Strain identifier

BacDive ID: 6437

Type strain: Yes

Species: Loigolactobacillus coryniformis

Strain Designation: 34

Strain history: CIP <- 1988, DSM <- I.G. Abo-Elgana: strain 34

NCBI tax ID(s): 1610 (species)

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General

@ref: 8417

BacDive-ID: 6437

DSM-Number: 20001

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

description: Loigolactobacillus coryniformis 34 is a facultative anaerobe, mesophilic bacterium that was isolated from silage.

NCBI tax id

  • NCBI tax id: 1610
  • Matching level: species

strain history

@refhistory
8417<- I. G. Abo-Elnaga, 34
67770T. Mitsuoka S8-10 <-- DSM 20001 <-- I. G. Abo-Elnaga 34.
118760CIP <- 1988, DSM <- I.G. Abo-Elgana: strain 34

doi: 10.13145/bacdive6437.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Loigolactobacillus
  • species: Loigolactobacillus coryniformis
  • full scientific name: Loigolactobacillus coryniformis (Abo-Elnaga and Kandler 1965) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus coryniformis

@ref: 8417

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Loigolactobacillus

species: Loigolactobacillus coryniformis subsp. coryniformis

full scientific name: Loigolactobacillus coryniformis subsp. coryniformis (Abo-Elnaga and Kandler 1965) Zheng et al. 2020

strain designation: 34

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.027
69480100positive
118760nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8417MRS 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
35495MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118760CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41
118760CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8417positivegrowth30mesophilic
35495positivegrowth37mesophilic
67770positivegrowth30mesophilic
118760positivegrowth25-37mesophilic
118760nogrowth15psychrophilic
118760nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118760
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.949

murein

  • @ref: 8417
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

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
68371cellobiose-builds acid from17057
68371salicin+builds acid from17814
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-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
118760nitrate-reduction17632
118760nitrite-reduction16301
118760nitrate+respiration17632

metabolite production

  • @ref: 118760
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 118760
  • 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
118760oxidase-
118760alcohol dehydrogenase-1.1.1.1
118760catalase-1.11.1.6
118760lysine decarboxylase-4.1.1.18
118760ornithine decarboxylase-4.1.1.17
118760urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50203C14:0414
    50203C15:01.315
    50203C16:027.416
    50203C18:03.718
    50203C16:1 ω7c8.815.819
    50203C17:0 CYCLO2.916.888
    50203C18:1 ω7c /12t/9t33.217.824
    50203C18:1 ω9c317.769
    50203C18:2 ω6,9c/C18:0 ANTE7.617.724
    50203C19:0 CYCLO ω9c7.218.87
    50203Unidentified0.813.244
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118760-----++---++---+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8417+/----------++++-+/---+---+--++-+--+------------------
8417----------++++----+---+--++-+--+------------------
8417----------++++-+/---+---+---+-+--+------------------
118760---------++++-+/---++--+-++/-+-+/---+------------------

Isolation, sampling and environmental information

isolation

@refsample type
8417silage
50203Silage
67770Silage
118760Other, Silage

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Animal feed
#Engineered#Biodegradation#Composting
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5528.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_2172;97_3279;98_4127;99_5528&stattab=map
  • Last taxonomy: Loigolactobacillus coryniformis
  • 16S sequence: LC064900
  • Sequence Identity:
  • Total samples: 9201
  • soil counts: 965
  • aquatic counts: 2103
  • animal counts: 5503
  • plant counts: 630

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
84171Risk group (German classification)
1187601Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus coryniformis 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA integenic spacer gene, complete sequence; and 23S ribosomal RNA gene, partial sequenceDQ314274339ena913848
20218Lactobacillus coryniformis strain DSM 20001 16S ribosomal RNA gene, partial sequenceM588131516ena1610
20218Lactobacillus coryniformis subsp. coryniformis gene for 16S rRNA, partial sequence, strain: JCM 1164AB289063687ena913848
67770Lactobacillus coryniformis subsp. coryniformis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1164LC0649001501ena913848

