Strain identifier

BacDive ID: 139755

Type strain: Yes

Species: Catenibacillus scindens

Strain Designation: CG19-1

Strain history: DSM 106146 <-- A. Braune; Dept. of Gastrointestinal Microbiol., German Inst. of Human Nutrition, Germany; CG19-1.

NCBI tax ID(s): 673271 (species)

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General

@ref: 42366

BacDive-ID: 139755

DSM-Number: 106146

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

description: Catenibacillus scindens CG19-1 is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from healthy human feces.

NCBI tax id

  • NCBI tax id: 673271
  • Matching level: species

strain history

@refhistory
42366<- A. Braune, Dept. Gastrointestinal Microbiology, German Inst. of Human Nutrition (DIFE), Nuthetal, Germany; CG19-1 <- A. Braune {2008}
67770DSM 106146 <-- A. Braune; Dept. of Gastrointestinal Microbiol., German Inst. of Human Nutrition, Germany; CG19-1.

doi: 10.13145/bacdive139755.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Catenibacillus
  • species: Catenibacillus scindens
  • full scientific name: Catenibacillus scindens Braune and Blaut 2018

@ref: 42366

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Catenibacillus

species: Catenibacillus scindens

full scientific name: Catenibacillus scindens Braune and Blaut 2018

strain designation: CG19-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66717positive1.0-2.0 µm0.6-1.0 µmrod-shapedno
69480no92.488
69480positive100

colony morphology

  • @ref: 66717
  • type of hemolysis: gamma
  • colony size: 0.5 mm
  • colony color: matte greyish
  • colony shape: circular
  • incubation period: 4 days
  • medium used: sheep-blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
42366RCM MEDIUM (N2/CO2) (DSMZ Medium 634c)yeshttps://mediadive.dsmz.de/medium/634cName: RCM MEDIUM (N2/CO2) (DSMZ Medium 634c) Composition: dehydrated RCM medium 38.0 g/l Sodium carbonate 1.0 g/l Sodium resazurin 0.0005 g/l Distilled water
66717reinforced clostridial medium (RCM mod)yescontained (g/l): yeast extract (3.0), meat extract (10), peptone (10), glucose (5.0), soluble starch (1.0), NaCl (5.0), sodium acetate (5.0) and cysteine hydrochloride (0.5)
66717sheep-blood agaryesat 37° C
66717starch-free RCM mod.yessupplemented with 40 mM pyruvate
66717starch-free RCMmod.yes

culture temp

@refgrowthtypetemperaturerange
42366positivegrowth37mesophilic
66717positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
66717anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
66717no
69480no99.982

murein

  • @ref: 66717
  • murein short key: A21.04
  • type: A4ß L-Orn-D-Asp

observation

@refobservation
66717Capsules, slime or polyphosphate granules are not produced.
66717Doubling time at optimal growth is 2.7 h.
66717using a gas phase of N 2 /CO 2 (80 : 20, v/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
667174853esculin-builds acid from
667176731melezitose-builds acid from
667178391D-gluconate-builds acid from
6671712936D-galactose-builds acid from
6671715443inulin-builds acid from
6671715824D-fructose-builds acid from
6671715963ribitol-builds acid from
6671716024D-mannose-builds acid from
6671716443D-tagatose-builds acid from
6671716634raffinose-builds acid from
66717168082-dehydro-D-gluconate-builds acid from
6671716813galactitol-builds acid from
6671716899D-mannitol-builds acid from
6671716988D-ribose-builds acid from
6671717057cellobiose-builds acid from
6671717113erythritol-builds acid from
6671717151xylitol-builds acid from
6671717266L-sorbose-builds acid from
6671717268myo-inositol-builds acid from
6671717306maltose-builds acid from
6671717634D-glucose-builds acid from
6671717716lactose-builds acid from
6671717754glycerol-builds acid from
6671717814salicin-builds acid from
6671717924D-sorbitol-builds acid from
6671717992sucrose-builds acid from
6671718222xylose-builds acid from
6671718305arbutin-builds acid from
6671722599arabinose-builds acid from
6671722605arabinitol-builds acid from
6671727082trehalose-builds acid from
6671727613amygdalin-builds acid from
6671728017starch-builds acid from
6671728053melibiose-builds acid from
6671728066gentiobiose-builds acid from
6671728087glycogen-builds acid from
6671732528turanose-builds acid from
6671733984fucose-builds acid from
6671743943methyl alpha-D-mannoside-builds acid from
66717581435-dehydro-D-gluconate-builds acid from
6671759640N-acetylglucosamine-builds acid from
6671762318D-lyxose-builds acid from
6671762345L-rhamnose-builds acid from
6671774863methyl beta-D-xylopyranoside-builds acid from
66717320061methyl alpha-D-glucopyranoside-builds acid from
6671717968butyrate+fermentation
6671716632vanillate-growth
6671729749ferulate-growth
66717132111syringate-growth
6671717234glucose+growth
6671750144sodium pyruvate+growth
667175291gelatin-hydrolysis
6671715354choline-hydrolysis
66717174404-nitrophenyl phosphate-hydrolysis
6671717968butyrate-hydrolysis
6671725646octanoate-hydrolysis
6671737572alpha-L-arabinofuranoside-hydrolysis
6671761631N-acetyl-beta-D-glucosaminide-hydrolysis
66717901284-nitrophenyl 6-O-phosphono-beta-D-galactoside-hydrolysis
66717901464-nitrophenyl beta-D-glucuronide-hydrolysis
66717901484-nitrophenyl beta-D-xylopyranoside-hydrolysis
66717902492-naphthyl tetradecanoate-hydrolysis
66717902534-nitrophenyl alpha-L-fucoside-hydrolysis
66717902554-nitrophenyl beta-L-fucoside-hydrolysis
66717902594-nitrophenyl beta-D-glucopyranoside-hydrolysis
66717902604-nitrophenyl beta-lactoside-hydrolysis
66717903434-Nitrophenyl N-acetyl-beta-D-glucosaminide-hydrolysis
6671790347glycine 2-naphthylamide-hydrolysis
6671790350L-arginine-2-naphthylamide-hydrolysis
6671790426L-cysteine 2-naphthylamide-hydrolysis
6671790447L-histidine 2-naphthylamide-hydrolysis
6671790476L-leucine 2-naphthylamide-hydrolysis
6671790478L-lysine 2-naphthylamide-hydrolysis
6671790599L-phenylalanine 2-naphthylamide-hydrolysis
6671790600L-proline 2-naphthylamide-hydrolysis
6671790601L-pyroglutamic acid 2-naphthylamide-hydrolysis
6671790603L-serine 2-naphthylamide-hydrolysis
6671790607L-tyrosine 2-naphthylamide-hydrolysis
6671790608L-valine 2-naphthylamide-hydrolysis
6671790611L-alanyl-L-alanine 2-naphthylamide-hydrolysis
6671790727L-glutamyl-L-glutamic acid 2-naphthylamide-hydrolysis
6671790730N-glutaryl-L-phenylalanine 2-naphthylamide-hydrolysis
6671790741L-leucylglycine 2-naphthylamide-hydrolysis
6671791062N-benzoyl-DL-arginine 2-naphthylamide-hydrolysis
66717911224-nitrophenyl alpha-D-glucopyranoside-hydrolysis
667173557154-nitrophenyl beta-D-galactopyranoside-hydrolysis
667175468404-nitrophenyl alpha-D-galactoside-hydrolysis
66717gamma-L-glutamate-4-nitroanilide-hydrolysis
66717L-alanine 4-nitroanilide-hydrolysis
66717L-proline-4-nitroanilide-hydrolysis
6671716632vanillate-reduction
6671717632nitrate-reduction
66717199503-O-methylgallate-reduction
6671778019triphenyltetrazolium chloride-reduction
66717132111syringate-reduction
6671729749ferulate+reduction

