Strain identifier

BacDive ID: 6668

Type strain: Yes

Species: Agrilactobacillus composti

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

NCBI tax ID(s): 398555 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
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 8.1 (current version)

General

@ref: 7578

BacDive-ID: 6668

DSM-Number: 18527

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

description: Agrilactobacillus composti DSM 18527 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from composting material of distilled shochu residue.

NCBI tax id

  • NCBI tax id: 398555
  • Matching level: species

strain history

@refhistory
7578<- Akihito Endo, NRIC 0689
67770A. Endo NRIC 0689.
118715CIP <- 2007, JCM <- 2006, NRIC

doi: 10.13145/bacdive6668.20230509.8.1

Name and taxonomic classification

LPSN

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

    • @ref: 20215
    • synonym: Lactobacillus composti

@ref: 7578

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Agrilactobacillus

species: Agrilactobacillus composti

full scientific name: Agrilactobacillus composti (Endo and Okada 2007) Zheng et al. 2020

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31976positive02-06 µm0.8 µmrod-shapedno
69480no94.21
69480positive100
118715positiverod-shapedno

pigmentation

  • @ref: 31976
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7578MRS 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
37769MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
118715CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
7578positivegrowth30mesophilic
31976positivegrowth10-37
31976positiveoptimum23.5psychrophilic
37769positivegrowth37mesophilic
67770positivegrowth30mesophilic
118715positivegrowth10-37
118715nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31976positivegrowth3.5-9alkaliphile
31976positiveoptimum6.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7578microaerophile
31976anaerobe
118715facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

observation

  • @ref: 31976
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3197622599arabinose+carbon source
3197628757fructose+carbon source
3197628260galactose+carbon source
3197617234glucose+carbon source
3197617306maltose+carbon source
3197629864mannitol+carbon source
3197637684mannose+carbon source
3197628053melibiose+carbon source
3197626546rhamnose+carbon source
3197617814salicin+carbon source
3197630911sorbitol+carbon source
3197617992sucrose+carbon source
3197627082trehalose+carbon source
3197618222xylose+carbon source
68371Potassium 5-ketogluconate-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
6837116634raffinose-builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+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
6837117113erythritol-builds acid from
11871517632nitrate-reduction
11871516301nitrite-reduction
11871517632nitrate+respiration

metabolite tests

  • @ref: 118715
  • 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
118715oxidase-
118715alcohol dehydrogenase-1.1.1.1
118715catalase-1.11.1.6
118715lysine decarboxylase-4.1.1.18
118715ornithine 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
118715--+--++---+++--++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
7578----+-+--+++++++--++--+-+++-+-+/-++-+-----+---+-----
7578-+/---+-+--+++++++--++--+-+++-+--++-+-----+---+--++-
118715--+/-+-+--+++++++--++--+-+++-+--++-+-+/----+---+--+/-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7578composting material of distilled shochu residueMiyazaki prefectureJapanJPNAsia
67770Compost of distilled shochu residue
118715Environment, Compost of distilled shochu residueMiyazaki, KyushuJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8049.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_3720;97_4572;98_5867;99_8049&stattab=map
  • Last taxonomy: Agrilactobacillus composti subclade
  • 16S sequence: LC480800
  • Sequence Identity:
  • Total samples: 2461
  • soil counts: 76
  • aquatic counts: 201
  • animal counts: 1912
  • plant counts: 272

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75781Risk group (German classification)
1187151Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7578Lactobacillus composti gene for 16S rRNA, partial sequence, strain:NRIC 0689AB2681181522ena398555
67770Lactobacillus composti JCM 14202 gene for 16S ribosomal RNA, partial sequenceLC4808001499ena398555

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus composti DSM 18527 = JCM 142021423734.3wgspatric1423734
66792Lactobacillus composti JCM 142021236950.3wgspatric1423734
66792Agrilactobacillus composti JCM 142022576861770draftimg1423734
66792Agrilactobacillus composti DSM 185272700989152draftimg1423734
67770Agrilactobacillus composti DSM 18527 = JCM 14202GCA_001436375scaffoldncbi1423734
67770Agrilactobacillus composti DSM 18527 = JCM 14202GCA_000583695contigncbi1423734

GC content

@refGC-contentmethod
757847
6777047high performance liquid chromatography (HPLC)
6777044genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.571yes
gram-positiveyes95.603yes
anaerobicno91.81no
halophileyes71.517no
spore-formingno86.329no
thermophileno98.068yes
glucose-utilyes89.711yes
aerobicno94.439yes
flagellatedno95.173yes
glucose-fermentyes83.448no

External links

@ref: 7578

culture collection no.: DSM 18527, JCM 14202, NRIC 0689, CIP 109571

straininfo link

  • @ref: 76142
  • straininfo: 302642

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392222Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a compost of distilled shochu residue.Endo A, Okada SInt J Syst Evol Microbiol10.1099/ijs.0.64743-02007Alcoholic Beverages/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, 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
Enzymology28623564An NADPH-dependent Lactobacillus composti short-chain dehydrogenase/reductase: characterization and application to (R)-1-phenylethanol synthesis.Wang YJ, Ying BB, Chen M, Shen W, Liu ZQ, Zheng YGWorld J Microbiol Biotechnol10.1007/s11274-017-2311-92017Acetophenones/metabolism, Amino Acid Sequence, Bacterial Proteins/genetics/metabolism, Biocatalysis, Cloning, Molecular/*drug effects, Hydrogen-Ion Concentration, Lactobacillus/*enzymology/genetics, Molecular Weight, NADH, NADPH Oxidoreductases/*genetics/*metabolism, Open Reading Frames, Substrate Specificity, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7578Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18527)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18527
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
31976Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2823128776041
37769Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7329
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
76142Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302642.1StrainInfo: A central database for resolving microbial strain identifiers
118715Curators of the CIPCollection of Institut Pasteur (CIP 109571)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109571