Strain identifier

BacDive ID: 132591

Type strain: Yes

Species: Varibaculum anthropi

Strain history: E. Moore.

NCBI tax ID(s): 1177728 (species)

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General

@ref: 24380

BacDive-ID: 132591

DSM-Number: 27023

keywords: 16S sequence, Bacteria, anaerobe, mesophilic

description: Varibaculum anthropi DSM 27023 is an anaerobe, mesophilic bacterium that was isolated from human urine.

NCBI tax id

  • NCBI tax id: 1177728
  • Matching level: species

strain history

@refhistory
24380<- E. Moore, CCUG; CCUG 31793 <- E. Falsen <- Sahlgrenska Univ. Hospital, Bacteriol. Lab
67770E. Moore.

doi: 10.13145/bacdive132591.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Varibaculum
  • species: Varibaculum anthropi
  • full scientific name: Varibaculum anthropi Glaeser et al. 2017

@ref: 24380

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Varibaculum

species: Varibaculum anthropi

full scientific name: Varibaculum anthropi Glaeser et al. 2017

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 24380
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
50730positivegrowth37mesophilic
24380positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50730anaerobe
50730microaerophile

metabolite utilization

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

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
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
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-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease+3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
24380+--+-+-----+------+-+/-+/--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
24380human urineGothenburgSwedenSWEEurope
50730Human urine,8-month-old or 101-yr-old ?SwedenSWEEurope1993-08-09
67770Human urineGöteborgSwedenSWEEurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_6694.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_520;96_2630;97_3222;98_4937;99_6694&stattab=map
  • Last taxonomy: Varibaculum massiliense
  • 16S sequence: JQ780830
  • Sequence Identity:
  • Total samples: 7247
  • soil counts: 58
  • aquatic counts: 103
  • animal counts: 7075
  • plant counts: 11

Sequence information

16S sequences

  • @ref: 24380
  • description: Varibaculum anthropi strain CCUG 31793 16S ribosomal RNA gene, partial sequence
  • accession: JQ780830
  • length: 1329
  • database: ena
  • NCBI tax ID: 1177728

GC content

@refGC-contentmethod
2438052.8sequence analysis
6777052.8genome sequence analysis

External links

@ref: 24380

culture collection no.: DSM 27023, CCUG 31793, JCM 19104

straininfo link

  • @ref: 90908
  • straininfo: 51419

literature

  • topic: Phylogeny
  • Pubmed-ID: 27745752
  • title: Varibaculum anthropi sp. nov. represented by three genetically different genomovars isolated from clinical material and emended description of the genus Varibaculum.
  • authors: Glaeser SP, Doijad S, Hijazin M, Chakraborty T, Falsen E, Hall V, Kampfer P
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2016.09.002
  • year: 2016
  • mesh: Actinomycetaceae/*classification/*genetics/isolation & purification, Adolescent, Adult, Base Sequence, DNA, Bacterial/*genetics, Female, Genome, Bacterial/*genetics, Humans, Male, Middle Aged, Multilocus Sequence Typing, Nucleic Acid Hybridization, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
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
24380Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27023Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27023)
50730Curators of the CCUGhttps://www.ccug.se/strain?id=31793Culture Collection University of Gothenburg (CCUG) (CCUG 31793)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90908Reimer, 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-ID51419.1