Strain identifier

BacDive ID: 6643

Type strain: Yes

Species: Lentilactobacillus farraginis

Strain history: CIP <- 2007, JCM <- 2006, NRIC

NCBI tax ID(s): 390841 (species)

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

@ref: 7364

BacDive-ID: 6643

DSM-Number: 18382

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

description: Lentilactobacillus farraginis DSM 18382 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from composting material of distilled shochu residue.

NCBI tax id

  • NCBI tax id: 390841
  • Matching level: species

strain history

@refhistory
7364<- Akihito Endo, NRIC 0676
67770A. Endo NRIC 0676.
119287CIP <- 2007, JCM <- 2006, NRIC

doi: 10.13145/bacdive6643.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lentilactobacillus
  • species: Lentilactobacillus farraginis
  • full scientific name: Lentilactobacillus farraginis (Endo and Okada 2007) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus farraginis

@ref: 7364

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lentilactobacillus

species: Lentilactobacillus farraginis

full scientific name: Lentilactobacillus farraginis (Endo and Okada 2007) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31901positive03-06 µm0.8 µmrod-shapedno
69480no92.44
69480positive100
119287positiverod-shapedno

pigmentation

  • @ref: 31901
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7364MRS 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
36536MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
119287CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
7364positivegrowth30mesophilic
31901positivegrowth15-45
31901positiveoptimum30mesophilic
36536positivegrowth37mesophilic
67770positivegrowth30mesophilic
119287positivegrowth15-45
119287nogrowth10psychrophilic

culture pH

@refabilitytypepHPH range
31901positivegrowth04-09alkaliphile
31901positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7364microaerophile
31901facultative anaerobe
119287facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.982

observation

  • @ref: 31901
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3190122599arabinose+carbon source
3190128260galactose+carbon source
3190128053melibiose+carbon source
3190116634raffinose+carbon source
3190117992sucrose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+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
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-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
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11928717632nitrate+reduction
11928716301nitrite-reduction
11928717632nitrate+respiration

metabolite tests

  • @ref: 119287
  • 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
119287oxidase-
119287alcohol dehydrogenase+1.1.1.1
119287catalase-1.11.1.6
119287lysine decarboxylase-4.1.1.18
119287ornithine 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
119287-+++-+-+--++++-++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7364----++----+++-----+---------++++--++-----------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7364composting material of distilled shochu residueMiyazaki prefectureJapanJPNAsia
67770Compost of distilled shochu residue
119287Environment, Compost of distilled shochu residueJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Food production#Fermented
#Engineered#Food production#Beverage

taxonmaps

  • @ref: 69479
  • File name: preview.99_1951.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_367;97_831;98_1249;99_1951&stattab=map
  • Last taxonomy: Lentilactobacillus farraginis
  • 16S sequence: LC383828
  • Sequence Identity:
  • Total samples: 18053
  • soil counts: 1305
  • aquatic counts: 1092
  • animal counts: 14859
  • plant counts: 797

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
73641Risk group (German classification)
1192871Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7364Lactobacillus farraginis gene for 16S rRNA, partial sequence, strain: NRIC 0676AB2627311514ena390841
67770Lactobacillus farraginis JCM 14108 gene for 16S ribosomal RNA, partial sequenceLC3838281512ena390841

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus farraginis DSM 18382 = JCM 141081423743.5wgspatric1423743
66792Lactobacillus farraginis JCM 141081236511.3wgspatric1423743
66792Lentilactobacillus farraginis JCM 141082576861775draftimg1423743
66792Lentilactobacillus farraginis DSM 183822681813158draftimg1423743
67770Lentilactobacillus farraginis DSM 18382 = JCM 14108GCA_001435875scaffoldncbi1423743
67770Lentilactobacillus farraginis DSM 18382 = JCM 14108GCA_000583655contigncbi1423743

GC content

@refGC-contentmethod
736440
3190141
6777041high performance liquid chromatography (HPLC)
6777042.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.025no
gram-positiveyes97.025no
anaerobicno91.501no
halophileyes87.065no
spore-formingno90.721no
glucose-utilyes89.697no
thermophileno99.446yes
aerobicno94.319yes
flagellatedno98.021no
glucose-fermentyes85.542no

External links

@ref: 7364

culture collection no.: DSM 18382, JCM 14108, NRIC 0676, CIP 109567

straininfo link

  • @ref: 76117
  • straininfo: 302641

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392191Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue.Endo A, Okada SInt J Syst Evol Microbiol10.1099/ijs.0.64618-02007Alcoholic Beverages/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fermentation, Japan, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Genetics24675866Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shochu Residue.Yuki M, Oshima K, Suda W, Kitahara M, Kitamura K, Iida T, Hattori M, Ohkuma MGenome Announc10.1128/genomeA.00257-142014Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7364Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18382)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18382
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
31901Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2815928776041
36536Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7324
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
76117Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302641.1StrainInfo: A central database for resolving microbial strain identifiers
119287Curators of the CIPCollection of Institut Pasteur (CIP 109567)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109567