enzymes

@refvalueactivityec
66717acid phosphatase-3.1.3.2
66717alanine aminopeptidase-
66717alkaline phosphatase-3.1.3.1
66717arginine dihydrolase-3.5.3.6
66717beta-mannosidase-3.2.1.25
66717carbohydrates-1.14.14.9
66717catalase-1.11.1.6
66717cytochrome oxidase-1.9.3.1
66717glutamate decarboxylase-4.1.1.15
66717L-arginine arylamidase-
66717leucine arylamidase-3.4.11.1
66717tryptophanase-4.1.99.1
66717urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66717C18:0 DMA5
    66717C18:1 w9c21
    66717C16:026.3
    66717C16:0 DMA6.1
    66717C18:0 12OH7.8
    66717C18:1 w9c DMA8.8
  • type of FA analysis: whole cell analysis
  • incubation medium: peptone – yeast extract –glucose medium
  • incubation temperature: 37
  • incubation time: 1
  • incubation_oxygen: anaerobic
  • system: MIS MIDI
  • method/protocol: Kämpfer & Kroppenstedt 1996

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
42366healthy human fecesBergholz-RehbrückeGermanyDEUEurope
66717from faeces of a healthy humanNuthetalGermanyDEUEuropereinforced clostridial medium (RCM mod )contained (g/L): yeast extract (3.0), meat extract (10), peptone (10), glucose (5.0), soluble starch (1.0), NaCl (5.0), sodium acetate (5.0) and cysteine hydrochloride (0.5)24-48 h37
67770Feces of a healthy humanNuthetalGermanyDEUEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_97041.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_39619;97_50491;98_66509;99_97041&stattab=map
  • Last taxonomy: Catenibacillus scindens subclade
  • 16S sequence: FJ711049
  • Sequence Identity:
  • Total samples: 1857
  • soil counts: 5
  • aquatic counts: 92
  • animal counts: 1760

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
42366Intestinal bacterium CG19-1 16S ribosomal RNA gene, partial sequenceFJ7110491454ena673271
66717Intestinal bacterium CG19-1 16S ribosomal RNA gene, partial sequenceFJ711049.11454ena673271

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Catenibacillus scindens DSM 106146GCA_014202115scaffoldncbi673271
66792Catenibacillus scindens strain DSM 106146673271.3wgspatric673271
66792Catenibacillus scindens DSM 1061462861335840draftimg673271

GC content

@refGC-contentmethod
4236647.1
6777047.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno79no
flagellatedno92.278yes
gram-positiveyes86.915no
anaerobicyes99.631no
aerobicno98.712yes
halophileno82.228no
spore-formingno62.238yes
glucose-utilyes90.535yes
motileno91.482yes
glucose-fermentyes64.64no
thermophileno96.062yes

External links

@ref: 42366

culture collection no.: DSM 106146, CCUG 71490, JCM 33534

straininfo link

  • @ref: 96201
  • straininfo: 406272

literature

  • topic: Phylogeny
  • Pubmed-ID: 30179152
  • title: Catenibacillus scindens gen. nov., sp. nov., a C-deglycosylating human intestinal representative of the Lachnospiraceae.
  • authors: Braune A, Blaut M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003001
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Germany, Humans, Intestines/*microbiology, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

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
42366Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106146Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106146)
66717Annett Braune, Michael BlautCatenibacillus scindens gen. nov., sp. nov., a C-deglycosylating human intestinal representative of the Lachnospiraceae10.1099/ijsem.0.003001IJSEM 68: 3356-3361 201830179152
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
96201Reimer, 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-ID406272.1