Strain identifier

BacDive ID: 133154

Type strain: Yes

Species: Butyricimonas faecihominis

Strain Designation: 180-3

Strain history: Y. Tanaka 180-3.

NCBI tax ID(s): 1472416 (species)

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General

@ref: 42682

BacDive-ID: 133154

DSM-Number: 105721

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

description: Butyricimonas faecihominis 180-3 is a mesophilic, Gram-positive, motile bacterium that forms circular colonies and was isolated from healthy human’s faeces .

NCBI tax id

  • NCBI tax id: 1472416
  • Matching level: species

strain history

@refhistory
42682<- JCM RIKEN BioResource Center, Tsukuba; JCM 18676 <- Y. Tanaka; 180-3
67770Y. Tanaka 180-3.

doi: 10.13145/bacdive133154.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Odoribacteraceae
  • genus: Butyricimonas
  • species: Butyricimonas faecihominis
  • full scientific name: Butyricimonas faecihominis Sakamoto et al. 2014

@ref: 42682

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Odoribacteraceae

genus: Butyricimonas

species: Butyricimonas faecihominis

full scientific name: Butyricimonas faecihominis Sakamoto et al. 2014 emend. Le Roy et al. 2019

strain designation: 180-3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
24928positive1.7-2.3 µm0.8-1.1 µmrod-shapedyes
24928positive1.3 µm0.7 µmcoccus-shapedno

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium usedtype of hemolysis
249281.0-2.0 mmyellowishcircular3 daysyeast extract-casein hydrolysate-fatty acids (YCFAG) agar plate
24928white to colourlesscircular3 daysyeast extract-casein hydrolysate-fatty acids (YCFAG) agar plategamma
24928irregular

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
24928yeast extract-casein hydrolysate-fatty acids (YCFAG) agar plateyes
24928yeast extract-casein hydrolysate-fatty acids (YCFAG) agar plateyessupplemented with 1.0 % glucose
24928sulfide-indole motility mediumyes
24928inositol-enriched mediumyes
42682PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yesName: 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 waterhttps://mediadive.dsmz.de/medium/104

culture temp

@refgrowthtypetemperaturerange
42682positivegrowth37mesophilic
63241positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
24928
63241anaerobe

murein

  • @ref: 24928
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2492827613amygdalin-fermentation
2492822599arabinose-fermentation
2492817057cellobiose-builds acid from
2492817057cellobiose-fermentation
2492817108D-arabinose-builds acid from
2492817634D-glucose-builds acid from
2492816899D-mannitol-builds acid from
2492816024D-mannose-builds acid from
2492865327D-xylose-builds acid from
2492817113erythritol-fermentation
249284853esculin-fermentation
249284853esculin-hydrolysis
2492828757fructose-fermentation
249285291gelatin-hydrolysis
2492817234glucose-fermentation
2492817754glycerol-builds acid from
2492828087glycogen-fermentation
2492818287L-fucose-builds acid from
2492817716lactose-builds acid from
2492817716lactose-fermentation
2492817306maltose-builds acid from
2492817306maltose-fermentation
2492829864mannitol-fermentation
2492837684mannose-fermentation
249286731melezitose-builds acid from
249286731melezitose-fermentation
2492828053melibiose-fermentation
2492817632nitrate-reduction
2492817309pectin-fermentation
2492816634raffinose-builds acid from
2492816634raffinose-fermentation
249288806resazurin-reduction
2492826546rhamnose-builds acid from
2492826546rhamnose-fermentation
2492833942ribose-fermentation
2492817814salicin-fermentation
2492817814salicin-builds acid from
2492830911sorbitol-builds acid from
2492830911sorbitol-fermentation
2492828017starch-hydrolysis
2492817992sucrose-fermentation
2492817992sucrose-builds acid from
2492827082trehalose-builds acid from
2492827082trehalose-fermentation
2492818222xylose-fermentation
2492817634D-glucose+builds acid from
2492817268myo-inositol+fermentation

metabolite production

@refChebi-IDmetaboliteproduction
2492816136hydrogen sulfideno
2492830089acetateyes
2492817968butyrateyes
2492835581indoleyes
2492824996lactateyes
2492830031succinateyes

