Strain identifier

BacDive ID: 158397

Type strain: Yes

Species: Parolsenella catena

Strain Designation: 2CBE6H3, 2CBEGH3

Strain history: M. Sakamoto; RIKEN BRC-JCM, Japan; 2CBEGH3.

NCBI tax ID(s): 2003188 (species)

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General

@ref: 65073

BacDive-ID: 158397

DSM-Number: 105194

keywords: genome sequence, 16S sequence, Bacteria, obligate anaerobe, mesophilic, Gram-positive, coccus-shaped, colony-forming

description: Parolsenella catena 2CBE6H3 is an obligate anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Feces of man.

NCBI tax id

  • NCBI tax id: 2003188
  • Matching level: species

strain history

@refhistory
65073<- M. Sakamoto, JCM, RIKEN BioResource Center, Tsukuba, Japan; 2CBEGH3
67770M. Sakamoto; RIKEN BRC-JCM, Japan; 2CBEGH3.

doi: 10.13145/bacdive158397.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Coriobacteriales
  • family: Atopobiaceae
  • genus: Parolsenella
  • species: Parolsenella catena
  • full scientific name: Parolsenella catena Sakamoto et al. 2018

@ref: 65073

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Parolsenella

species: Parolsenella catena

full scientific name: Parolsenella catena Sakamoto et al. 2018

strain designation: 2CBE6H3, 2CBEGH3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
65377positivecoccus-shapedno
69480no90.491
69480positive99.999

colony morphology

  • @ref: 65377
  • colony size: 1-3 mm
  • colony color: grey to off-white-grey
  • colony shape: circular
  • incubation period: 4 days
  • medium used: Eggerth-Gagnon agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65073PYG 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
65377Eggerth-Gagnon agaryes

culture temp

@refgrowthtypetemperaturerange
65073positivegrowth37mesophilic
65377positivegrowth30-45
65377positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
65377positivegrowth6-8
65377positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
65377obligate anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
65377no
69480no99.996
69481no100

observation

  • @ref: 65377
  • observation: coccobacilli found as chains and 0.8-1.5 (average, 1.0) 2.4-2.8 (average, 2.6) µm.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6537717057cellobiose-builds acid from
6537717634D-glucose+builds acid from
6537716899D-mannitol-builds acid from
6537716024D-mannose+builds acid from
6537717924D-sorbitol-builds acid from
6537765327D-xylose-builds acid from
653774853esculin-hydrolysis
653775291gelatin+assimilation
6537717754glycerol-builds acid from
6537730849L-arabinose-builds acid from
6537762345L-rhamnose-builds acid from
6537717716lactose-builds acid from
6537717306maltose+builds acid from
6537737684mannose-fermentation
653776731melezitose-builds acid from
6537717632nitrate-reduction
6537716634raffinose-builds acid from
6537716634raffinose-fermentation
6537717814salicin-builds acid from
6537717992sucrose-builds acid from
6537727082trehalose-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6537716136hydrogen sulfideno
6537735581indoleno

enzymes

@refvalueactivityec
65377catalase-1.11.1.6
65377urease-3.5.1.5
65377arginine dihydrolase-3.5.3.6
65377alpha-glucosidase-3.2.1.20
65377alpha-galactosidase-3.2.1.22
65377beta-galactosidase-3.2.1.23
653776-phospho-beta-galactosidase-3.2.1.85
65377beta-glucosidase-3.2.1.21
65377alpha-arabinosidase-3.2.1.55
65377beta-glucuronidase-3.2.1.31
65377alkaline phosphatase-3.1.3.1
65377leucyl glycin arylamidase-3.4.11.1
65377pyroglutamic acid arylamidase-
65377glutamyl-glutamate arylamidase-
65377esterase-
65377esterase Lipase (C 8)-
65377lipase (C 14)-
65377valine arylamidase-
65377cystine arylamidase-3.4.11.3
65377trypsin-3.4.21.4
65377chymotrypsin-3.4.4.5
65377alpha-mannosidase-3.2.1.24
65377alpha-fucosidase+3.2.1.51
65377arginine arylamidase+
65377proline-arylamidase+3.4.11.5
65377leucine arylamidase+3.4.11.1
65377tyrosine arylamidase+
65377phenylalanine arylamidase+
65377glycin arylamidase+
65377histidine arylamidase+
65377serine arylamidase+
65377acid phosphatase+3.1.3.2
65377naphthol-AS-BI-phosphohydrolase+
65377glutamate decarboxylase-4.1.1.15

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    65377C12:02.4
    65377C14:06.6
    65377C16:05.6
    65377C18:05.7
    65377C16:0 DMA10.9
    65377C18:0 DMA3.7
    65377C18:1ω9c32.5
    65377C18:1ω9c DMA25.6
    65377unknown and/or C 17:1ω8c2.617
  • type of FA analysis: whole cell analysis
  • incubation medium: Eggerth–Gagnon agar
  • agar/liquid: agar
  • incubation temperature: 37
  • incubation time: 4
  • software version: Sherlock 6.2B
  • library/peak naming table: BHIBLA 3.80
  • system: MIS MIDI
  • method/protocol: Miller 1982

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
65073Feces of manTsukubaJapanJPNAsia
65377faecal sample of a healthy Japanese man in his thirties
67770Feces of a man in the thirtiesJapanJPNAsia

isolation source categories

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

Sequence information

16S sequences

  • @ref: 65073
  • description: Parolsenella catena gene for 16S ribosomal RNA, partial sequence
  • accession: LC270126
  • length: 1478
  • database: ena
  • NCBI tax ID: 2003188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parolsenella catena JCM 31932GCA_003966955completencbi2003188
66792Parolsenella catena strain JCM 319322003188.3completepatric2003188
66792Parolsenella catena JCM 319322837160246completeimg2003188

GC content

@refGC-contentmethod
6507368.4
6537768.4genome sequence analysis
6777065.6genome sequence analysis
6777068.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.038yes
flagellatedno97.761yes
gram-positiveyes95.613yes
anaerobicyes99.18yes
aerobicno98.384yes
halophileno82.62no
spore-formingno95.454yes
thermophileno94.041yes
glucose-utilyes89.292no
glucose-fermentyes68.863no

External links

@ref: 65073

culture collection no.: DSM 105194, JCM 31932

straininfo link

  • @ref: 111201
  • straininfo: 396827

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29458507Parolsenella catena gen. nov., sp. nov., isolated from human faeces.Sakamoto M, Iino T, Hamada M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0026452018Actinobacteria/*classification/genetics/isolation & purification, Adult, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, Japan, Male, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny30762516Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov.Sakamoto M, Ikeyama N, Murakami T, Mori H, Yuki M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0032832019Actinobacteria/*classification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Genomics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

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
65073Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105194Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105194)
65377Mitsuo Sakamoto, Takao Iino, Moriyuki Hamada, Moriya OhkumaParolsenella catena gen. nov., sp. nov., isolated from human faeces10.1099/ijsem.0.002645IJSEM 68: 1165-1172 201829458507
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111201Reimer, 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-ID396827.1