Strain identifier

BacDive ID: 11755

Type strain: Yes

Species: Aggregatibacter segnis

Strain Designation: HK316

Strain history: CIP <- 1989, NCTC <- 1975, M. Kilian, Arhus, Denmark: strain HK 316, Haemophilus segnis

NCBI tax ID(s): 888057 (strain), 739 (species)

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General

@ref: 15694

BacDive-ID: 11755

DSM-Number: 21418

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, rod-shaped

description: Aggregatibacter segnis HK316 is a microaerophile, mesophilic, rod-shaped bacterium that was isolated from dental plaque.

NCBI tax id

NCBI tax idMatching level
739species
888057strain

strain history

@refhistory
15694<- CCUG; HK316 {2008} <- NCTC <- M. Kilian
67771<- DSM <- CCUG, HK316(2008) <- NCTC <- M Kilian
122549CIP <- 1989, NCTC <- 1975, M. Kilian, Arhus, Denmark: strain HK 316, Haemophilus segnis

doi: 10.13145/bacdive11755.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pasteurellales
  • family: Pasteurellaceae
  • genus: Aggregatibacter
  • species: Aggregatibacter segnis
  • full scientific name: Aggregatibacter segnis (Kilian 1977) Nørskov-Lauritsen and Kilian 2006

  • synonyms

    • @ref: 20215
    • synonym: Haemophilus segnis

@ref: 15694

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pasteurellales

family: Pasteurellaceae

genus: Aggregatibacter

species: Aggregatibacter segnis

full scientific name: Aggregatibacter segnis (Kilian 1977) Nørskov-Lauritsen and Kilian 2006

strain designation: HK316

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stainconfidence
67771rod-shapedno
67771pleomorphic-shaped
67771negative
69480negative99.983

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15694HAEMOPHILUS MEDIUM (DSMZ Medium 804)yeshttps://mediadive.dsmz.de/medium/804Name: HAEMOPHILUS MEDIUM (DSMZ Medium 804) Composition: Mueller-Hinton broth 21.0 g/l Yeast extract 5.0 g/l Distilled water
40097MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and NeisseriayesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml);PolyVitex mischung (10.000 ml)
122549CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
15694positivegrowth37mesophilic
40097positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15694microaerophile
67771microaerophile

spore formation

@refspore formationconfidence
69481no100
69480no99.982

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837717634D-glucose+builds acid from
6837715824D-fructose+builds acid from
6837717306maltose+builds acid from
6837718257ornithine-degradation
6837716199urea-hydrolysis
6837727897tryptophan-energy source

metabolite production

  • @ref: 68377
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68377
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase-3.4.11.5
68377beta-galactosidase-3.2.1.23
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17

fatty acid profile

  • @reffatty acidpercentageECL
    65595C12:00.312
    65595C14:027.414
    65595C16:025.416
    65595C18:00.718
    65595C13:0 ISO 2OH0.513.814
    65595C14:0 3OH/C16:1 ISO I9.415.485
    65595C16:1 ω7c29.215.819
    65595C18:1 ω9c317.769
    65595C18:2 ω6,9c/C18:0 ANTE3.517.724
    65595unknown 14.5030.414.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    65597C12:00.312
    65597C14:026.814
    65597C16:026.316
    65597C18:00.918
    65597C12:0 ALDE ?0.710.915
    65597C13:0 ISO 2OH0.513.814
    65597C14:0 3OH/C16:1 ISO I7.715.485
    65597C16:1 ω5c0.215.908
    65597C16:1 ω7c2815.819
    65597C18:1 ω9c4.317.769
    65597C18:2 ω6,9c/C18:0 ANTE3.317.724
    65597Unidentified0.113.767
    65597Unidentified0.513.944
    65597Unidentified0.215.171
    65597unknown 14.5030.414.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
15694++++---+-----
15694-++++---+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
15694dental plaqueDenmarkDNKEurope
67771From dental plaqueDenmarkDNKEurope
122549Other, Dental plateDenmarkDNKEurope1973

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Plaque

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
156942Risk group (German classification)
1225492Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15694
  • description: Aggregatibacter segnis ATCC 33393 16S ribosomal RNA gene, partial sequence
  • accession: M75043
  • length: 1479
  • database: ena
  • NCBI tax ID: 888057

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aggregatibacter segnis ATCC 33393 NCTC 10977GCA_900476035completencbi888057
66792Aggregatibacter segnis ATCC 33393GCA_000185305scaffoldncbi888057
66792Aggregatibacter segnis ATCC 33393888057.3wgspatric888057
66792Aggregatibacter segnis ATCC 33393 strain NCTC10977 strain NCTC 10977888057.20completepatric888057
66792Aggregatibacter segnis strain FDAARGOS_987739.212completepatric739
66792Aggregatibacter segnis ATCC 33393649989906draftimg888057
66792Aggregatibacter segnis NCTC 109772811995232completeimg888057

GC content

  • @ref: 67771
  • GC-content: 43.0-44.0
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.104no
gram-positiveno98.276yes
anaerobicno95.178yes
aerobicno93.868no
halophileyes55.722no
spore-formingno98.839no
thermophileno98.341no
glucose-utilno58.416no
motileno89.409yes
glucose-fermentno51.005no

External links

@ref: 15694

culture collection no.: DSM 21418, ATCC 33393, CCUG 10787, CCUG 12838, CIP 103292, KCTC 5968, NCTC 10977, CCM 6052

straininfo link

  • @ref: 80973
  • straininfo: 47018

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957111Reclassification of Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, Haemophilus paraphrophilus and Haemophilus segnis as Aggregatibacter actinomycetemcomitans gen. nov., comb. nov., Aggregatibacter aphrophilus comb. nov. and Aggregatibacter segnis comb. nov., and emended description of Aggregatibacter aphrophilus to include V factor-dependent and V factor-independent isolates.Norskov-Lauritsen N, Kilian MInt J Syst Evol Microbiol10.1099/ijs.0.64207-02006Actinobacillus/*classification/enzymology/genetics, DNA, Bacterial/*analysis, Haemophilus/*classification/enzymology/genetics, Molecular Sequence Data, Nicotinamide Phosphoribosyltransferase, Pentosyltransferases/*genetics, RNA, Ribosomal, 16SEnzymology
Pathogenicity24640241The antibacterial activity of various saturated and unsaturated fatty acids against several oral pathogens.Choi JS, Park NH, Hwang SY, Sohn JH, Kwak I, Cho KK, Choi ISJ Environ Biol2013Aggregatibacter segnis/drug effects, Anti-Bacterial Agents/*pharmacology, Fatty Acids/*pharmacology, Fatty Acids, Unsaturated/*pharmacology, Porphyromonas gingivalis/drug effects

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
15694Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21418)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21418
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
40097Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15073
65595Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 10787)https://www.ccug.se/strain?id=10787
65597Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 12838)https://www.ccug.se/strain?id=12838
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)
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68377Automatically annotated from API NH
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80973Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47018.1StrainInfo: A central database for resolving microbial strain identifiers
122549Curators of the CIPCollection of Institut Pasteur (CIP 103292)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103292