Strain identifier

BacDive ID: 6844

Type strain: Yes

Species: Weissella confusa

Strain Designation: 548-D

Strain history: CIP <- 1988, NCIB, Lactobacillus confusus <- 1961, NRRL: B-1064 <- C.S. McCleskey: strain 548D, Leuconostoc mesenteroides

NCBI tax ID(s): 1583 (species)

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General

@ref: 8469

BacDive-ID: 6844

DSM-Number: 20196

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Weissella confusa 548-D is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sugar cane.

NCBI tax id

  • NCBI tax id: 1583
  • Matching level: species

strain history

@refhistory
8469<- ATCC <- C.S. McCleskey, 548-D
67770T. Mitsuoka S8-9 <-- DSM 20196 <-- ATCC 10881 (Leuconostoc mesenteroides) <-- C. S. McCleskey 548-D.
118727CIP <- 1988, NCIB, Lactobacillus confusus <- 1961, NRRL: B-1064 <- C.S. McCleskey: strain 548D, Leuconostoc mesenteroides

doi: 10.13145/bacdive6844.20250331.9.3

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 confusa
  • full scientific name: Weissella confusa corrig. (Holzapfel and Kandler 1969) Collins et al. 1994

  • synonyms

    @refsynonym
    20215Lactobacillus confusus
    20215Lactobacillus confusa
    20215Lactobacillus coprophilus subsp. confusus

@ref: 8469

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Leuconostocaceae

genus: Weissella

species: Weissella confusa

full scientific name: Weissella confusa (Holzapfel and Kandler 1969) Collins et al. 1994

strain designation: 548-D

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118727positiverod-shapedno
125438no93
125438positive95.504
125439positive95.9

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8469MRS 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
34122MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118727CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperature
8469positivegrowth30
34122positivegrowth30
49916positivegrowth30-37
67770positivegrowth30
118727positivegrowth15-45
118727nogrowth10

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
49916aerobe
49916microaerophile
118727facultative anaerobe
125439microaerophile97.5

halophily

@refsaltgrowthtested relationconcentration
118727NaClpositivegrowth0-4 %
118727NaClnogrowth6 %
118727NaClnogrowth8 %
118727NaClnogrowth10 %

murein

  • @ref: 8469
  • murein short key: A11.04
  • type: A3alpha L-Lys-L-Ala

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11872716947citrate-carbon source
11872717632nitrate-reduction
11872716301nitrite-reduction
11872717632nitrate+respiration
6837118305arbutin-builds acid from
6837127613amygdalin+builds acid from
68371Potassium 5-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

antibiotic resistance

  • @ref: 118727
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 118727
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
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
118727oxidase-
118727alcohol dehydrogenase+1.1.1.1
118727gelatinase-
118727caseinase-3.4.21.50
118727catalase-1.11.1.6
118727lysine decarboxylase-4.1.1.18
118727ornithine decarboxylase-4.1.1.17
68382alpha-galactosidase-3.2.1.22

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118727-+---+---+++----+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8469-----++---++++--------++-+-++---------------------
8469------+---++++--------++-++++------------------+/-+/--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
8469sugar cane
67770Sugar cane
118727Other, Sugarcane juiceUnited States of AmericaUSANorth America1946

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7464.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_155;96_519;97_786;98_910;99_7464&stattab=map
  • Last taxonomy: Weissella
  • 16S sequence: AB023241
  • Sequence Identity:
  • Total samples: 13671
  • soil counts: 505
  • aquatic counts: 937
  • animal counts: 11257
  • plant counts: 972

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
8469yes, in single casesyes, in single cases1Risk group (German classification)
1187271Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Weissella confusa DNA for 16S ribosomal RNA, strain JCM 1093AB0232411477nuccore1583
20218Weissella confusa gene for 16S rRNA, partial sequence, strain: JCM 1093AB5969441499nuccore1583
20218Lactobacillus confusus gene for 16S ribosomal RNA, partial sequenceD31684230nuccore1583
67770Weissella confusa gene for 16S ribosomal RNA, partial sequence, strain: JCM 1093LC0631641538nuccore1583
67770L.confusus 16S small subunit ribosomal RNAM230361525nuccore1583
124043Weissella confusa gene for 16S rRNA, partial sequence, strain: NBRC 106469.AB6824491502nuccore1583

