Strain identifier

BacDive ID: 10433

Type strain: Yes

Species: Alysiella crassa

Strain Designation: S6

Strain history: CIP <- 1989, NCTC <- 1962, P.D.M. Steed, Brisbane, UK: strain S6

NCBI tax ID(s): 1120980 (strain), 153491 (species)

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General

@ref: 1128

BacDive-ID: 10433

DSM-Number: 2578

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Alysiella crassa S6 is a Gram-negative bacterium that was isolated from sheep saliva.

NCBI tax id

NCBI tax idMatching level
1120980strain
153491species

strain history

@refhistory
1128<- ATCC <- NCTC <- P. Steed, S6
67770IAM 14969 <-- ATCC 15533 <-- NCTC 10283 <-- P. Steed S6.
118776CIP <- 1989, NCTC <- 1962, P.D.M. Steed, Brisbane, UK: strain S6

doi: 10.13145/bacdive10433.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Neisseriaceae
  • genus: Alysiella
  • species: Alysiella crassa
  • full scientific name: Alysiella crassa (Schmid 1922) Xie and Yokota 2005

  • synonyms

    • @ref: 20215
    • synonym: Simonsiella crassa

@ref: 1128

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Neisseriaceae

genus: Alysiella

species: Alysiella crassa

full scientific name: Alysiella crassa (Schmid 1922) Xie and Yokota 2005

strain designation: S6

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 97.554

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_2578_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2578_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2578_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2578_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_2578_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1128TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
1128COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
1128NUTRIENT BROTH WITH 10% HORSE SERUM (DSMZ Medium 302)yeshttps://mediadive.dsmz.de/medium/302Name: NUTRIENT BROTH WITH 10% HORSE SERUM (DSMZ Medium 302) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Horse serum Distilled water
38126MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
118776CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
1128positivegrowth37
38126positivegrowth37
67770positivegrowth37

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 91.848

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837717634D-glucose+builds acid from
6837715824D-fructose-builds acid from
6837717306maltose-builds acid from
6837717992sucrose-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
68377alkaline phosphatase-3.1.3.1
68377lipase+
68377urease-3.5.1.5
68377ornithine decarboxylase+4.1.1.17
68377beta-lactamase-3.5.2.6
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    48297C12:04.212
    48297C14:022.314
    48297C16:012.416
    48297C18:01.218
    48297C12:0 3OH2.313.455
    48297C13:0 ISO 2OH1.713.814
    48297C14:0 3OH/C16:1 ISO I1.215.485
    48297C16:1 ω7c21.315.819
    48297C18:1 ω7c /12t/9t30.717.824
    48297C18:1 ω9c0.917.769
    48297C18:2 ω6,9c/C18:0 ANTE1.917.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
48297--++-+----+---------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
48297-+---+-+-----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
1128sheep salivaAustraliaAUSAustralia and Oceania
48297Sheep saliva
67770Sheep saliva
118776Animal, Sheep, salivaAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body Product#Oral cavity and Airways#Saliva

taxonmaps

  • @ref: 69479
  • File name: preview.99_888.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_528;97_609;98_700;99_888&stattab=map
  • Last taxonomy: Alysiella crassa
  • 16S sequence: AB087264
  • Sequence Identity:
  • Total samples: 1965
  • soil counts: 9
  • aquatic counts: 294
  • animal counts: 1638
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
11281Risk group (German classification)
1187761Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Alysiella crassa gene for 16S rRNA, strain: IAM 14969AB0872641492nuccore153491
20218Alysiella crassa gene for 16S rRNA, partial sequence, strain: NBRC 102455AB6817971462nuccore153491

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alysiella crassa DSM 25781120980.3wgspatric1120980
66792Alysiella crassa strain NCTC10283153491.3wgspatric153491
66792Alysiella crassa NCTC 102832808606660draftimg153491
66792Alysiella crassa DSM 25782571042010draftimg1120980
67770Alysiella crassa DSM 2578GCA_000745955scaffoldncbi1120980
67770Alysiella crassa NCTC10283GCA_900445245contigncbi153491
66792Alysiella crassa S6GCA_022871045completencbi153491

GC content

  • @ref: 1128
  • GC-content: 43.9

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno97.554no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.602no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no51.881no
69480spore-formingspore-formingAbility to form endo- or exosporesno91.848no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.962yes
69480flagellatedmotile2+Ability to perform flagellated movementno81.928no

External links

@ref: 1128

culture collection no.: DSM 2578, ATCC 15533, NCTC 10283, CCUG 25927, JCM 21440, CIP 103341, IAM 14969, LMG 7829, NBRC 102455, CIP 108879

straininfo link

  • @ref: 79714
  • straininfo: 4972

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny697509Isolation, characterization, and numerical taxonomy of Simonsiella strains from the oral cavities of cats, dogs, sheep, and humans.Kuhn DA, Gregory DA, Buchanan GE Jr, Nyby MD, Daly KRArch Microbiol10.1007/BF004291111978Animals, Bacteroidetes/classification/*isolation & purification/physiology, Cats/*microbiology, Computers, Dogs/*microbiology, Humans, Mouth/*microbiology, Sheep/*microbiologyPathogenicity
Phylogeny34797758Paralysiella testudinis gen. nov., sp. nov., isolated from the cloaca of a toad-headed turtle (Mesoclemmys nasuta).Busse HJ, Kampfer P, Szostak MP, Ruckert C, Spergser JInt J Syst Evol Microbiol10.1099/ijsem.0.0051142021Animals, Bacterial Typing Techniques, Base Composition, Cloaca/microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Neisseriaceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Turtles/microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1128Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2578)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2578
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
38126Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15128
48297Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 25927)https://www.ccug.se/strain?id=25927
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/
68377Automatically annotated from API NH
68382Automatically annotated from API zym
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
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)
79714Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4972.1StrainInfo: A central database for resolving microbial strain identifiers
118776Curators of the CIPCollection of Institut Pasteur (CIP 103341)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103341