Strain identifier

BacDive ID: 140312

Type strain: Yes

Species: Galliscardovia ingluviei

Strain Designation: RP51

Strain history: <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; RP51 <- R. Pechar

NCBI tax ID(s): 1769422 (species)

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General

@ref: 42919

BacDive-ID: 140312

DSM-Number: 100235

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

description: Galliscardovia ingluviei RP51 is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from crop of a 13-month-old Hisex Brown hybrid laying hen Gallus gallus f. domestica.

NCBI tax id

  • NCBI tax id: 1769422
  • Matching level: species

strain history

  • @ref: 42919
  • history: <- J. Killer, Inst. Animal Physiol. and Genetics, Czech Acad. Sci., Prague; RP51 <- R. Pechar

doi: 10.13145/bacdive140312.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Galliscardovia
  • species: Galliscardovia ingluviei
  • full scientific name: Galliscardovia ingluviei Pechar et al. 2017

@ref: 42919

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Galliscardovia

species: Galliscardovia ingluviei

full scientific name: Galliscardovia ingluviei Pechar et al. 2017

strain designation: RP51

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43287positive1.3-2.1 µm0.4-0.6 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 43287
  • colony size: 1.1-2.6 mm
  • colony color: creamy yellowish
  • colony shape: circular
  • incubation period: 3 days
  • medium used: TPY agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43287TPY agaryes
42919BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

culture temp

@refgrowthtypetemperaturerange
43287positiveoptimum39mesophilic
43287positivegrowth15-49
42919positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
43287positivegrowth4.0-8.5alkaliphile
43287positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43287anaerobe
43287microaerophile
69480anaerobe97.54

spore formation

@reftype of sporespore formationconfidence
43287sporeno
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
432875291gelatin-hydrolysis
4328717634D-glucose+fermentation
4328715824D-fructose+fermentation
4328730849L-arabinose+fermentation
4328716988D-ribose+fermentation
4328765327D-xylose+fermentation
4328732528turanose+fermentation
4328727613amygdalin+fermentation
4328717814salicin+fermentation
4328717057cellobiose+fermentation
4328727082trehalose+fermentation
432876731melezitose+fermentation
4328728087glycogen+fermentation
432874853esculin+fermentation
4328728053melibiose+fermentation
4328728066gentiobiose+fermentation
4328717306maltose+fermentation
4328717992sucrose+fermentation
4328728017starch+fermentation
4328716634raffinose+fermentation
4328717754glycerol-builds acid from
4328717113erythritol-builds acid from
4328717108D-arabinose-builds acid from
4328765328L-xylose-builds acid from
4328715963ribitol-builds acid from
4328774863methyl beta-D-xylopyranoside-builds acid from
4328716024D-mannose-builds acid from
4328717266L-sorbose-builds acid from
4328762345L-rhamnose-builds acid from
4328716813galactitol-builds acid from
4328717268myo-inositol-builds acid from
4328716899D-mannitol-builds acid from
4328717924D-sorbitol-builds acid from
4328743943methyl alpha-D-mannoside-builds acid from
43287320061methyl alpha-D-glucopyranoside-builds acid from
4328718305arbutin-builds acid from
43287506227N-acetylglucosamine-builds acid from
4328715443inulin-builds acid from
4328717151xylitol-builds acid from
4328762318D-lyxose-builds acid from
4328716443D-tagatose-builds acid from
4328728847D-fucose-builds acid from
4328718287L-fucose-builds acid from
4328718333D-arabitol-builds acid from
4328718403L-arabitol-builds acid from
4328732032potassium gluconate-builds acid from
43287potassium 5-dehydro-D-gluconate-builds acid from
43287potassium 2-dehydro-D-gluconate-builds acid from
4328717632nitrate-reduction
43287D-galactose-fermentation
4328717716lactose-fermentation
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

