Strain identifier

BacDive ID: 140268

Type strain: Yes

Species: Faecalimonas umbilicata

Strain Designation: EGH7

Strain history: M. Sakamoto; RIKEN BRC-JCM, Japan; EGH7.

NCBI tax ID(s): 1912855 (species)

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General

@ref: 42875

BacDive-ID: 140268

DSM-Number: 103426

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

description: Faecalimonas umbilicata EGH7 is an obligate anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from human faeces, healthy Japanese man .

NCBI tax id

  • NCBI tax id: 1912855
  • Matching level: species

strain history

@refhistory
42875<- M. Sakamoto, RIKEN BRC-JCM, Japan; EGH7
67770M. Sakamoto; RIKEN BRC-JCM, Japan; EGH7.

doi: 10.13145/bacdive140268.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Faecalimonas
  • species: Faecalimonas umbilicata
  • full scientific name: Faecalimonas umbilicata Sakamoto et al. 2017

@ref: 42875

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Eubacteriales

family: Lachnospiraceae

genus: Faecalimonas

species: Faecalimonas umbilicata

full scientific name: Faecalimonas umbilicata Sakamoto et al. 2017

strain designation: EGH7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43183positive2.4 µm0.8-1.5 µmcoccus-shapedno
69480positive100

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
43183Eggerth-Gagnon (EG) agar (Merck)yes
43183PYG brothyes
42875PYG 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
43183positiveoptimum37mesophilic
43183positivegrowth30-40
42875positivegrowth37mesophilic
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
43183obligate anaerobe
69480anaerobe99.63

spore formation

@refspore formationconfidence
43183no
69480no98.501

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
431834853esculin+hydrolysis
431835291gelatin-degradation
4318317634D-glucose+builds acid from
4318317716lactose+builds acid from
4318317306maltose+builds acid from
4318316634raffinose+builds acid from
4318317814salicin+builds acid from
4318317992sucrose+builds acid from
4318365327D-xylose+builds acid from
4318330849L-arabinose-builds acid from
4318317057cellobiose-builds acid from
4318317754glycerol-builds acid from
4318316899D-mannitol-builds acid from
4318316024D-mannose-builds acid from
431836731melezitose-builds acid from
4318362345L-rhamnose-builds acid from
4318317924D-sorbitol-builds acid from
4318327082trehalose-builds acid from
4318316634raffinose+fermentation
4318337684mannose-fermentation
4318317632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
4318316136hydrogen sulfideyes
4318335581indoleno

enzymes

@refvalueactivityec
43183catalase-1.11.1.6
43183alpha-galactosidase+3.2.1.22
43183beta-galactosidase+3.2.1.23
43183alpha-glucosidase+3.2.1.20
43183beta-glucosidase+3.2.1.21
43183beta-glucuronidase+3.2.1.31
43183alkaline phosphatase+3.1.3.1
43183arginine arylamidase+
43183phenylalanine arylamidase+
43183leucine arylamidase+3.4.11.1
43183tyrosine arylamidase+
43183alanine arylamidase+3.4.11.2
43183histidine arylamidase+
43183serine arylamidase+
43183urease-3.5.1.5
43183arginine dihydrolase-3.5.3.6
431836-phospho-beta-galactosidase-3.2.1.85
43183alpha-arabinosidase-3.2.1.55
43183N-acetyl-beta-glucosaminidase-3.2.1.52
43183glutamate decarboxylase-4.1.1.15
43183proline-arylamidase-3.4.11.5
43183leucyl glycin arylamidase-3.4.11.1
43183pyroglutamic acid arylamidase-
43183glycin arylamidase-
43183glutamyl-glutamate arylamidase-
43183esterase+
43183esterase Lipase (C 8)+
43183valine arylamidase+
43183acid phosphatase+3.1.3.2
43183naphthol-AS-BI-phosphohydrolase+
43183lipase-
43183cystine arylamidase-3.4.11.3
43183trypsin-3.4.21.4
43183alpha-chymotrypsin-3.4.21.1
43183alpha-mannosidase-3.2.1.24

fatty acid profile

  • fatty acids

    @reffatty acidpercentageSDECL
    43183C12:01.30.1
    43183C14:05.80.4
    43183C16:021.30.9
    43183C18:04.10.3
    43183C16:0 DMA3.10.7
    43183C18:0 DMA1.30.8
    43183C18:1ω9c34.24.3
    43183C18:2ω6,9c2.70.5
    43183C18:1ω7c DMA2.61.6
    43183C18:1ω9c DMA15.20.9
    43183unknown / C17:1ω8c3.10.217
    43183unknown / C18:0ω11c/9t/6t FAME6.90.717834
  • 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
42875human faeces, healthy Japanese man (45-years-old)Tsukuba, IbarakiJapanJPNAsia
43183human faeces
67770Feces of a man in the forties

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_1016;97_1183;98_1414;99_4314&stattab=map
  • Last taxonomy: Faecalimonas umbilicata subclade
  • 16S sequence: LC192831
  • Sequence Identity:
  • Total samples: 53459
  • soil counts: 369
  • aquatic counts: 856
  • animal counts: 51940
  • plant counts: 294

Safety information

risk assessment

  • @ref: 42875
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42875
  • description: Faecalimonas umbilicata gene for 16S ribosomal RNA, partial sequence, strain: EGH7
  • accession: LC192831
  • length: 1492
  • database: ena
  • NCBI tax ID: 1912855

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Faecalimonas umbilicata strain DSM 1034261912855.8wgspatric1912855
66792Faecalimonas umbilicata strain EGH71912855.5wgspatric1912855
66792Faecalimonas umbilicata EGH72832053327draftimg1912855
66792Faecalimonas umbilicata DSM 1034262784746781draftimg1912855
67770Faecalimonas umbilicata EGH7GCA_003402615contigncbi1912855
67770Faecalimonas umbilicata DSM 103426GCA_004346095scaffoldncbi1912855

GC content

  • @ref: 42875
  • GC-content: 46.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes55no
motileno92.727yes
gram-positiveyes96.079no
anaerobicyes99.499no
aerobicno98.157no
halophileno80.322no
spore-formingno72.075yes
glucose-utilyes88.341no
flagellatedno95.309no
thermophileno95.93yes
glucose-fermentyes73.375no

External links

@ref: 42875

culture collection no.: DSM 103426, JCM 30896

straininfo link

  • @ref: 96574
  • straininfo: 407291

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Genetics30533935Draft Genome Sequence of Faecalimonas umbilicata JCM 30896(T), an Acetate-Producing Bacterium Isolated from Human Feces.Sakamoto M, Ikeyama N, Yuki M, Ohkuma MMicrobiol Resour Announc10.1128/MRA.01091-182018Phylogeny

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
42875Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103426Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103426)
43183Mitsuo Sakamoto, Takao Iino, Moriya OhkumaFaecalimonas 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.10.1099/ijsem.0.001790IJSEM 67: 1219-1227 201728556772
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/
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/
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
96574Reimer, 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-ID407291.1