Strain identifier

BacDive ID: 140290

Type strain: Yes

Species: Boudabousia liubingyangii

Strain Designation: VUL4_1

Strain history: <- X. Meng, Chinese Center for Disease Control and Prevention, Beijing, China; VUL4_1

NCBI tax ID(s): 1921764 (species)

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General

@ref: 42897

BacDive-ID: 140290

DSM-Number: 104050

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

description: Boudabousia liubingyangii VUL4_1 is a facultative anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from faeces from a wild vulture Gypaetus barbatus.

NCBI tax id

  • NCBI tax id: 1921764
  • Matching level: species

strain history

  • @ref: 42897
  • history: <- X. Meng, Chinese Center for Disease Control and Prevention, Beijing, China; VUL4_1

doi: 10.13145/bacdive140290.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Boudabousia
  • species: Boudabousia liubingyangii
  • full scientific name: Boudabousia liubingyangii (Meng et al. 2017) Yang et al. 2021

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces liubingyangii

@ref: 42897

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Boudabousia

species: Boudabousia liubingyangii

full scientific name: Boudabousia liubingyangii (Meng et al. 2017) Yang et al. 2021

strain designation: VUL4_1

type strain: yes

Morphology

cell morphology

  • @ref: 43236
  • gram stain: positive
  • cell length: 0.8-1.2 µm
  • cell width: 0.6-1.0 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43236
  • colony size: <1 mm
  • colony color: greyish white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: sheep-blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43236sheep-blood agaryes
42897PYG 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
42897BBL ACTINOMYCES BROTH (DSMZ Medium 1029)yeshttps://mediadive.dsmz.de/medium/1029Name: BBL ACTINOMYCES BROTH (DSMZ Medium 1029) Composition: Infusion Broth 1.425 g/l Potassium Phosphate 0.855 g/l Dextrose 0.285 g/l Yeast extract 0.285 g/l Pancreatic digest of casein 0.228 g/l L-Cysteine HCl 0.057 g/l Starch 0.057 g/l Ammonium Sulfate 0.057 g/l Magnesium sulfate 0.0114 g/l Calcium Chloride 0.00057 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43236positiveoptimum37mesophilic
42897positivegrowth37mesophilic

culture pH

  • @ref: 43236
  • ability: positive
  • type: optimum
  • pH: 6-7

Physiology and metabolism

oxygen tolerance

  • @ref: 43236
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 43236
  • type of spore: spore
  • spore formation: no

halophily

  • @ref: 43236
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4323617754glycerol+builds acid from
4323665327D-xylose+builds acid from
4323612936D-galactose+builds acid from
4323617634D-glucose+builds acid from
4323615824D-fructose+builds acid from
4323616024D-mannose+builds acid from
43236506227N-acetylglucosamine+builds acid from
4323617306maltose+builds acid from
4323617716lactose+builds acid from
43236potassium 5-dehydro-D-gluconate+/-builds acid from
4323617113erythritol-builds acid from
4323617108D-arabinose-builds acid from
4323630849L-arabinose-builds acid from
4323616988D-ribose-builds acid from
4323665328L-xylose-builds acid from
4323615963ribitol-builds acid from
43236methyl alpha-D-xylopyranoside-builds acid from
4323617266L-sorbose-builds acid from
4323662345L-rhamnose-builds acid from
4323616813galactitol-builds acid from
4323643943methyl alpha-D-mannoside-builds acid from
43236320061methyl alpha-D-glucopyranoside-builds acid from
4323617814salicin-builds acid from
4323617057cellobiose-builds acid from
4323628053melibiose-builds acid from
4323617992sucrose-builds acid from
4323627082trehalose-builds acid from
4323615443inulin-builds acid from
432366731melezitose-builds acid from
4323616634raffinose-builds acid from
4323628017starch-builds acid from
4323628087glycogen-builds acid from
4323617151xylitol-builds acid from
4323628066gentiobiose-builds acid from
4323632528turanose-builds acid from
4323662318D-lyxose-builds acid from
4323628847D-fucose-builds acid from
4323618287L-fucose-builds acid from
4323618403L-arabitol-builds acid from
4323618333D-arabitol-builds acid from
4323632032potassium gluconate-builds acid from
43236potassium 2-dehydro-D-gluconate-builds acid from
43236320055methyl beta-D-glucopyranoside-builds acid from
43236606565hippurate+hydrolysis
432365291gelatin-hydrolysis