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Weissella confusa NBRC 106469GCA_007991875contigncbi1583
66792Weissella confusa strain DSM 201961583.306wgspatric1583
66792Weissella confusa strain DSM 201961583.20wgspatric1583
66792Weissella confusa strain NBRC 1064691583.181wgspatric1583
66792Weissella confusa DSM 201962660238305draftimg1583
67770Weissella confusa DSM 20196GCA_001436895scaffoldncbi1583

GC content

@refGC-contentmethod
846945.0
6777045thermal denaturation, midpoint method (Tm)
6777046.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes95.504no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no82.78yes
125438spore-formingspore-formingAbility to form endo- or exosporesno89.386no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.836yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no91.328no
125438motile2+flagellatedAbility to perform flagellated movementno93no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno88.6
125439BacteriaNetmotilityAbility to perform movementno81
125439BacteriaNetgram_stainReaction to gram-stainingpositive95.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile97.5

External links

@ref: 8469

culture collection no.: DSM 20196, ATCC 10881, NCDO 1586, NCIB 9311, CCUG 30113, JCM 1093, BCRC 14002, CECT 4707, CIP 103172, LMG 9497, NBRC 106469, NCIMB 9311, NRIC 0207, NRRL B-1064, VTT E-90393

straininfo link

  • @ref: 76309
  • straininfo: 3269

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism4259626Some slime-forming heterofermentative species of the genus Lactobacillus.Sharpe ME, Garvie EI, Tilbury RHAppl Microbiol10.1128/am.23.2.389-397.19721972Ammonia/biosynthesis, Arginine/metabolism, Carbohydrate Metabolism, Chromatography, Gas, Chromatography, Paper, Fermentation, Flavonoids/metabolism, Fructose-Bisphosphate Aldolase/analysis, Glycoside Hydrolases, L-Lactate Dehydrogenase/analysis, Lactates/biosynthesis, Lactobacillus/analysis/*classification/enzymology/growth & development/*metabolism, Leuconostoc/classification, Penicillium/enzymology, Phosphofructokinase-1/analysis, Polysaccharides, Bacterial/analysis/biosynthesis, Pyruvate Oxidase/analysis, Species Specificity, Spectrophotometry, Terminology as TopicPhylogeny
8910918Lactobacillus- and bifidobacterium-mediated antigenotoxicity in the colon of rats.Pool-Zobel BL, Neudecker C, Domizlaff I, Ji S, Schillinger U, Rumney C, Moretti M, Vilarini I, Scassellati-Sforzolini R, Rowland INutr Cancer10.1080/0163558960951449219961,2-Dimethylhydrazine, Animals, *Anticarcinogenic Agents, *Antimutagenic Agents, Bifidobacterium/*physiology, Carcinogens/administration & dosage, Colon/*microbiology, Colonic Neoplasms/genetics/prevention & control, DNA Damage, Dimethylhydrazines/administration & dosage, Immunohistochemistry, Lactobacillus/*physiology, Lactobacillus acidophilus/physiology, Male, Methylnitronitrosoguanidine/administration & dosage, Proliferating Cell Nuclear Antigen/analysis, Rats, Rats, Sprague-Dawley
Metabolism27233126Molecular cloning of kman coding for mannanase from Klebsiella oxytoca KUB-CW2-3 and its hybrid mannanase characters.Pongsapipatana N, Damrongteerapap P, Chantorn S, Sintuprapa W, Keawsompong S, Nitisinprasert SEnzyme Microb Technol10.1016/j.enzmictec.2016.03.0052016Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/*metabolism, Cloning, Molecular, Escherichia coli/enzymology/genetics, Genes, Bacterial, Klebsiella oxytoca/*enzymology/*genetics, Mannans/metabolism, Models, Molecular, Protein Conformation, Recombinant Proteins/chemistry/genetics/metabolism, Substrate Specificity, beta-Mannosidase/chemistry/*genetics/*metabolismEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8469Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20196)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20196
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
34122Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14940
49916Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30113)https://www.ccug.se/strain?id=30113
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)
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
76309Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3269.1StrainInfo: A central database for resolving microbial strain identifiers
118727Curators of the CIPCollection of Institut Pasteur (CIP 103172)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103172
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1