Strain identifier

BacDive ID: 5323

Type strain: Yes

Species: Enterococcus saccharolyticus

Strain Designation: HF 62

Strain history: CIP <- 1988, NCFB <- 1982, Nat. Inst. Res. Dairying, Shinfield, UK: strain HF 62, Streptococcus saccharolyticus

NCBI tax ID(s): 1139996 (strain), 41997 (species)

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General

@ref: 9036

BacDive-ID: 5323

DSM-Number: 20726

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, animal pathogen

description: Enterococcus saccharolyticus HF 62 is a microaerophile, mesophilic, Gram-positive animal pathogen that was isolated from straw bedding.

NCBI tax id

NCBI tax idMatching level
1139996strain
41997species

strain history

@refhistory
9036<- NCDO <- J. Kruze, HF 62 (Streptococcus bovis)
67770ATCC 43076 <-- NCDO 2594 <-- J. Kruze HF62.
122335CIP <- 1988, NCFB <- 1982, Nat. Inst. Res. Dairying, Shinfield, UK: strain HF 62, Streptococcus saccharolyticus

doi: 10.13145/bacdive5323.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Enterococcaceae
  • genus: Enterococcus
  • species: Enterococcus saccharolyticus
  • full scientific name: Enterococcus saccharolyticus (Farrow et al. 1985) Rodrigues and Collins 1991

  • synonyms

    • @ref: 20215
    • synonym: Streptococcus saccharolyticus

@ref: 9036

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Enterococcus

species: Enterococcus saccharolyticus subsp. saccharolyticus

full scientific name: Enterococcus saccharolyticus subsp. saccharolyticus (Farrow et al. 1985) Chen et al. 2013

strain designation: HF 62

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
122335positivecoccus-shapedno

colony morphology

@reftype of hemolysisincubation period
9036gamma1-2 days
122335

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9036COLUMBIA 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
9036TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
40583MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
122335CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
9036positivegrowth37mesophilic
40583positivegrowth37mesophilic
67770positivegrowth37mesophilic
122335positivegrowth25-45
122335nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
9036microaerophile
122335facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.36

halophily

  • @ref: 122335
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 9036
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1223354853esculin+hydrolysis
122335606565hippurate+hydrolysis
12233517632nitrate+reduction
12233516301nitrite-reduction
6838129016arginine-hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol+builds acid from
6838130911sorbitol+builds acid from
6838117716lactose+builds acid from
6838127082trehalose+builds acid from
6838116634raffinose+builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838140585alpha-cyclodextrin+builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen-builds acid from
6838127941pullulan-builds acid from
6838117306maltose+builds acid from
6838128053melibiose+builds acid from
683816731melezitose+builds acid from
68381320055methyl beta-D-glucopyranoside+builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

  • @ref: 68381
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6838115688acetoin+
12233515688acetoin-

enzymes

@refvalueactivityec
9036catalase-1.11.1.6
9036cytochrome-c oxidase-1.9.3.1
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
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
122335oxidase-
122335beta-galactosidase+3.2.1.23
122335alcohol dehydrogenase+1.1.1.1
122335gelatinase-
122335amylase-
122335catalase-1.11.1.6
122335lysine decarboxylase-4.1.1.18
122335ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122335--+--+----+-+--+----

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
9036-+--+--++++++-+++----+---++++---
9036-+--+--++++++--++---+/-+---++++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
9036straw bedding
67770Straw bedding
122335Other, Straw beddingUnited KingdomGBREurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_759.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_19;97_19;98_605;99_759&stattab=map
  • Last taxonomy: Enterococcus
  • 16S sequence: U30931
  • Sequence Identity:
  • Total samples: 18861
  • soil counts: 573
  • aquatic counts: 1598
  • animal counts: 15794
  • plant counts: 896

