Strain identifier

BacDive ID: 6849

Type strain: Yes

Species: Weissella viridescens

Strain Designation: S38A, S 38A

Strain history: CIP <- 1987, DSMZ, Lactobacillus viridescens <- Difco Lab., Detroit, USA <- ATCC <- J.B. Evans: strain S 38A

NCBI tax ID(s): 1629 (species)

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General

@ref: 8796

BacDive-ID: 6849

DSM-Number: 20410

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

description: Weissella viridescens S38A is a facultative anaerobe, mesophilic bacterium that was isolated from cured meat products.

NCBI tax id

  • NCBI tax id: 1629
  • Matching level: species

strain history

@refhistory
8796<- Difco Lab. <- ATCC <- J.B. Evans, S38A
67770ATCC 12706 <-- J. B. Evans S38A.
123861CIP <- 1987, DSMZ, Lactobacillus viridescens <- Difco Lab., Detroit, USA <- ATCC <- J.B. Evans: strain S 38A

doi: 10.13145/bacdive6849.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Weissella
  • species: Weissella viridescens
  • full scientific name: Weissella viridescens (Niven and Evans 1957) Collins et al. 1994

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus viridescens

@ref: 8796

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Weissella

species: Weissella viridescens

full scientific name: Weissella viridescens (Niven and Evans 1957) Collins et al. 1994

strain designation: S38A, S 38A

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.873
69480100positive
123861nopositiverod-shaped

colony morphology

  • @ref: 123861

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8796MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water
41868MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
123861CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8796positivegrowth30mesophilic
41868positivegrowth30mesophilic
67770positivegrowth37mesophilic
123861positivegrowth15-37
123861nogrowth10psychrophilic
123861nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123861
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

@refsaltgrowthtested relationconcentration
123861NaClpositivegrowth0-4 %
123861NaClnogrowth6 %
123861NaClnogrowth8 %
123861NaClnogrowth10 %

murein

  • @ref: 8796
  • murein short key: A11.13
  • type: A3alpha L-Lys-L-Ala-L-Ser

observation

  • @ref: 67770
  • observation: Assay of Thiamine

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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-sorbitol-builds acid from17924
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-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
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
123861citrate-carbon source16947
123861nitrate-reduction17632
123861nitrite-reduction16301
123861nitrate+respiration17632

antibiotic resistance

  • @ref: 123861
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123861
  • metabolite: polysaccharides
  • production: no

metabolite tests

  • @ref: 123861
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
123861oxidase-
123861alcohol dehydrogenase-1.1.1.1
123861gelatinase-
123861caseinase-3.4.21.50
123861catalase-1.11.1.6
123861lysine decarboxylase-4.1.1.18
123861ornithine 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
123861-+--------++--------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8796-----------+++--------+-----+---------------------
8796-----------+++--------+-----+---------------------

Isolation, sampling and environmental information

isolation

@refsample type
8796cured meat products
67770Cured meat products
123861Food, Cured meat product

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Meat

taxonmaps

  • @ref: 69479
  • File name: preview.99_1853.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_155;96_1045;97_1221;98_1467;99_1853&stattab=map
  • Last taxonomy: Weissella
  • 16S sequence: LC065037
  • Sequence Identity:
  • Total samples: 5394
  • soil counts: 382
  • aquatic counts: 562
  • animal counts: 4100
  • plant counts: 350

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
87961Risk group (German classification)
1238611Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus plantarum ATCC 12706 16S ribosomal RNA gene, partial sequenceAF429488507ena1590
20218Lactobacillus plantarum strain ATCC 12706 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF429575517ena1590
20218Lactobacillus viridescens gene for 16S ribosomal RNA, partial sequenceD31699229ena1629
20218Lactobacillus viridescens 16S ribosomal RNAX525681515ena1629
20218Weissella viridescens DNA for 16S ribosomal RNA, strain NRIC 1536AB0232361479ena1629
67770Weissella viridescens gene for 16S ribosomal RNA, partial sequence, strain: JCM 1174LC0650371479ena1629
67770L.viridescens 16S small subunit ribosomal RNAM230401582ena1629

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Weissella viridescens strain DSM 204101629.5wgspatric1629
66792Weissella viridescens strain NCTC136451629.13wgspatric1629
66792Weissella viridescens NCDO 16552713896977draftimg1629
66792Weissella viridescens NCTC 136452808606721draftimg1629
66792Weissella viridescens DSM 204102690315949draftimg1629
67770Weissella viridescens NCDO 1655GCA_001460875scaffoldncbi1629
67770Weissella viridescens DSM 20410GCA_001437355scaffoldncbi1629
67770Weissella viridescens NCTC13645GCA_900460455contigncbi1629

