Strain identifier

BacDive ID: 6455

Type strain: Yes

Species: Companilactobacillus farciminis

Strain Designation: Rv4 na, Rv4na

Strain history: CIP <- 1988, DSM <- G. Reuter: strain Rv4na

NCBI tax ID(s): 1612 (species)

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General

@ref: 8460

BacDive-ID: 6455

DSM-Number: 20184

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

description: Companilactobacillus farciminis Rv4 na is a facultative anaerobe, mesophilic bacterium that was isolated from sausage.

NCBI tax id

  • NCBI tax id: 1612
  • Matching level: species

strain history

@refhistory
8460<- G. Reuter, Rv4 na
67770T. Mitsuoka S8-22 <-- DSM 20184 <-- G. Reuter Rv4 na.
119281CIP <- 1988, DSM <- G. Reuter: strain Rv4na

doi: 10.13145/bacdive6455.20230509.8.1

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 farciminis
  • full scientific name: Companilactobacillus farciminis (Reuter 1983 ex Reuter 1970) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus farciminis

@ref: 8460

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Companilactobacillus

species: Companilactobacillus farciminis

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

strain designation: Rv4 na, Rv4na

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.643
69480100positive
119281nopositiverod-shaped

colony morphology

  • @ref: 119281

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8460MRS 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
38122MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
119281CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41
119281CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8460positivegrowth30mesophilic
38122positivegrowth30mesophilic
67770positivegrowth30mesophilic
119281positivegrowth15-37
119281nogrowth10psychrophilic
119281nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119281
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

murein

  • @ref: 8460
  • 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
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
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
119281nitrate-reduction17632
119281nitrite-reduction16301
119281nitrate+respiration17632

antibiotic resistance

  • @ref: 119281
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite tests

  • @ref: 119281
  • 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
119281oxidase-
119281alcohol dehydrogenase-1.1.1.1
119281catalase-1.11.1.6
119281lysine decarboxylase-4.1.1.18
119281ornithine 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
119281-+---++---++---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8460----------++++-------++-++++++-++------+--+-------
119281---------++++-------++-+/-+/-+/-+/-+/-+-++---------+-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119281---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8460sausage
50208Sausage
67770Sausage
119281Food, Sausage

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5978.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_954;97_1113;98_1324;99_5978&stattab=map
  • Last taxonomy: Lactobacillaceae
  • 16S sequence: LC063168
  • Sequence Identity:
  • Total samples: 3707
  • soil counts: 237
  • aquatic counts: 342
  • animal counts: 2894
  • plant counts: 234

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
84601Risk group (German classification)
1192811Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus farciminis strain ATCC 29644 16S ribosomal RNA gene, partial sequenceM588171515ena1612
20218Lactobacillus farciminis gene for 16S ribosomal RNA, partial sequenceAB8405891515ena1612
20218Lactobacillus farciminis 16S-23S ribosomal RNA small intergenic spacer region, complete sequenceAF500490194ena936140
20218Lactobacillus farciminis 16S-23S ribosomal RNA large intergenic spacer region; and tRNA-Ile and tRNA-Ala genes, complete sequenceAF500491388ena936140
20218Lactobacillus farciminis partial 23S rRNA gene and 16S-23S IGS, strain DSM 20184AJ616017663ena936140
20218Lactobacillus farciminis gene for 16S rRNA, partial sequence, strain: JCM 1097AB289103682ena936140
20218Lactobacillus farciminis gene for 16S ribosomal RNA, partial sequenceD31688177ena936140
67770Lactobacillus farciminis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1097LC0631681528ena936140

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Companilactobacillus farciminis KCTC 3681 = DSM 20184GCA_002706745completencbi936140
66792Lactobacillus farciminis KCTC 3681936140.3wgspatric936140
66792Lactobacillus farciminis KCTC 3681 = DSM 20184936140.5wgspatric936140
66792Lactobacillus farciminis KCTC 3681 = DSM 20184936140.8completepatric936140
66792Lactobacillus farciminis KCTC 3681 = DSM 20184 strain KCTC3681936140.9plasmidpatric936140
66792Lactobacillus farciminis strain ATCC 296441612.42wgspatric1612
66792Lactobacillus farciminis DSM 201842667527616draftimg936140
66792Lactobacillus farciminis KCTC 3681651324060draftimg936140
66792Lactobacillus farciminis DSM 201842814123232completeimg936140
67770Companilactobacillus farciminis KCTC 3681 = DSM 20184GCA_000184535scaffoldncbi936140
67770Companilactobacillus farciminis KCTC 3681 = DSM 20184GCA_001434775contigncbi936140
67770Companilactobacillus farciminis ATCC 29644GCA_004354695contigncbi1612

