Strain identifier

BacDive ID: 6682

Type strain: Yes

Species: Lactiplantibacillus fabifermentans

Strain Designation: R-34115

Strain history: <- L. De Vuyst and K. De Bruyne <- N. Camu, Vrije Univ. Brussels, Belgium; R-34115

NCBI tax ID(s): 1413187 (strain), 483011 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 15486

BacDive-ID: 6682

DSM-Number: 21115

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

description: Lactiplantibacillus fabifermentans R-34115 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from cocoa bean heap fermentation.

NCBI tax id

NCBI tax idMatching level
483011species
1413187strain

strain history

  • @ref: 15486
  • history: <- L. De Vuyst and K. De Bruyne <- N. Camu, Vrije Univ. Brussels, Belgium; R-34115

doi: 10.13145/bacdive6682.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactiplantibacillus
  • species: Lactiplantibacillus fabifermentans
  • full scientific name: Lactiplantibacillus fabifermentans (De Bruyne et al. 2009) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus fabifermentans

@ref: 15486

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactiplantibacillus

species: Lactiplantibacillus fabifermentans

full scientific name: Lactiplantibacillus fabifermentans (De Bruyne et al. 2009) Zheng et al. 2020

strain designation: R-34115

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28904positive10 µm2 µmrod-shapedno
125438positive92.159

pigmentation

  • @ref: 28904
  • production: no

Culture and growth conditions

culture medium

  • @ref: 15486
  • name: MRS MEDIUM (DSMZ Medium 11)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/11
  • composition: Name: 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

culture temp

@refgrowthtypetemperature
15486positivegrowth30
28904positivegrowth10-37
28904positiveoptimum23.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
15486microaerophile
28904facultative anaerobe
125439microaerophile95.4

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 93.1

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2890422599arabinose+carbon source
2890417057cellobiose+carbon source
2890428757fructose+carbon source
2890428260galactose+carbon source
2890417234glucose+carbon source
2890417306maltose+carbon source
2890429864mannitol+carbon source
2890437684mannose+carbon source
2890433942ribose+carbon source
2890417814salicin+carbon source
2890417992sucrose+carbon source
2890427082trehalose+carbon source
2890418222xylose+carbon source
289044853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
6837127613amygdalin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+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
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
6837159640N-acetylglucosamine+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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
15486----+-----++++----+---+++++++--++-----------------
15486----+++---++++----+---+++++++--++------+----------

Isolation, sampling and environmental information

isolation

  • @ref: 15486
  • sample type: cocoa bean heap fermentation
  • country: Ghana
  • origin.country: GHA
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_195.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_140;97_151;98_168;99_195&stattab=map
  • Last taxonomy: Lactobacillaceae
  • 16S sequence: AM905388
  • Sequence Identity:
  • Total samples: 38637
  • soil counts: 2696
  • aquatic counts: 4479
  • animal counts: 29069
  • plant counts: 2393

Safety information

risk assessment

  • @ref: 15486
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus fabifermentans gene for 16S rRNA, partial sequence, strain: DSM 21115AB6260751491nuccore483011
15486Lactobacillus fabifermentans partial 16S rRNA gene, type strain LMG 24284TAM9053881532nuccore483011

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactiplantibacillus fabifermentans DSM 21115GCA_000498955scaffoldncbi1413187
66792Lactobacillus fabifermentans DSM 211151578.21wgspatric1413187
66792Lactiplantibacillus fabifermentans DSM 211152563367174draftimg1413187

GC content

  • @ref: 15486
  • GC-content: 44.9

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.159yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no86.392yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.392yes
125438spore-formingspore-formingAbility to form endo- or exosporesno79.754no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.077no
125438motile2+flagellatedAbility to perform flagellated movementno87no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno93.1
125439BacteriaNetmotilityAbility to perform movementno73.5
125439BacteriaNetgram_stainReaction to gram-stainingpositive85.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile95.4

External links

@ref: 15486

culture collection no.: DSM 21115, LMG 24284

straininfo link

  • @ref: 76156
  • straininfo: 311003

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126714Lactobacillus fabifermentans sp. nov. and Lactobacillus cacaonum sp. nov., isolated from Ghanaian cocoa fermentations.De Bruyne K, Camu N, De Vuyst L, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.001172-02009Bacterial Proteins/chemistry/genetics, Bacterial Typing Techniques, Cacao/*metabolism/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fermentation, Genes, rRNA, Ghana, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityMetabolism
Phylogeny23950151Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough.Gu CT, Li CY, Yang LJ, Huo GCInt J Syst Evol Microbiol10.1099/ijs.0.054296-02013Bacterial Typing Techniques, Base Composition, Bread/microbiology, 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

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15486Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21115)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21115
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
28904Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125343
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)
68371Automatically annotated from API 50CH acid
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
76156Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID311003.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1