GC content

@refGC-content
879642.7
6777043

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.389no
gram-positiveyes95.547no
anaerobicno87.801no
aerobicno94.18no
halophileyes94.353no
spore-formingno96.344no
thermophileno99.838no
glucose-utilyes90.328no
flagellatedno98.583no
glucose-fermentyes86.36no

External links

@ref: 8796

culture collection no.: DSM 20410, ATCC 12706, CCM 56, NCDO 1655, NCIB 8965, WDCM 00105, JCM 1174, BCRC 11650, CCUG 21533, CCUG 30502, CECT 283, CIP 102810, IAM 13546, KCTC 3504, LMG 3507, NCCB 71015, NCFB 1655, NCIMB 8965, NCTC 13645, NCTC 13770, NRIC 1536, NRRL B-1951, VKM B-1528, VTT E-98966

straininfo link

  • @ref: 76314
  • straininfo: 3386

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism6160478Nucleotide sequence of Lactobacillus viridescens 5S RNA.Alexander LJ, Stewart TSNucleic Acids Res10.1093/nar/8.5.9791980Bacillus megaterium/metabolism, Bacillus subtilis/metabolism, Base Sequence, Binding Sites, Escherichia coli/metabolism, Lactobacillus/*metabolism, Nucleic Acid Conformation, RNA, Bacterial/*metabolism, RNA, Transfer/metabolism, Species SpecificityPhylogeny
Pathogenicity12915033Thermal resistances and lactate and diacetate sensitivities of bacteria causing bologna discolouration.Peirson MD, Guan TY, Holley RAInt J Food Microbiol10.1016/s0168-1605(02)00548-22003Acetates/*pharmacology, Animals, Colony Count, Microbial, Color, Colorimetry, Disinfectants/*pharmacology, Food Handling/methods, Food Microbiology, Hot Temperature, Lactobacillaceae/drug effects/*growth & development, Lactobacillus/drug effects/growth & development, Meat Products/*microbiology/standards, Sodium Lactate/*pharmacology, Streptococcaceae/drug effects/*growth & development, SwineBiotechnology
Phylogeny21216921Weissella ceti sp. nov., isolated from beaked whales (Mesoplodon bidens).Vela AI, Fernandez A, Bernaldo de Quiros Y, Herraez P, Dominguez L, Fernandez-Garayzabal JFInt J Syst Evol Microbiol10.1099/ijs.0.028522-02011Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Weissella/*classification/genetics/*isolation & purification, Whales/*microbiologyGenetics
Phylogeny25180092Weissella uvarum sp. nov., isolated from wine grapes.Nisiotou A, Dourou D, Filippousi ME, Banilas G, Tassou CInt J Syst Evol Microbiol10.1099/ijs.0.066209-02014Base Composition, DNA, Bacterial/genetics, Electrophoresis, Gel, Pulsed-Field, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Restriction Mapping, Sequence Analysis, DNA, Spain, Vitis/*microbiology, Weissella/*classification/genetics/isolation & purification, WineEnzymology
Biotechnology26318409A novel real-time PCR assay for the specific identification and quantification of Weissella viridescens in blood sausages.Gomez-Rojo EM, Romero-Santacreu L, Jaime I, Rovira JInt J Food Microbiol10.1016/j.ijfoodmicro.2015.08.0022015DNA Primers, Food Microbiology/*methods, Meat Products/*microbiology, *Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, Weissella/*genetics/isolation & purificationEnzymology
Metabolism26341641Production of Antilisterial Bacteriocins from Lactic Acid Bacteria in Dairy-Based Media: A Comparative Study.Unlu G, Nielsen B, Ionita CProbiotics Antimicrob Proteins10.1007/s12602-015-9200-z2015Animals, Anti-Bacterial Agents/*biosynthesis/pharmacology, Bacteriocins/*biosynthesis/pharmacology, Bacteriological Techniques, Cheese, Culture Media/*metabolism, Food Microbiology, Lactobacillus/*metabolism, Listeria monocytogenes/*drug effects, Milk/metabolism, Pediococcus/*metabolism, Whey/metabolismBiotechnology
Genetics28931059Whole-genome sequencing of mutants with increased resistance against the two-peptide bacteriocin plantaricin JK reveals a putative receptor and potential docking site.Ekblad B, Nissen-Meyer J, Kristensen TPLoS One10.1371/journal.pone.01852792017Bacterial Proteins/chemistry/*metabolism, Bacteriocins/chemistry/metabolism/*pharmacology, Binding Sites, Drug Resistance, Bacterial/drug effects/genetics, Genome, Bacterial, Lactobacillus plantarum/*genetics, Molecular Docking Simulation, Mutation, Weissella/drug effects/*geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8796Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20410)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20410
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
41868Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14538
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/
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
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
76314Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3386.1StrainInfo: A central database for resolving microbial strain identifiers
123861Curators of the CIPCollection of Institut Pasteur (CIP 102810)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102810