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, mesophilic

description: Alysiella crassa S6 is a mesophilic bacterium that was isolated from sheep saliva.

NCBI tax id

NCBI tax idMatching level
153491species
1120980strain

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/bacdive10433.20230509.8.1

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

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

@refgrowthtypetemperaturerange
1128positivegrowth37mesophilic
38126positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

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 14969AB0872641492ena153491
20218Alysiella crassa gene for 16S rRNA, partial sequence, strain: NBRC 102455AB6817971462ena153491

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

traitpredictionconfidencetraining_data
flagellatedno96.607no
gram-positiveno98.215no
anaerobicno97.982no
aerobicno90.335no
halophileno85.006no
spore-formingno96.595no
motileno89.798no
glucose-fermentno89.581no
thermophileno98.471yes
glucose-utilyes74.302no

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
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