Strain identifier

BacDive ID: 6410

Type strain: Yes

Species: Companilactobacillus alimentarius

Strain Designation: R 13, R13

Strain history: CIP <- 1987, DSM <- G. Reuter: strain R13

NCBI tax ID(s): 1423720 (strain), 1602 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 8660

BacDive-ID: 6410

DSM-Number: 20249

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, lactate production

description: Companilactobacillus alimentarius R 13 is an anaerobe, mesophilic bacterium that produces lactate and was isolated from marinated fish product.

NCBI tax id

NCBI tax idMatching level
1423720strain
1602species

strain history

@refhistory
8660<- G. Reuter, R 13
67770T. Mitsuoka S8-17 <-- DSM 20249 (Lactobacillus sp.) <-- G. Reuter R13.
116236CIP <- 1987, DSM <- G. Reuter: strain R13

doi: 10.13145/bacdive6410.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Companilactobacillus
  • species: Companilactobacillus alimentarius
  • full scientific name: Companilactobacillus alimentarius (Reuter 1983 ex Reuter 1970) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus alimentarius

@ref: 8660

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Companilactobacillus

species: Companilactobacillus alimentarius

full scientific name: Companilactobacillus alimentarius (Reuter 1983) Zheng et al. 2020

strain designation: R 13, R13

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.425
69480100positive
116236nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8660MRS 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
40496MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116236CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8660positivegrowth30mesophilic
40496positivegrowth30mesophilic
50209positivegrowth30mesophilic
67770positivegrowth30mesophilic
116236positivegrowth30-37mesophilic
116236nogrowth10psychrophilic
116236nogrowth15psychrophilic
116236nogrowth22psychrophilic
116236nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 50209
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

compound production

  • @ref: 8660
  • compound: L(+) lactic acid

murein

  • @ref: 8660
  • 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
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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
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
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116236nitrate-reduction17632
116236nitrite-reduction16301
116236nitrate+respiration17632

metabolite tests

  • @ref: 116236
  • 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
116236oxidase-
116236alcohol dehydrogenase-1.1.1.1
116236catalase-1.11.1.6
116236lysine decarboxylase-4.1.1.18
116236ornithine 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
116236----------++----+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8660----+------+++--------++++++---++-----------------
8660----++----++++--------+++++++--++------+-------++-
116236---+/-+/------+/-+/-+/---------+/-+/--+/-+/-+/----+/-+/-------+/--------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116236------------------+-------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample type
8660marinated fish product
50209Marinated fish product
67770Marinated fish product
116236Food, Marinated fish product

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Food
#Host#Fishes

taxonmaps

  • @ref: 69479
  • File name: preview.99_7133.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_954;97_1113;98_2270;99_7133&stattab=map
  • Last taxonomy: Companilactobacillus alimentarius
  • 16S sequence: LC063166
  • Sequence Identity:
  • Total samples: 631
  • soil counts: 61
  • aquatic counts: 47
  • animal counts: 461
  • plant counts: 62

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
86601Risk group (German classification)
1162361Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus alimentarius 16S-23S ribosomal RNA small intergenic spacer region, complete sequenceAF500492230ena1602
20218Lactobacillus alimentarius 16S-23S ribosomal RNA large intergenic spacer region; and tRNA-Ile and tRNA-Ala genes, complete sequenceAF500493425ena1602
20218Lactobacillus alimentarius strain DSM 20249 16S ribosomal RNA gene, partial sequenceM588041514ena1602
20218Lactobacillus alimentarius gene for 16S rRNA, partial sequence, strain: JCM 1095AB289025694ena1602
20218Lactobacillus alimentarius gene for 16S ribosomal RNA, partial sequenceD31677187ena1602
20218Lactobacillus alimentarius partial 23S rRNA gene and 16S-23S IGS, strain LMG 9187AJ616015701ena1602
67770Lactobacillus alimentarius gene for 16S ribosomal RNA, partial sequence, strain: JCM 1095LC0631661528ena1602

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Companilactobacillus alimentarius DSM 20249GCA_002849895completencbi1423720
66792Lactobacillus alimentarius DSM 202491423720.3wgspatric1423720
66792Lactobacillus alimentarius DSM 202491423720.4patric1423720
66792Lactobacillus alimentarius strain NBRC 1064641602.4wgspatric1602
66792Lactobacillus alimentarius DSM 202492700989133draftimg1423720
66792Lactobacillus alimentarius DSM 202492802429297completeimg1423720
67770Companilactobacillus alimentarius DSM 20249GCA_001434745scaffoldncbi1423720
67770Companilactobacillus alimentarius NBRC 106464GCA_007991795contigncbi1602

GC content

@refGC-contentmethod
866037.0
6777035.4genome sequence analysis
6777037

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno98.271no
gram-positiveyes97.307no
anaerobicno83.944yes
aerobicno93.552yes
halophileyes88.308no
spore-formingno95.307no
thermophileno99.342yes
glucose-utilyes92.419no
motileno94.677no
glucose-fermentyes90.737no

External links

@ref: 8660

culture collection no.: DSM 20249, ATCC 29643, CCUG 30672, JCM 1095, BCRC 12932, CECT 570, CIP 102986, KACC 12425, KCTC 3593, LMG 9187, NBRC 106464, NCFB 2329, NCIMB 11994, NRIC 1640, NCDO 2329

straininfo link

  • @ref: 75883
  • straininfo: 8644

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11034488Lactobacillus kimchii sp. nov., a new species from kimchi.Yoon JH, Kang SS, Mheen TI, Ahn JS, Lee HJ, Kim TK, Park CS, Kho YH, Kang KH, Park YHInt J Syst Evol Microbiol10.1099/00207713-50-5-17892000Bacterial Typing Techniques, Bacteriocins/biosynthesis, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Korea, Lactobacillus/chemistry/*classification/*genetics/physiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/*microbiologyBiotechnology
Phylogeny12710620Lactobacillus versmoldensis sp. nov., isolated from raw fermented sausage.Krockel L, Schillinger U, Franz CMAP, Bantleon A, Ludwig WInt J Syst Evol Microbiol10.1099/ijs.0.02387-02003Fermentation, *Food Microbiology, Lactobacillus/chemistry/*classification/genetics/physiology, Meat/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Sequence Analysis, DNABiotechnology
Phylogeny23194598Lactobacillus alimentarius sp. nov., nom rev. and Lactobacillus farciminis sp. nov., nom. rev.Reuter GSyst Appl Microbiol10.1016/S0723-2020(83)80055-11983
Phylogeny31668878Polyphasic characterization of two novel Lactobacillus spp. isolated from blown salami packages: Description of Lactobacillus halodurans sp. nov. and Lactobacillus salsicarnum sp. nov.Schuster JA, Klingl A, Vogel RF, Ehrmann MASyst Appl Microbiol10.1016/j.syapm.2019.1260232019Animals, Base Composition, Fatty Acids/analysis, Fermented Foods/*microbiology, *Food Microbiology, Genes, Bacterial/genetics, Genome, Bacterial/genetics, Lactobacillus/chemistry/*classification/genetics/ultrastructure, Meat Products/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, SwineBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8660Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20249)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20249
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
40496Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14732
50209Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30672)https://www.ccug.se/strain?id=30672
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
75883Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8644.1StrainInfo: A central database for resolving microbial strain identifiers
116236Curators of the CIPCollection of Institut Pasteur (CIP 102986)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102986