Strain identifier

BacDive ID: 6644

Type strain: Yes

Species: Lentilactobacillus parafarraginis

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

NCBI tax ID(s): 390842 (species)

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

@ref: 7519

BacDive-ID: 6644

DSM-Number: 18390

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

description: Lentilactobacillus parafarraginis DSM 18390 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from composting material of distilled shochun residue.

NCBI tax id

  • NCBI tax id: 390842
  • Matching level: species

strain history

@refhistory
7519<- Akihito Endo, NRIC 0677
67770A. Endo NRIC 0677.
121553CIP <- 2007, JCM <- 2006, NRIC

doi: 10.13145/bacdive6644.20230509.8.1

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

    • @ref: 20215
    • synonym: Lactobacillus parafarraginis

@ref: 7519

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lentilactobacillus

species: Lentilactobacillus parafarraginis

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

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31901positive02-04 µm0.8 µmrod-shaped
121553positiverod-shapedno

pigmentation

  • @ref: 31901
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7519MRS 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
36080MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121553CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
7519positivegrowth30mesophilic
31901positivegrowth20-37
31901positiveoptimum28.5mesophilic
36080positivegrowth37mesophilic
67770positivegrowth30mesophilic
121553positivegrowth22-37
121553nogrowth10psychrophilic
121553nogrowth15psychrophilic
121553nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31901positivegrowth4-8.5alkaliphile
31901positiveoptimum6.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7519microaerophile
31901facultative anaerobe
121553facultative anaerobe

halophily

  • @ref: 31901
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 5 %

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
3190118222xylose+carbon source
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
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
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-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
12155317632nitrate-reduction
12155316301nitrite-reduction
12155317632nitrate+respiration

metabolite tests

  • @ref: 121553
  • 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
121553oxidase-
121553alcohol dehydrogenase-1.1.1.1
121553catalase-1.11.1.6
121553lysine decarboxylase-4.1.1.18
121553ornithine 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
121553----------+++++++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7519----+++---++++----+---------+-++--++---------+-+-+
121553---+++---++++/-----+/----------++/-++--++---------+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7519composting material of distilled shochun residueMiyazaki prefectureJapanJPNAsia
67770Compost of distilled shochu residue
121553Environment, 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_1582.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_367;97_831;98_1249;99_1582&stattab=map
  • Last taxonomy: Lentilactobacillus parafarraginis
  • 16S sequence: LC096238
  • Sequence Identity:
  • Total samples: 2392
  • soil counts: 201
  • aquatic counts: 226
  • animal counts: 1720
  • plant counts: 245

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75191Risk group (German classification)
1215531Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7519Lactobacillus parafarraginis gene for 16S rRNA, partial sequence, strain: NRIC 0677AB2627341556ena390842
67770Lactobacillus parafarraginis gene for 16S ribosomal RNA, partial sequence, strain: JCM 14109LC0962381510ena390842

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus parafarraginis DSM 18390 = JCM 141091423786.4wgspatric1423786
66792Lactobacillus parafarraginis DSM 18390 = JCM 141091423786.3wgspatric1423786
66792Lentilactobacillus parafarraginis DSM 183902700989151draftimg1423786
66792Lentilactobacillus parafarraginis JCM 141092728369682draftimg1423786
67770Lentilactobacillus parafarraginis DSM 18390 = JCM 14109GCA_001435895scaffoldncbi1423786
67770Lentilactobacillus parafarraginis DSM 18390 = JCM 14109GCA_001311355contigncbi1423786

GC content

@refGC-contentmethod
751940
6777045.2genome sequence analysis
6777040high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.347no
gram-positiveyes96.957no
anaerobicno93.568yes
halophileyes90.021no
spore-formingno91.669no
thermophileno99.615yes
glucose-utilyes89.466no
aerobicno94.202no
flagellatedno97.863no
glucose-fermentyes83.645no

External links

@ref: 7519

culture collection no.: DSM 18390, JCM 14109, NRIC 0677, CIP 109568

straininfo link

  • @ref: 76118
  • straininfo: 302674

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
Phylogeny23223818Lactobacillus curieae sp. nov., isolated from stinky tofu brine.Lei X, Sun G, Xie J, Wei DInt J Syst Evol Microbiol10.1099/ijs.0.041830-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Food Microbiology, Genes, Bacterial, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salts, Sequence Analysis, DNA, Soy Foods/*microbiologyBiotechnology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7519Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18390)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18390
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
36080Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7326
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
76118Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302674.1StrainInfo: A central database for resolving microbial strain identifiers
121553Curators of the CIPCollection of Institut Pasteur (CIP 109568)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109568