref: 24377
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24377
  • description: Ruthenibacterium lactatiformans strain 585-1 16S ribosomal RNA gene, partial sequence
  • accession: KM098109
  • length: 1519
  • database: ena
  • NCBI tax ID: 1550024

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruthenibacterium lactatiformans 585-1GCA_000949455contigncbi1550024
66792Ruthenibacterium lactatiformans 585-12630968832draftimg1550024

GC content

@refGC-contentmethod
4308756.4-56.6
2437756.5sequence analysis

External links

@ref: 24377

culture collection no.: DSM 100348, VKM B-2901

straininfo link

  • @ref: 90905
  • straininfo: 401423

literature

  • topic: Phylogeny
  • Pubmed-ID: 27154556
  • title: Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces.
  • authors: Shkoporov AN, Chaplin AV, Shcherbakova VA, Suzina NE, Kafarskaia LI, Bozhenko VK, Efimov BA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001143
  • year: 2016
  • mesh: Adult, Bacterial Typing Techniques, Base Composition, Child, Preschool, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Gram-Positive Bacteria/genetics, Humans, Lactic Acid/*biosynthesis, Male, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA
  • topic2: Pathogenicity

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
24377Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100348Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100348)
43087Andrei N. Shkoporov, Andrei V. Chaplin, Victoria A. Shcherbakova, Natalia E. Suzina, Lyudmila I. Kafarskaia, Vladimir K. Bozhenko and Boris A. EfimovRuthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces10.1099/ijsem.0.001143IJSEM 66: 3041-3049 201627154556
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
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/
90905Reimer, 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-ID401423.1