Strain identifier

BacDive ID: 2248

Type strain: Yes

Species: Allofustis seminis

Strain Designation: 01-570-1

Strain history: CIP <- 2002, CCUG <- M.D. Collins, Univ. Reading, Reading, UK: strain 01-570-1

NCBI tax ID(s): 1120978 (strain), 166939 (species)

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General

@ref: 6121

BacDive-ID: 2248

DSM-Number: 15817

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

description: Allofustis seminis 01-570-1 is an anaerobe, mesophilic bacterium that was isolated from stored porcine semen.

NCBI tax id

NCBI tax idMatching level
166939species
1120978strain

strain history

@refhistory
6121<- E. Falsen, CCUG <- M. D. Collins, Univ. of Reading <- R. Higgins
122555CIP <- 2002, CCUG <- M.D. Collins, Univ. Reading, Reading, UK: strain 01-570-1

doi: 10.13145/bacdive2248.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Allofustis
  • species: Allofustis seminis
  • full scientific name: Allofustis seminis Collins et al. 2003

@ref: 6121

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Allofustis

species: Allofustis seminis

full scientific name: Allofustis seminis Collins et al. 2003

strain designation: 01-570-1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.19
69480100positive
122555nopositiverod-shaped

colony morphology

@refincubation period
567862-3 days
122555

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15817_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15817_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15817_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15817_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15817_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6121PYG 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
6121COLUMBIA 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
33126MEDIUM 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)
122555CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
6121positivegrowth37mesophilic
33126positivegrowth37mesophilic
56786positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6121anaerobe
56786anaerobe
56786microaerophile

spore formation

@refspore formationconfidence
69481no98
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12255517632nitrate-reduction
12255516301nitrite-reduction
12255517632nitrate-respiration

metabolite production

  • @ref: 122555
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122555oxidase-
122555beta-galactosidase-3.2.1.23
122555gelatinase-
122555amylase-
122555DNase-
122555caseinase-3.4.21.50
122555catalase-1.11.1.6
122555tween esterase-
122555lecithinase-
122555lipase-
122555protease-
122555urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122555--+--+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6121stored porcine semenMontrealCanadaCANNorth America
56786Porcine semen,environmental contaminant ?MontrealCanadaCANNorth America
122555Animal, Porcine semenUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Urogenital tract#Semen

taxonmaps

  • @ref: 69479
  • File name: preview.99_6725.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_596;96_3178;97_3896;98_4954;99_6725&stattab=map
  • Last taxonomy: Allofustis seminis subclade
  • 16S sequence: AJ410303
  • Sequence Identity:
  • Total samples: 1239
  • soil counts: 105
  • aquatic counts: 120
  • animal counts: 966
  • plant counts: 48

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
61211Risk group (German classification)
1225551Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Allofustis seminis 16S rRNA gene, type strain CCUG 45438TAJ4584461500ena166939
6121Alloiococcus sp. CCUG 45438 16S rRNA gene, strain CCUG 45438AJ4103031500ena166939

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Allofustis seminis DSM 15817GCA_000374325scaffoldncbi1120978
66792Allofustis seminis DSM 158171120978.3wgspatric1120978
66792Allofustis seminis DSM 158172518285549draftimg1120978

GC content

  • @ref: 6121
  • GC-content: 39

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno95.962no
flagellatedno98.733no
gram-positiveyes96.009no
anaerobicno88.862no
aerobicno95.492yes
halophileyes87.371no
spore-formingno94.166no
glucose-utilyes87.803no
thermophileno92.747yes
glucose-fermentyes71.305no

External links

@ref: 6121

culture collection no.: DSM 15817, CCUG 45438, CIP 107425

straininfo link

  • @ref: 71807
  • straininfo: 87828

literature

  • topic: Phylogeny
  • Pubmed-ID: 12807205
  • title: Allofustis seminis gen. nov., sp. nov., a novel Gram-positive, catalase-negative, rod-shaped bacterium from pig semen.
  • authors: Collins MD, Higgins R, Messier S, Fortin M, Hutson RA, Lawson PA, Falsen E
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02484-0
  • year: 2003
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cell Wall/chemistry, DNA, Ribosomal/analysis, Gram-Positive Rods/chemistry/*classification/genetics/*isolation & purification, Male, Molecular Sequence Data, Peptidoglycan/analysis, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Semen/*microbiology, Sequence Analysis, DNA, *Swine
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6121Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15817)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15817
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
33126Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4859
56786Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 45438)https://www.ccug.se/strain?id=45438
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
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)
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
71807Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87828.1StrainInfo: A central database for resolving microbial strain identifiers
122555Curators of the CIPCollection of Institut Pasteur (CIP 107425)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107425