GC content

@refGC-contentmethod
846036.3
6777036
6777036.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.954no
gram-positiveyes92.551no
anaerobicno93.123no
aerobicno96.121no
halophileyes87.957no
spore-formingno94.798no
glucose-utilyes90.266no
thermophileno99.326no
motileno94.366no
glucose-fermentyes86.891no

External links

@ref: 8460

culture collection no.: DSM 20184, ATCC 29644, NCIB 11717, CCUG 30671, JCM 1097, BCRC 14043, CECT 571, CIP 103136, KCTC 3681, LMG 9200, NBRC 107150, NCFB 2330, NCIMB 11717, NRRL B-4566, VTT E-991267, NCDO 2330, IMET 11462

straininfo link

  • @ref: 75928
  • straininfo: 3284

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
Genetics21257766Genome sequence of Lactobacillus farciminis KCTC 3681.Nam SH, Choi SH, Kang A, Kim DW, Kim RN, Kim A, Kim DS, Park HSJ Bacteriol10.1128/JB.00003-112011Food Microbiology, *Genome, Bacterial, Lactobacillus/*classification/*genetics, Molecular Sequence DataBiotechnology
Phylogeny23194598Lactobacillus alimentarius sp. nov., nom rev. and Lactobacillus farciminis sp. nov., nom. rev.Reuter GSyst Appl Microbiol10.1016/S0723-2020(83)80055-11983
Metabolism23329323In vitro characterization of aggregation and adhesion properties of viable and heat-killed forms of two probiotic Lactobacillus strains and interaction with foodborne zoonotic bacteria, especially Campylobacter jejuni.Tareb R, Bernardeau M, Gueguen M, Vernoux JPJ Med Microbiol10.1099/jmm.0.049965-02013*Antibiosis, *Bacterial Adhesion, Carbohydrate Metabolism, Cell Line, Enterobacteriaceae/*physiology, Epithelial Cells/microbiology, Humans, Lactobacillus/*physiology, Lectins/metabolism, Listeria monocytogenes/*physiology, Microscopy, Electron, *Probiotics, Protein BindingPathogenicity
Phylogeny23728376Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle.Gu CT, Li CY, Yang LJ, Huo GCInt J Syst Evol Microbiol10.1099/ijs.0.053355-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, *Food Microbiology, Genes, Bacterial, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vegetables/microbiologyBiotechnology
Metabolism23986487A C69-family cysteine dipeptidase from Lactobacillus farciminis JCM1097 possesses strong Gly-Pro hydrolytic activity.Sakamoto T, Otokawa T, Kono R, Shigeri Y, Watanabe KJ Biochem10.1093/jb/mvt0692013Cysteine/*metabolism, Dipeptidases/chemistry/genetics/*metabolism, Dipeptides/*chemistry/*metabolism, Hydrolysis, Lactobacillus/*enzymology, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Protein, Substrate SpecificityGenetics
Phylogeny25281727Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal.Chang CH, Chen YS, Lee TT, Chang YC, Yu BInt J Syst Evol Microbiol10.1099/ijs.0.070938-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Fermentation, Genes, Bacterial, Lactic Acid, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/*microbiologyGenetics
Pathogenicity30637506Structure and biological activities of a hexosamine-rich cell wall polysaccharide isolated from the probiotic Lactobacillus farciminis.Maes E, Sadovskaya I, Leveque M, Elass-Rochard E, Payre B, Grard T, Theodorou V, Guerardel Y, Mercier-Bonin MGlycoconj J10.1007/s10719-018-09854-y2019Cell Wall/*chemistry/ultrastructure, Cytokines/metabolism, HEK293 Cells, Hexosamines/analysis, Humans, Lactobacillus/*chemistry, Polysaccharides, Bacterial/*chemistry/immunology/pharmacology, Probiotics/*chemistry, Signal Transduction/immunology, Toll-Like Receptors/metabolismMetabolism
Phylogeny30900972Lactobacillus zhachilii sp. nov., a lactic acid bacterium isolated from Zha-Chili.Zhang Z, Hou Q, Wang Y, Li W, Zhao H, Sun Z, Guo ZInt J Syst Evol Microbiol10.1099/ijsem.0.0033622019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermented Foods/*microbiology, Lactic Acid, Lactobacillus/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny33502298Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed.Jung JY, Kang HK, Jin HM, Han SS, Kwon YC, Eun JJ, Kim SC, Seo MJ, Ryu BG, Chung EJInt J Syst Evol Microbiol10.1099/ijsem.0.0046702021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8460Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20184)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20184
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
38122Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14900
50208Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 30671)https://www.ccug.se/strain?id=30671
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
75928Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3284.1StrainInfo: A central database for resolving microbial strain identifiers
119281Curators of the CIPCollection of Institut Pasteur (CIP 103136)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103136