Strain identifier

BacDive ID: 18083

Type strain: Yes

Species: Pseudoflavonifractor capillosus

Strain history: <- CCUG <- ATCC <- EP Cato, VPI R2-29-1

NCBI tax ID(s): 411467 (strain), 106588 (species)

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General

@ref: 17449

BacDive-ID: 18083

DSM-Number: 23940

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, rod-shaped

description: Pseudoflavonifractor capillosus DSM 23940 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
411467strain
106588species

strain history

@refhistory
17449<- CCUG <- ATCC <- E. P. Cato, Virginia Polytechnical Institute and State University, Blacksburg, V., USA; VPI R2-29-1
67770CCUG 15402 A <-- ATCC 29799 <-- E. P. Cato VPI R2-29-1.
67771<- CCUG <- ATCC <- EP Cato, VPI R2-29-1

doi: 10.13145/bacdive18083.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Oscillospiraceae
  • genus: Pseudoflavonifractor
  • species: Pseudoflavonifractor capillosus
  • full scientific name: Pseudoflavonifractor capillosus (Tissier 1908) Carlier et al. 2010

  • synonyms

    @refsynonym
    20215Bacteroides capillosus
    20215Bacillus capillosus

@ref: 17449

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Pseudoflavonifractor

species: Pseudoflavonifractor capillosus

full scientific name: Pseudoflavonifractor capillosus (Tissier 1908) Carlier et al. 2010

type strain: yes

Morphology

cell morphology

@refcell shapegram stainmotilityconfidence
68367rod-shaped
68367negative
67771rod-shapedno
67771curved-shaped
67771negative
125439negative94.8

colony morphology

@reftype of hemolysisincubation period
17449gamma
462422 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17449COLUMBIA 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
17449FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

culture temp

@refgrowthtypetemperature
17449positivegrowth37
46242positivegrowth37
67770positivegrowth37
67771positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
17449anaerobe
46242anaerobe
67771anaerobe
125438anaerobe92.612
125439anaerobe99.8

spore formation

@refspore formationconfidence
68367no
67771no
125439no94.2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838017632nitrate-reduction
6838016199urea-hydrolysis
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

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6836735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

enzymes

@refvalueactivityec
17449catalase-1.11.1.6
17449cytochrome-c oxidase-1.9.3.1
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380glycin arylamidase-
68380tyrosine arylamidase-
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
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-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68367urease-3.5.1.5
68380histidine arylamidase-
68380alanine arylamidase-3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380beta-glucosidase+3.2.1.21
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase-

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRESPORGRAMCOCC
17449--+----++--+-+----++---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
17449---+-+/-+----------------------

Isolation, sampling and environmental information

isolation

@refsample type
17449human faeces
46242Human feces
67770Human feces
67771From human feces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3504.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_91;96_299;97_2188;98_2685;99_3504&stattab=map
  • Last taxonomy: Pseudoflavonifractor capillosus subclade
  • 16S sequence: AY136666
  • Sequence Identity:
  • Total samples: 14741
  • soil counts: 154
  • aquatic counts: 58
  • animal counts: 14487
  • plant counts: 42

Safety information

risk assessment

  • @ref: 17449
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17449
  • description: Bacteroides capillosus 16S ribosomal RNA gene, partial sequence
  • accession: AY136666
  • length: 1483
  • database: nuccore
  • NCBI tax ID: 411467

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoflavonifractor capillosus ATCC 29799411467.62wgspatric411467
66792Pseudoflavonifractor capillosus ATCC 29799640963014draftimg411467
67770Pseudoflavonifractor capillosus ATCC 29799GCA_000169255contigncbi411467

GC content

@refGC-contentmethod
1744960high performance liquid chromatography (HPLC)
6777160.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes59.508yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes92.612no
125438spore-formingspore-formingAbility to form endo- or exosporesno58.372no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no95.238yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.39yes
125438motile2+flagellatedAbility to perform flagellated movementno86.143yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno94.2
125439BacteriaNetmotilityAbility to perform movementno61.4
125439BacteriaNetgram_stainReaction to gram-stainingnegative94.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe99.8

External links

@ref: 17449

culture collection no.: DSM 23940, ATCC 29799, CCUG 15402 A, VPI R2-29-1, KCTC 15156, JCM 32126, CCUG 15402A

straininfo link

  • @ref: 87071
  • straininfo: 39725

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654357Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Seguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.Carlier JP, Bedora-Faure M, K'ouas G, Alauzet C, Mory FInt J Syst Evol Microbiol10.1099/ijs.0.016725-02009Bacterial Infections/*microbiology, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, Clostridium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Eubacterium/*classification/genetics/isolation & purification, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny29745868Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces.Sakamoto M, Iino T, Yuki M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijsem.0.0028002018Adult, Bacterial Typing Techniques, Base Composition, Butyrates/*metabolism, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Female, Humans, Japan, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17449Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23940)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23940
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
46242Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15402 A)https://www.ccug.se/strain?id=15402
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
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
87071Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID39725.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1