metabolite production

  • @ref: 43287
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43287fructose-6-phosphate phosphoketolase+4.1.2.22
43287catalase-1.11.1.6
43287cytochrome oxidase-1.9.3.1
43287alpha-glucosidase+3.2.1.20
43287beta-glucosidase+3.2.1.21
43287alpha-galactosidase+3.2.1.22
43287beta-galactosidase+3.2.1.23
43287L-arginine arylamidase+
43287leucine arylamidase+3.4.11.1
43287serine arylamidase+
43287tyrosine arylamidase+
43287proline-arylamidase-3.4.11.5
43287urease-3.5.1.5
43287arginine dihydrolase-3.5.3.6
432876-phospho-beta-galactosidase-3.2.1.85
43287beta-glucuronidase-3.2.1.31
43287N-acetyl-beta-glucosaminidase-3.2.1.52
43287glutamate decarboxylase-4.1.1.15
43287alpha-mannosidase-3.2.1.24
43287alkaline phosphatase-3.1.3.1
43287leucyl glycin arylamidase-3.4.11.1
43287pyroglutamic acid arylamidase-
43287glutamyl-glutamate arylamidase-
43287valine arylamidase-
43287cystine arylamidase-3.4.11.3
43287esterase Lipase (C 8)-
43287lipase (C 14)-
43287alpha-chymotrypsin-3.4.21.1
43287trypsin-3.4.21.4
43287alpha-arabinosidase+3.2.1.55
43287leucyl glycin arylamidase+/-3.4.11.1
43287phenylalanine arylamidase+
43287phenylalanine arylamidase-
43287glycin arylamidase+/-
43287esterase (C 4)+
43287acid phosphatase-3.1.3.2

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
42919----+++----+---------+-++++++-+++-++++-++---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
42919crop of a 13-month-old Hisex Brown hybrid laying hen Gallus gallus f. domesticaGallus gallus f. domesticaCentral Bohemia, PragueCzech RepublicCZEEurope
43287sample from crop of a 13-month-old Hisex Brown hybrid laying hen

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_122159.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_47998;97_61721;98_82184;99_122159&stattab=map
  • Last taxonomy: Galliscardovia ingluviei subclade
  • 16S sequence: KT343146
  • Sequence Identity:
  • Total samples: 13331
  • soil counts: 140
  • aquatic counts: 340
  • animal counts: 12791
  • plant counts: 60

Safety information

risk assessment

  • @ref: 42919
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4328716S rRNA - 23S rRNA intergenic spacer regionKT343138391ena1769422
42919Galliscardovia ingluviei strain RP51 16S ribosomal RNA gene, partial sequenceKT3431461444ena1769422

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Galliscardovia ingluviei CCM 8606GCA_014635685contigncbi1769422
66792Galliscardovia ingluviei strain CCM 86061769422.3wgspatric1769422

GC content

@refGC-contentmethod
4328744.3
4291944.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.767yes
gram-positiveyes91.477yes
anaerobicyes94.004no
halophileno60.707no
spore-formingno95.153no
glucose-utilyes82.08no
flagellatedno95.437yes
thermophileno97.597no
aerobicno97.152no
glucose-fermentyes85.116yes

External links

@ref: 42919

culture collection no.: DSM 100235, CCM 8606, LMG 28778

straininfo link

  • @ref: 96617
  • straininfo: 400241

literature

  • topic: Phylogeny
  • Pubmed-ID: 28742007
  • title: Galliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica).
  • authors: Pechar R, Killer J, Svejstil R, Salmonova H, Geigerova M, Bunesova V, Rada V, Benada O
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001972
  • year: 2017
  • mesh: Actinobacteria/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Chickens/*microbiology, Crop, Avian/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Genes, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

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
42919Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100235Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100235)
43287R. Pechar, J. Killer, R. vejstil, H. Salmonová, M. Geigerová, V. Buneová, V. Rada and O. BenadaGalliscardovia ingluviei gen. nov., sp. nov., a thermophilic bacterium of the family Bifidobacteriaceae isolated from the crop of a laying hen (Gallus gallus f. domestica)10.1099/ijsem.0.001972IJSEM 67: 2403-2411 201728742007
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
68371Automatically annotated from API 50CH acid
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96617Reimer, 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-ID400241.1