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Loigolactobacillus coryniformis subsp. coryniformis KCTC 3167 = DSM 20001GCA_002706425completencbi913848
66792Lactobacillus coryniformis subsp. coryniformis KCTC 3167913848.3wgspatric913848
66792Lactobacillus coryniformis subsp. coryniformis KCTC 3167 = DSM 20001913848.7completepatric913848
66792Lactobacillus coryniformis subsp. coryniformis KCTC 3167 = DSM 20001913848.6wgspatric913848
66792Loigolactobacillus coryniformis coryniformis DSM 200012667528105draftimg913848
66792Loigolactobacillus coryniformis coryniformis DSM 200012814123233completeimg913848
66792Loigolactobacillus coryniformis coryniformis KCTC 3167651324058draftimg913848
67770Loigolactobacillus coryniformis subsp. coryniformis KCTC 3167 = DSM 20001GCA_000166795scaffoldncbi913848
67770Loigolactobacillus coryniformis subsp. coryniformis KCTC 3167 = DSM 20001GCA_001433765scaffoldncbi913848

GC content

@refGC-contentmethod
841746.4
6777042.9genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.29no
gram-positiveyes95.625no
anaerobicno86.451no
aerobicno97.936no
halophileyes77.295no
spore-formingno90.831no
glucose-utilyes88.78no
thermophileno99.083no
motileno93.657no
glucose-fermentyes83.742no

External links

@ref: 8417

culture collection no.: CCUG 30666, DSM 20001, ATCC 25602, NCIB 9711, JCM 1164, BCRC 12935, CECT 982, CIP 103133, KCTC 3167, LMG 9196, NCFB 2741, NCIMB 9711, NRRL B-4391, VTT E-93487, NCDO 2741

straininfo link

  • @ref: 75911
  • straininfo: 3271

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism15574903Characterization of Lactobacillus coryniformis DSM 20001T surface protein Cpf mediating coaggregation with and aggregation among pathogens.Schachtsiek M, Hammes WP, Hertel CAppl Environ Microbiol10.1128/AEM.70.12.7078-7085.20042004Amino Acid Sequence, Animals, *Bacterial Adhesion, Bacterial Proteins/genetics/*metabolism, Campylobacter coli/genetics/physiology, Campylobacter jejuni/genetics/physiology, Cattle, Escherichia coli/genetics/physiology, Gene Expression Regulation, Bacterial, Humans, Lactobacillus/genetics/metabolism/physiology, Membrane Proteins/chemistry/genetics/*metabolism, Molecular Sequence Data, Sequence Analysis, DNA, Transcription, GeneticPathogenicity
Genetics21148735Genome sequence of Lactobacillus coryniformis subsp. coryniformis KCTC 3167.Nam SH, Choi SH, Kang A, Kim DW, Kim DS, Kim RN, Kim A, Park HSJ Bacteriol10.1128/JB.01394-102010Fermentation, *Food Microbiology, *Genome, Bacterial, Lactobacillus/*genetics/*isolation & purification/metabolism, Molecular Sequence DataBiotechnology
Metabolism23332852Antimicrobial potential for the combination of bovine lactoferrin or its hydrolysate with lactoferrin-resistant probiotics against foodborne pathogens.Chen PW, Jheng TT, Shyu CL, Mao FCJ Dairy Sci10.3168/jds.2012-61122013Animals, Anti-Infective Agents/administration & dosage/*therapeutic use, Bifidobacterium/metabolism, Cattle, Enterococcus faecalis/drug effects, Escherichia coli/drug effects, Lactobacillus/metabolism, Lactobacillus acidophilus/metabolism, Lactobacillus rhamnosus/metabolism, Lactoferrin/administration & dosage/drug effects/*therapeutic use, Pediococcus/metabolism, Probiotics/administration & dosage/*therapeutic use, Protein Hydrolysates, Salmonella typhimurium/drug effectsPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8417Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20001)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20001
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
35495Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14897
50203Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30666)https://www.ccug.se/strain?id=30666
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
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
75911Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3271.1StrainInfo: A central database for resolving microbial strain identifiers
118760Curators of the CIPCollection of Institut Pasteur (CIP 103133)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103133