Strain identifier

BacDive ID: 1591

Type strain: Yes

Species: Bacteroides helcogenes

Strain Designation: P 36-108

Strain history: Y. Benno P36-108.

NCBI tax ID(s): 693979 (strain), 290053 (species)

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General

@ref: 8961

BacDive-ID: 1591

DSM-Number: 20613

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, animal pathogen

description: Bacteroides helcogenes P 36-108 is an anaerobe, mesophilic animal pathogen that was isolated from pig abscess.

NCBI tax id

NCBI tax idMatching level
693979strain
290053species

strain history

@refhistory
8961<- Y. Benno, P 36-108
67770Y. Benno P36-108.

doi: 10.13145/bacdive1591.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides helcogenes
  • full scientific name: Bacteroides helcogenes Benno et al. 1983

@ref: 8961

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides helcogenes

full scientific name: Bacteroides helcogenes Benno et al. 1983 emend. Hahnke et al. 2016

strain designation: P 36-108

type strain: yes

Morphology

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20613_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8961COLUMBIA 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
8961CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
8961PYG 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

culture temp

@refgrowthtypetemperaturerange
8961positivegrowth37mesophilic
46251positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8961anaerobe
46251anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+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
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
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+3.2.1.23
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8961---++/-++--++--+--+--+----+--+-
8961--+++++--+++-+--+--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample type
8961pig abscess
46251Pig abscess
67770Pig abscess

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_3198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_1664;97_1992;98_2451;99_3198&stattab=map
  • Last taxonomy: Bacteroides helcogenes subclade
  • 16S sequence: AB510702
  • Sequence Identity:
  • Total samples: 16335
  • soil counts: 150
  • aquatic counts: 105
  • animal counts: 16050
  • plant counts: 30

Safety information

risk assessment

  • @ref: 8961
  • pathogenicity animal: yes
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides helcogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 6297AB5107021486ena290053
8961Bacteroides helcogenes gene for 16S rRNA, partial sequence, strain: JCM 6927AB2002271405ena290053
8961Bacteroides helcogenes strain JCM6297 16S ribosomal RNA gene, partial sequenceEU1366922115ena693979

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides helcogenes P 36-108GCA_000186225completencbi693979
66792Bacteroides helcogenes P 36-108693979.3completepatric693979
66792Bacteroides helcogenes P 36-108, DSM 20613649633012completeimg693979

GC content

@refGC-contentmethod
896145.7
896144.7sequence analysis
6777045high performance liquid chromatography (HPLC)
6777045.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.371no
flagellatedno97.045no
gram-positiveno97.842no
anaerobicyes99.048yes
aerobicno98.094yes
halophileno90.071no
spore-formingno94.275no
glucose-utilyes87.594no
thermophileno97.939yes
glucose-fermentyes73.702no

External links

@ref: 8961

culture collection no.: DSM 20613, ATCC 35417, CCUG 15421, JCM 6297

straininfo link

  • @ref: 71236
  • straininfo: 41065

literature

  • topic: Genetics
  • Pubmed-ID: 21475586
  • title: Complete genome sequence of Bacteroides helcogenes type strain (P 36-108).
  • authors: Pati A, Gronow S, Zeytun A, Lapidus A, Nolan M, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brambilla E, Rohde M, Goker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas S
  • journal: Stand Genomic Sci
  • DOI: 10.4056/sigs.1513795
  • year: 2011

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8961Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20613)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20613
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
46251Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15421)https://www.ccug.se/strain?id=15421
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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/
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
71236Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41065.1StrainInfo: A central database for resolving microbial strain identifiers