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Strain identifier

BacDive ID: 2621

Type strain: Yes

Species: Faecalicatena orotica

Strain history: ATCC 13619 <-- H. C. Friedman ("Zymobacterium oroticum") <-- A. Kornberg.

NCBI tax ID(s): 1544 (species)

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General

@ref: 607

BacDive-ID: 2621

DSM-Number: 1287

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

description: Faecalicatena orotica DSM 1287 is an anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from mud.

NCBI tax id

  • NCBI tax id: 1544
  • Matching level: species

strain history

doi: 10.13145/bacdive2621.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Faecalicatena
  • species: Faecalicatena orotica
  • full scientific name: Faecalicatena orotica (Wachsman and Barker 1954) Sakamoto et al. 2017

  • synonyms

    @refsynonym
    20215Clostridium oroticum
    20215Zymobacterium oroticum

@ref: 607

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Faecalicatena

species: Faecalicatena orotica

full scientific name: Faecalicatena orotica (Wachsman and Barker 1954) Sakamoto et al. 2017

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43183positiverod-shapedyes
69480positive90.408

colony morphology

  • @ref: 43183
  • colony size: 1-3 mm
  • colony color: white to ivory
  • colony shape: circular
  • incubation period: 4 days
  • medium used: Eggerth-Gagnon (EG) agar (Merck)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
607CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
607FAECALICATENA OROTICA MEDIUM (DSMZ Medium 249)yeshttps://mediadive.dsmz.de/medium/249Name: FAECALICATENA OROTICA MEDIUM (DSMZ Medium 249) Composition: K2HPO4 6.95 g/l Tryptone 5.0 g/l Na-orotate 2.5 g/l KH2PO4 1.36 g/l Yeast extract 0.5 g/l Na-thioglycolate 0.5 g/l Riboflavin 0.015 g/l Resazurin 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
607positivegrowth37mesophilic
43183positiveoptimum37mesophilic
43183positivegrowth20-40
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
43183positivegrowth6.0-8.0
43183positiveoptimum7

Physiology and metabolism

tolerance

  • @ref: 43183
  • compound: bile
  • concentration: 20.0 % (w/v)

oxygen tolerance

@refoxygen toleranceconfidence
607anaerobe
43183obligate anaerobe
69480anaerobe99.319

spore formation

@refspore formationconfidence
43183yes
69480yes50

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 98.797

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
431834853esculin+hydrolysis
4318330849L-arabinose+builds acid from
4318317057cellobiose+builds acid from
4318317716lactose+builds acid from
4318317306maltose+builds acid from
4318316899D-mannitol+builds acid from
4318316024D-mannose+builds acid from
4318316634raffinose+builds acid from
4318362345L-rhamnose+builds acid from
4318317924D-sorbitol+builds acid from
4318337684mannose-fermentation
4318316634raffinose-fermentation

metabolite production

  • @ref: 43183
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
43183urease-3.5.1.5
43183acid phosphatase+3.1.3.2
43183esterase Lipase (C 8)+
43183alpha-fucosidase+3.2.1.51
43183beta-galactosidase+3.2.1.23
43183alpha-glucosidase+3.2.1.20
43183beta-glucosidase+3.2.1.21
43183beta-glucuronidase+3.2.1.31
43183proline-arylamidase+3.4.11.5
43183N-acetyl-beta-glucosaminidase-3.2.1.52
43183alkaline phosphatase-3.1.3.1
43183alanine arylamidase-3.4.11.2
43183arginine arylamidase-
43183histidine arylamidase-
43183leucine arylamidase-3.4.11.1
43183phenylalanine arylamidase-
43183serine arylamidase-
43183tyrosine arylamidase-
43183valine arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentageSDECL
    43183C12:01.60.2
    43183C14:060.1
    43183C16:0120.4
    43183C18:01.40.8
    43183C16:0 DMA21.1
    43183C18:0 DMA1.10.6
    43183C18:1ω9c25.92.2
    43183C18:2ω6,9c1.50.9
    43183C18:1ω7c DMA2.41.4
    43183C18:1ω9c DMA373.9
    43183C18:1ω11t3.72.1
    43183unknown / C17:1ω8c8.61.517
    43183unknown / C18:0ω11c/9t/6t FAME3.42
  • type of FA analysis: whole cell analysis
  • incubation medium: EG
  • agar/liquid: agar
  • incubation temperature: 37
  • incubation time: 4
  • software version: Sherlock 6.2B
  • system: MIS MIDI
  • method/protocol: Miller 1982
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
607mudSan Francisco BayUSAUSANorth America
67770MudSan Francisco Bay, CAUSAUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_29505.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_942;97_1096;98_21996;99_29505&stattab=map
  • Last taxonomy: Faecalicatena orotica subclade
  • 16S sequence: AB818947
  • Sequence Identity:
  • Total samples: 846
  • soil counts: 2
  • aquatic counts: 3
  • animal counts: 841

Safety information

risk assessment

  • @ref: 607
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium oroticum strain ATCC 13619 16S ribosomal RNA gene, partial sequenceM591091537ena1544
607Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 1FR7499171525ena1544
607Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 2FR7499181525ena1544
607Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 3FR7499191525ena1544
607Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 4FR7499201525ena1544
607Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 5FR7499211525ena1544
607Clostridium oroticum partial 16S rRNA gene, type strain DSM 1287T, clone 6FR7499221526ena1544
67770Clostridium oroticum gene for 16S ribosomal RNA, partial sequence, strain: JCM 1429AB8189471494ena1544

Genome sequences

  • @ref: 66792
  • description: Clostridium oroticum DSM 1287
  • accession: 2928587524
  • assembly level: draft
  • database: img
  • NCBI tax ID: 1485

GC content

@refGC-contentmethod
60744.0
60749.9high performance liquid chromatography (HPLC)
6777044thermal denaturation, midpoint method (Tm)

External links

@ref: 607

culture collection no.: DSM 1287, ATCC 13619, ATCC 25750, JCM 1429, NCIB 10650, BCRC 14529, LMG 3286, NCCB 73016, NCIMB 10650, VPI 0565

straininfo link

@refpassport
20218http://www.straininfo.net/strains/7913
20218http://www.straininfo.net/strains/7911
20218http://www.straininfo.net/strains/7912
20218http://www.straininfo.net/strains/7914

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology2867744Enzyme elements involved in the interconversion of L-carbamylaspartate and L-dihydroorotate by dihydroorotase from Clostridium oroticum.Pettigrew DW, Mehta BJ, Bidigare RR, Choudhury RR, Scheffler JE, Sander EGArch Biochem Biophys10.1016/0003-9861(85)90521-11985Amidohydrolases/*metabolism, Aspartic Acid/*analogs & derivatives/metabolism, Catalysis, Clostridium/*enzymology, Cobalt, Cyclization, Diethyl Pyrocarbonate/pharmacology, Dihydroorotase/antagonists & inhibitors/*metabolism, Histidine/physiology, Hydrogen-Ion Concentration, Kinetics, Orotic Acid/*analogs & derivatives/metabolism, Zinc/physiologyMetabolism
Phylogeny28556772Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.Sakamoto M, Iino T, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0017902017Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/genetics/isolation & purification, Clostridium/classification, DNA, Bacterial/genetics, Eubacterium/classification, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
607Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1287)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1287
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
43183Mitsuo Sakamoto, Takao Iino, Moriya Ohkuma10.1099/ijsem.0.001790Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov.IJSEM 67: 1219-1227 201728556772
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)