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
9036yes2Risk group (German classification)
1223352Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterococcus saccharolyticus 16S ribosomal RNA gene, partial sequenceAF0610041506ena1139996
20218E.saccharolyticus 16S rRNA gene, partial (strain ATTC 43076 (CCUG 33311))Y12919366ena1139996
20218Enterococcus saccharolyticus strain CCUG 33311 clone 1 16S-23S ribosomal RNA intergenic spacer, partial sequenceDQ204538228ena1139996
20218Enterococcus saccharolyticus strain KCTC 3643 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceHM241937440ena1139996
20218Enterococcus saccharolyticus 16S rRNA gene, strain LMG 11427AJ3018391902ena1139996
20218Enterococcus saccharolyticus gene for 16S rRNA, partial sequence, strain: NBRC 100493AB6811911483ena1139996
20218Enterococcus saccharolyticus 16S ribosomal RNA partial sequenceU309311521ena41997
20218S.saccharolyticus 16S rRNA gene (5')X55766144ena1139996
20218S.saccharolyticus 16S rRNA geneX557671293ena1139996
20218Enterococcus saccharolyticus 16S rRNA geneY183571456ena1139996
9036Enterococcus saccharolyticus strain ATCC 43076 16S ribosomal RNA gene, partial sequenceDQ4118161480ena1139996
67770Enterococcus saccharolyticus gene for 16S ribosomal RNA, partial sequence, strain: JCM 8734LC0970721467ena41997

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterococcus saccharolyticus ATCC 43076 [PRJNA206268]1139996.3wgspatric1139996
66792Enterococcus saccharolyticus ATCC 43076 [PRJNA206365]1139996.4wgspatric1139996
66792Enterococcus saccharolyticus strain DSM 2072641997.3wgspatric41997
66792Enterococcus saccharolyticus ATCC 430762545824663draftimg1139996
66792Enterococcus saccharolyticus ATCC 430762541047445draftimg1139996
67770Enterococcus saccharolyticus subsp. saccharolyticus ATCC 43076GCA_000407005scaffoldncbi1139996
67770Enterococcus saccharolyticus subsp. saccharolyticus ATCC 43076GCA_000407285scaffoldncbi1139996
67770Enterococcus saccharolyticus DSM 20726GCA_001886235scaffoldncbi41997

GC content

  • @ref: 9036
  • GC-content: 37.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes85no
motileno91.427no
flagellatedno91.701no
gram-positiveyes94.811no
anaerobicno97.131yes
aerobicno92.452yes
halophileyes82.889no
spore-formingno88.59no
glucose-utilyes85.494no
thermophileno99.801yes
glucose-fermentyes82.544no

External links

@ref: 9036

culture collection no.: DSM 20726, ATCC 43076, CCUG 27643, CCUG 33311, CIP 103246, JCM 8734, LMG 11427, NBRC 100493, NCDO 2594, NCIMB 702594, CCM 4377, CECT 4309, CGMCC 1.2485, HAMBI 1576, KACC 10783, KCTC 3643

straininfo link

  • @ref: 74812
  • straininfo: 2281

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23959830Enterococcus saccharolyticus subsp. taiwanensis subsp. nov., isolated from broccoli.Chen YS, Lin YH, Pan SF, Ji SH, Chang YC, Yu CR, Liou MS, Wu HC, Otoguro M, Yanagida F, Liao CC, Chiu CM, Huang BQInt J Syst Evol Microbiol10.1099/ijs.0.052761-02013Bacterial Typing Techniques, Base Composition, Brassica/*microbiology, Carbohydrate Metabolism, DNA, Bacterial/genetics, Enterococcus/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny24812366Enterococcus olivae sp. nov., isolated from Spanish-style green-olive fermentations.Lucena-Padros H, Gonzalez JM, Caballero-Guerrero B, Ruiz-Barba JL, Maldonado-Barragan AInt J Syst Evol Microbiol10.1099/ijs.0.062208-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Enterococcus/*classification/genetics/isolation & purification, *Fermentation, *Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Olea/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, SpainBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9036Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20726)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20726
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
40583Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15022
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68381Automatically annotated from API rID32STR
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)
74812Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2281.1StrainInfo: A central database for resolving microbial strain identifiers
122335Curators of the CIPCollection of Institut Pasteur (CIP 103246)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103246