metabolite production

  • @ref: 43236
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: no

enzymes

@refvalueactivityec
43236catalase-1.11.1.6
43236alkaline phosphatase+3.1.3.1
43236leucine arylamidase+3.4.11.1
43236trypsin+/-3.4.21.4
43236acid phosphatase+/-3.1.3.2
43236naphthol-AS-BI-phosphohydrolase+
43236beta-galactosidase+3.2.1.23
43236alpha-glucosidase+3.2.1.20
43236N-acetyl-beta-glucosaminidase+3.2.1.52
43236pyrazinamidase+3.5.1.B15
43236tripeptide aminopeptidase+3.4.11.4
43236glycyl tryptophan arylamidase+
43236lipase (C 14)-
43236valine arylamidase-
43236cystine arylamidase-3.4.11.3
43236alpha-galactosidase-3.2.1.22
43236beta-glucuronidase-3.2.1.31
43236alpha-mannosidase-3.2.1.24
43236alpha-fucosidase-3.2.1.51
43236pyrrolidonyl arylamidase-3.4.19.3
43236arginine dihydrolase-3.5.3.6
43236pyroglutamic acid arylamidase-
43236beta-mannosidase-3.2.1.25
43236urease-3.5.1.5
43236beta-glucosidase-3.2.1.21

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
42897faeces (rectal swab) from a wild vulture Gypaetus barbatusGypaetus barbatusTibetan autonomous region, Qinghai provinceChinaCHNAsia
43236faecal sample of a wild vultureThe Tibetan autonomous region, Qinghai province, ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Birds
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host Body-Site#Gastrointestinal tract#Rectum
#Infection#Patient#Swab

taxonmaps

  • @ref: 69479
  • File name: preview.99_7567.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_224;96_3229;97_3962;98_5545;99_7567&stattab=map
  • Last taxonomy: Boudabousia
  • 16S sequence: KY268292
  • Sequence Identity:
  • Total samples: 3238
  • soil counts: 17
  • aquatic counts: 18
  • animal counts: 3202
  • plant counts: 1

Safety information

risk assessment

  • @ref: 42897
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42897
  • description: Actinomyces liubingyangii strain VUL4_1 16S ribosomal RNA gene, partial sequence
  • accession: KY268292
  • length: 1455
  • database: ena
  • NCBI tax ID: 1921764

Genome sequences

  • @ref: 66792
  • description: Boudabousia liubingyangii VUL4_1
  • accession: GCA_001907245
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1921764

GC content

@refGC-contentmethod
4323654.9genome sequence analysis
4289754.9sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.256no
gram-positiveyes94.93no
anaerobicno75.822no
aerobicno96.757no
halophileno90.319yes
spore-formingno96.552yes
glucose-utilyes86.171no
thermophileno96.774yes
motileno93.848yes
glucose-fermentyes87.083no

External links

@ref: 42897

culture collection no.: DSM 104050, CGMCC 4.7370

straininfo link

  • @ref: 96596
  • straininfo: 405285

literature

  • topic: Phylogeny
  • Pubmed-ID: 28629506
  • title: Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus.
  • authors: Meng X, Lu S, Lai XH, Wang Y, Wen Y, Jin D, Yang J, Xu J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001884
  • year: 2017
  • mesh: Actinomyces/genetics/isolation & purification, Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Falconiformes/*microbiology, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rectum/*microbiology, Sequence Analysis, DNA, Spiro Compounds, Tibet
  • 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
42897Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104050Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104050)
43236Xiangli Meng, Shan Lu, Xin-He Lai, Yiting Wang, Yumeng Wen, Dong Jin, Jing Yang and Jianguo XuActinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus10.1099/ijsem.0.001884IJSEM 67: 1873-1879 201728629506
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/
96596Reimer, 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-ID405285.1