Strain identifier

BacDive ID: 5375

Type strain: Yes

Species: Solobacterium moorei

Strain Designation: RCA59-74

Strain history: CIP <- 2000, JCM <- Y. Benno: strain RCA59-74

NCBI tax ID(s): 1123263 (strain), 102148 (species)

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General

@ref: 16566

BacDive-ID: 5375

DSM-Number: 22971

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Solobacterium moorei RCA59-74 is an anaerobe, mesophilic bacterium that was isolated from human feces.

NCBI tax id

NCBI tax idMatching level
102148species
1123263strain

strain history

@refhistory
16566<- JCM/RIKEN <- Y. Benno; RCA59-74
67770Y. Benno RCA59-74.
121136CIP <- 2000, JCM <- Y. Benno: strain RCA59-74

doi: 10.13145/bacdive5375.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Erysipelotrichaceae
  • genus: Solobacterium
  • species: Solobacterium moorei
  • full scientific name: Solobacterium moorei Kageyama and Benno 2000

@ref: 16566

domain: Bacteria

phylum: Firmicutes

class: Erysipelotrichia

order: Erysipelotrichales

family: Erysipelotrichaceae

genus: Solobacterium

species: Solobacterium moorei

full scientific name: Solobacterium moorei Kageyama and Benno 2000

strain designation: RCA59-74

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.052
69480100positive
121136nopositiverod-shaped

colony morphology

  • @ref: 121136

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_22971_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_22971_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_22971_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_22971_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_22971_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16566PYG 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
16566COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperaturerange
16566positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16566anaerobe
69480anaerobe96.883
121136anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose-builds acid from
683676731melezitose-builds acid from
6836716024D-mannose-builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose-builds acid from
6836717992sucrose-builds acid from
6836717716lactose-builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
12113615824D-fructose+degradation
12113617634D-glucose+degradation
12113665327D-xylose-degradation
12113617057cellobiose-degradation
12113617716lactose-degradation
12113617306maltose-degradation
12113617814salicin-degradation
12113617992sucrose+degradation
1211364853esculin+hydrolysis
12113617632nitrate-reduction
12113616301nitrite-reduction
12113617632nitrate+respiration
6838016199urea-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
12113635581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
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
68380beta-Galactosidase 6-phosphate-
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5
68367beta-glucosidase-3.2.1.21
68367gelatinase+
68367urease-3.5.1.5
121136oxidase-
121136beta-galactosidase-3.2.1.23
121136gelatinase+/-
121136amylase+
121136DNase-
121136caseinase+3.4.21.50
121136catalase+1.11.1.6
121136tween esterase+
121136lecithinase-
121136lipase-
121136protease-
121136urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121136--------------------

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16566--+-------+---------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURMNERAFNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerAbeta NAGGDCalpha FUC
16566---+-+-------+/-+---+----+--
16566-+---+/---------+---+----------
16566---+/--+--------+---+/-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16566human fecesJapanJPNAsia
67770Human fecesJapanJPNAsia
121136Human, IntestineJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
165662Risk group (German classification)
1211361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Solobacterium moorei gene for 16S ribosomal RNA, partial sequence, strain: JCM 10645AB5409871486ena102148
20218Solobacterium moorei strain JCM 10645 16S ribosomal RNA gene, partial sequenceAY0449161480ena102148
16566Solobacterium moorei gene for 16S rRNA, isolate:RCA59-74AB0310561487ena102148

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Solobacterium moorei DSM 229711123263.3wgspatric1123263
66792Solobacterium moorei DSM 229712524614654draftimg1123263
67770Solobacterium moorei DSM 22971GCA_000425005scaffoldncbi1123263

GC content

@refGC-contentmethod
1656637.8high performance liquid chromatography (HPLC)
6777037.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.58no
flagellatedno97.785no
gram-positiveyes93.054no
anaerobicyes98.775no
aerobicno99.304yes
halophileno52.813no
spore-formingno90.543no
thermophileno99.208yes
glucose-utilyes86.143no
glucose-fermentyes82.389no

External links

@ref: 16566

culture collection no.: DSM 22971, CIP 106864, JCM 10645, KCTC 15084

straininfo link

  • @ref: 74865
  • straininfo: 88236

literature

  • topic: Phylogeny
  • Pubmed-ID: 10832964
  • title: Phylogenic and phenotypic characterization of some Eubacterium-like isolates from human feces: description of Solobacterium moorei Gen. Nov., Sp. Nov.
  • authors: Kageyama A, Benno Y
  • journal: Microbiol Immunol
  • DOI: 10.1111/j.1348-0421.2000.tb02487.x
  • year: 2000
  • mesh: Bacteria, Anaerobic/*classification/genetics/*isolation & purification, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Eubacterium/classification/genetics/isolation & purification, Feces/*microbiology, Genes, rRNA/genetics, Gram-Positive Asporogenous Rods/*classification/genetics/*isolation & purification, Humans, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16566Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22971)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22971
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74865Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88236.1StrainInfo: A central database for resolving microbial strain identifiers
121136Curators of the CIPCollection of Institut Pasteur (CIP 106864)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106864