Strain identifier

BacDive ID: 24344

Type strain: Yes

Species: Hallella seregens

Strain history: CIP <- 2001, CCUG <- 1994, ATCC <- L.V. Moore: strain VPI D238B-15

NCBI tax ID(s): 1336250 (strain), 52229 (species)

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General

@ref: 21085

BacDive-ID: 24344

DSM-Number: 28061

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

description: Hallella seregens DSM 28061 is an anaerobe, mesophilic bacterium that was isolated from gingival crevice of periodontally healthy patient.

NCBI tax id

NCBI tax idMatching level
1336250strain
52229species

strain history

@refhistory
21085<- CCUG <- ATCC <- L. V. Moore; VPI D238B-15
122568CIP <- 2001, CCUG <- 1994, ATCC <- L.V. Moore: strain VPI D238B-15

doi: 10.13145/bacdive24344.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Hallella
  • species: Hallella seregens
  • full scientific name: Hallella seregens Moore and Moore 1994

@ref: 21085

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Hallella

species: Hallella seregens

full scientific name: Hallella seregens Moore and Moore 1994 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.422
6948099.994negative
122568nonegativerod-shaped

colony morphology

  • @ref: 21085
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21085COLUMBIA 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
36022MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
122568CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
21085positivegrowth37mesophilic
36022positivegrowth37mesophilic
51651positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
21085anaerobe
51651anaerobe
69480anaerobe99.723

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin-builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan-energy source
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleno
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole-
6836735581indole-

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
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68367beta-glucosidase-3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51651C12:00.412
    51651C14:06.714
    51651C15:01.715
    51651C16:013.916
    51651C18:02.918
    51651C13:0 2OH0.614.191
    51651C13:0 3OH/C15:1 i I/H0.414.469
    51651C13:1 at 12-130.512.931
    51651C14:0 3OH/C16:1 ISO I0.615.485
    51651C14:0 ISO12.713.618
    51651C15:0 ANTEISO3.614.711
    51651C16:0 3OH15.317.52
    51651C16:0 iso3.815.626
    51651C16:0 iso 3OH1.717.145
    51651C16:1 ω7c1.415.819
    51651C16:1 ω7c alcohol0.915.386
    51651C17:0 3OH0.518.535
    51651C17:1 ω5c ISO2.216.461
    51651C18:1 ω9c3.717.769
    51651C18:2 ω6,9c/C18:0 ANTE13.117.724
    51651Unidentified0.614.309
    51651Unidentified0.414.946
    51651Unidentified0.915.936
    51651Unidentified2.517.256
    51651Unidentified517.793
    51651Unidentified2.318.227
    51651Unidentified0.718.705
    51651Unidentified0.819.171
    51651Unidentified0.519.696
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
21085--+-+++-++----+-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
51651--++-+-+-+------+--+----+----
21085++++-++/-+-++---+-+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
21085gingival crevice of periodontally healthy patient
51651Gingival crevice of periodontally healthy patient
122568Gingival crevice of periodontally healthy patientUnited States of AmericaUSANorth America1994

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Oral cavity and airways#Gingiva

taxonmaps

  • @ref: 69479
  • File name: preview.99_223.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16035;96_159;97_170;98_190;99_223&stattab=map
  • Last taxonomy: Prevotella
  • 16S sequence: X81877
  • Sequence Identity:
  • Total samples: 18324
  • soil counts: 230
  • aquatic counts: 247
  • animal counts: 17748
  • plant counts: 99

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
210852Risk group (German classification)
1225681Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21085
  • description: H.seregens 16S rRNA gene
  • accession: X81877
  • length: 1463
  • database: ena
  • NCBI tax ID: 1336250

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hallella seregens ATCC 51272GCA_000518545scaffoldncbi1336250
66792Hallella seregens ATCC 512721336250.3wgspatric1336250
66792Hallella seregens ATCC 512722545555854draftimg1336250

GC content

  • @ref: 21085
  • GC-content: 56.0
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.365no
flagellatedno97.511no
gram-positiveno97.791no
anaerobicyes98.733yes
halophileno83.451no
spore-formingno97.022no
thermophileno97.981yes
glucose-utilyes86.178no
aerobicno98.51no
glucose-fermentyes65.942no

External links

@ref: 21085

culture collection no.: DSM 28061, ATCC 51272, CCUG 33639, CIP 107046, VPI D238B-15

straininfo link

  • @ref: 88270
  • straininfo: 42891

literature

  • topic: Phylogeny
  • Pubmed-ID: 8186083
  • title: Oribaculum catoniae gen. nov., sp. nov.; Catonella morbi gen. nov., sp. nov.; Hallella seregens gen. nov., sp. nov.; Johnsonella ignava gen. nov., sp. nov.; and Dialister pneumosintes gen. nov., comb. nov., nom. rev., Anaerobic gram-negative bacilli from the human gingival crevice.
  • authors: Moore LV, Moore WE
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-44-2-187
  • year: 1994
  • mesh: Bacterial Typing Techniques, Fatty Acids/analysis, Gingival Pocket/*microbiology, Gingivitis/*microbiology, Gram-Negative Anaerobic Bacteria/*classification/isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Periodontitis/*microbiology
  • topic2: Pathogenicity

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
21085Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28061Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28061)
36022Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19243
51651Curators of the CCUGhttps://www.ccug.se/strain?id=33639Culture Collection University of Gothenburg (CCUG) (CCUG 33639)
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
68367Automatically annotated from API 20A
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/
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
88270Reimer, 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-ID42891.1
122568Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107046Collection of Institut Pasteur (CIP 107046)