enzymes

@refvalueactivityec
24928acid phosphatase+3.1.3.2
24928alkaline phosphatase+3.1.3.1
24928alpha-chymotrypsin-3.4.21.1
24928alpha-fucosidase-3.2.1.51
24928alpha-galactosidase-3.2.1.22
24928alpha-glucosidase-3.2.1.20
24928alpha-mannosidase-3.2.1.24
24928beta-galactosidase-3.2.1.23
24928beta-glucosidase-3.2.1.21
24928beta-glucuronidase3.2.1.31
24928cystine arylamidase-3.4.11.3
24928esterase (C 4)-
24928esterase lipase (C 8)-
24928leucine arylamidase+3.4.11.1
24928lipase (C 14)-
24928N-acetyl-beta-glucosaminidase-3.2.1.52
24928naphthol-AS-BI-phosphohydrolase-
24928trypsin-3.4.21.4
24928urease-3.5.1.5
24928valine arylamidase-
24928catalase-1.11.1.6
24928cytochrome oxidase-1.9.3.1
24928lecithinase-
24928lipase-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperaturesampling date
24928healthy human’s faeces (who had not undergone antibiotic therapy in the previous 6 months)JapanJPNAsiayeast extract-casein hydrolysate-fatty acids (YCFA) brothsupplemented with 0.5 % carbohydrate [one of mucin (from porcine stomach; Wako Pure Chemical Industries), inulin (from chicory), arabinogalactan, xylan, lignin, pectin, cellulose, galactose, amylopectin, L-fucose, N-acetyl-D-galactosamine or N-acetyl-D-glucosamine]8-16 h37
63241Human fecesJapanJPNAsia2010-07-08
42682human faecesJapanJPNAsia
67770Human feces

isolation source categories

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

Safety information

risk assessment

  • @ref: 42682
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42682
  • description: Butyricimonas faecihominis gene for 16S ribosomal RNA, partial sequence, strain: 180-3
  • accession: AB916501
  • length: 1486
  • database: ena
  • NCBI tax ID: 1472416

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Butyricimonas faecihominis DSM 105721GCA_014196975contigncbi1472416
66792Butyricimonas faecihominis JCM 18676GCA_014647335contigncbi1472416
66792Butyricimonas faecihominis strain CCUG 655621472416.60wgspatric1472416
66792Butyricimonas faecihominis strain DSM 1057211472416.74wgspatric1472416
66792Butyricimonas faecihominis strain JCM 186761472416.75wgspatric1472416
66792Butyricimonas faecihominis DSM 1057212830045573draftimg1472416
67770Butyricimonas faecihominis CCUG 65562GCA_008830385contigncbi1472416

GC content

@refGC-contentmethod
2492855.6
2492835
6777045.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.093no
gram-positiveno94.47yes
anaerobicyes99.089no
aerobicno96.587yes
halophileno87.934no
spore-formingno92.068no
thermophileno98.9no
glucose-utilyes87.647no
flagellatedno96.567yes
glucose-fermentno56.185yes

External links

@ref: 42682

culture collection no.: DSM 105721, CCUG 65562, JCM 18676

straininfo link

  • @ref: 91381
  • straininfo: 400609

literature

  • topic: Phylogeny
  • Pubmed-ID: 24903545
  • title: Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas.
  • authors: Sakamoto M, Tanaka Y, Benno Y, Ohkuma M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.065318-0
  • year: 2014
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Genes, Bacterial, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistry
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
24928T. W. Takada, Koichi,Makino, Hiroshi,Kushiro, AkiraReclassification of Eubacterium desmolans as Butyricicoccus desmolans comb. nov., and description of Butyricicoccus faecihominis sp. nov., a butyrate-producing bacterium from human faeces10.1099/ijsem.0.001323IJSEM 66: 4125-4131 201627453394
42682Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105721Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105721)
63241Curators of the CCUGhttps://www.ccug.se/strain?id=65562Culture Collection University of Gothenburg (CCUG) (CCUG 65562)
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/
91381Reimer, 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-ID400609.1