Strain identifier

BacDive ID: 5262

Type strain: Yes

Species: Vagococcus fluvialis

Strain Designation: M-29c

Strain history: CIP <- 1987, NCFB, Lactococcus sp. <- H. Hashimoto: strain M-29 C, Streptococcus lactis

NCBI tax ID(s): 2738 (species)

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General

@ref: 2312

BacDive-ID: 5262

DSM-Number: 5731

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, oval-shaped, human pathogen

description: Vagococcus fluvialis M-29c is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from chicken faeces.

NCBI tax id

  • NCBI tax id: 2738
  • Matching level: species

strain history

@refhistory
2312<- NCFB <- H. Hashimoto, M-29c
119413CIP <- 1987, NCFB, Lactococcus sp. <- H. Hashimoto: strain M-29 C, Streptococcus lactis

doi: 10.13145/bacdive5262.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Enterococcaceae
  • genus: Vagococcus
  • species: Vagococcus fluvialis
  • full scientific name: Vagococcus fluvialis Collins et al. 1990

@ref: 2312

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Vagococcus

species: Vagococcus fluvialis

full scientific name: Vagococcus fluvialis Collins et al. 1990

strain designation: M-29c

type strain: yes

Morphology

cell morphology

  • @ref: 119413
  • gram stain: positive
  • cell shape: oval-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2312TRYPTICASE 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
38745MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119413CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
2312positivegrowth30mesophilic
38745positivegrowth37
51141positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51141aerobe
119413facultative anaerobe

murein

  • @ref: 2312
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside+builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
119413nitrate-reduction17632
119413nitrite-reduction16301

metabolite production

  • @ref: 119413
  • 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
119413oxidase-
119413catalase-1.11.1.6
119413urease-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
119413--++------++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119413+---+----+/-++/-+/-----++/--++++++++--++------++--------+/-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
2312chicken faecesJapanJPNAsia
51141Chicken feces
119413Animal, Chicken, feces

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_12024.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1881;97_2259;98_9029;99_12024&stattab=map
  • Last taxonomy: Vagococcus fluvialis
  • 16S sequence: Y18098
  • Sequence Identity:
  • Total samples: 9217
  • soil counts: 1044
  • aquatic counts: 1703
  • animal counts: 6217
  • plant counts: 253

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
2312yesyes2Risk group (German classification)
1194131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vagococcus fluvialis strain CCUG 32704 16S-23S ribosomal RNA intergenic spacer, partial sequenceJQ697980232ena2738
20218Vagococcus fluvialis 16S rRNA geneY180981469ena2738
20218Vagococcus fluvialis 16S ribosomal RNAX542581484ena2738

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vagococcus fluvialis NCDO 2497GCA_003987575contigncbi2738
66792Vagococcus fluvialis DSM 5731GCA_003337315scaffoldncbi2738
66792Vagococcus fluvialis strain DSM 57312738.3wgspatric2738
66792Vagococcus fluvialis DSM 57312770939496draftimg2738

GC content

  • @ref: 2312
  • GC-content: 33.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes51.949no
flagellatedno78.962no
gram-positiveyes83.627no
anaerobicno95.41yes
aerobicno91.988yes
halophileyes74.416no
spore-formingno77.626no
glucose-utilyes90.114no
thermophileno98.954yes
glucose-fermentyes80.732no

External links

@ref: 2312

culture collection no.: DSM 5731, ATCC 49515, NCDO 2497, CCUG 32704, CIP 102976, LMG 9464

straininfo link

  • @ref: 74752
  • straininfo: 5032

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny247963016S ribosomal ribonucleic acid sequence analyses of lactococci and related taxa. Description of Vagococcus fluvialis gen. nov., sp. nov.Collins MD, Ash C, Farrow JA, Wallbanks S, Williams AMJ Appl Bacteriol10.1111/j.1365-2672.1989.tb02516.x1989Animals, Base Sequence, Chickens, Feces, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal/*genetics, RNA, Ribosomal, 16S/*genetics, RNA-Directed DNA Polymerase, Sequence Homology, Nucleic Acid, Streptococcaceae/classification/*genetics, Streptococcus/classification/genetics, Water MicrobiologyGenetics
Phylogeny19897618Vagococcus penaei sp. nov., isolated from spoilage microbiota of cooked shrimp (Penaeus vannamei).Jaffres E, Prevost H, Rossero A, Joffraud JJ, Dousset XInt J Syst Evol Microbiol10.1099/ijs.0.012872-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Enterococcaceae/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Molecular Sequence Data, Penaeidae/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny32195646Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content.Ge Y, Yang J, Lai XH, Zhang G, Jin D, Lu S, Wang B, Huang Y, Huang Y, Ren Z, Zhang X, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0040612020Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cloaca/*microbiology, DNA, Bacterial/genetics, Enterococcaceae/*classification/isolation & purification, Fatty Acids/chemistry, Finches/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2312Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5731)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5731
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
38745Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14721
51141Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32704)https://www.ccug.se/strain?id=32704
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)
68371Automatically annotated from API 50CH acid
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
74752Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5032.1StrainInfo: A central database for resolving microbial strain identifiers
119413Curators of the CIPCollection of Institut Pasteur (CIP 102976)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102976