Strain identifier

BacDive ID: 6646

Type strain: Yes

Species: Ligilactobacillus apodemi

Strain Designation: ASB1, ASB-1

Strain history: CIP <- 2005, DSMZ <- R. Osawa, Kobe Univ., Kobe, Japan: strain ASB-1

NCBI tax ID(s): 307126 (species)

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

@ref: 6537

BacDive-ID: 6646

DSM-Number: 16634

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

description: Ligilactobacillus apodemi ASB1 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from feces, wild Japanese wood mouse.

NCBI tax id

  • NCBI tax id: 307126
  • Matching level: species

strain history

@refhistory
6537<- R. Osawa; ASB1
67770CIP 108913 <-- DSM 16634 <-- R. Osawa ASB1.
116423CIP <- 2005, DSMZ <- R. Osawa, Kobe Univ., Kobe, Japan: strain ASB-1

doi: 10.13145/bacdive6646.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Ligilactobacillus
  • species: Ligilactobacillus apodemi
  • full scientific name: Ligilactobacillus apodemi (Osawa et al. 2006) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus apodemi

@ref: 6537

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus apodemi

full scientific name: Ligilactobacillus apodemi (Osawa et al. 2006) Zheng et al. 2020

strain designation: ASB1, ASB-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31735positive05-06 µm0.5-1 µmrod-shapedno
69480positive100
116423positiverod-shapedno

pigmentation

  • @ref: 31735
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6537MRS 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
38184MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116423CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
6537positivegrowth37mesophilic
31735positivegrowth25-45
31735positiveoptimum25-37mesophilic
38184positivegrowth37mesophilic
67770positivegrowth37mesophilic
116423positivegrowth30-37mesophilic
116423nogrowth10psychrophilic
116423nogrowth15psychrophilic
116423nogrowth22psychrophilic

culture pH

@refabilitytypepH
31735positivegrowth7
31735positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6537anaerobe
6537microaerophile
31735anaerobe
116423facultative anaerobe

spore formation

@refspore formationconfidence
31735no
69481no100
69480no99.987

observation

  • @ref: 31735
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3173528757fructose+carbon source
3173528260galactose+carbon source
3173517234glucose+carbon source
3173524996lactate+carbon source
3173517716lactose+carbon source
3173517306maltose+carbon source
3173537684mannose+carbon source
3173528053melibiose+carbon source
31735506227N-acetylglucosamine+carbon source
3173516634raffinose+carbon source
3173517992sucrose+carbon source
3173527082trehalose+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
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127613amygdalin-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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11642317632nitrate-reduction
11642316301nitrite-reduction
11642317632nitrate+respiration

metabolite tests

  • @ref: 116423
  • 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
116423oxidase-
116423alcohol dehydrogenase-1.1.1.1
116423catalase-1.11.1.6
116423lysine decarboxylase-4.1.1.18
116423ornithine 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
116423-----++---++-+-+--+-

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6537-----+-----+++--------+-+++++++++--+--------------
6537----------++++--------+-+++++++++--+--------------
116423---------+/-+/-+/-+/---------+/--+/-+/-+/-+/-+/-+/-+/-+/-+/---+/---------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6537feces, wild Japanese wood mouseKyotanabeJapanJPNAsia
67770Wild mouse fecesKyotanabeJapanJPNAsia
116423Animal, Wild Japanese wood mouseKyotanabeJapanJPNAsia2002

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7017.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_871;97_1018;98_1201;99_7017&stattab=map
  • Last taxonomy: Ligilactobacillus apodemi
  • 16S sequence: LC519852
  • Sequence Identity:
  • Total samples: 68252
  • soil counts: 1119
  • aquatic counts: 731
  • animal counts: 66125
  • plant counts: 277

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65371Risk group (German classification)
1164231Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus apodemi gene for 16S ribosomal RNA, partial sequence, strain: DSM 16634AB3708741487ena307126
6537Lactobacillus apodemi 16S rRNA gene, type strain ASB1TAJ8711781532ena307126
67770Lactobacillus apodemi JCM 16172 gene for 16S rRNA, partial sequenceLC5198521504ena307126

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus apodemi DSM 16634 = JCM 161721423724.4wgspatric1423724
66792Lactobacillus apodemi JCM 161721236952.3wgspatric1423724
66792Ligilactobacillus apodemi JCM 161722585427873draftimg1423724
66792Ligilactobacillus apodemi DSM 166342675903500draftimg1423724
67770Ligilactobacillus apodemi DSM 16634 = JCM 16172GCA_001434405scaffoldncbi1423724
67770Ligilactobacillus apodemi DSM 16634 = JCM 16172GCA_000615885contigncbi1423724

GC content

@refGC-contentmethod
653738.5
6777038.5high performance liquid chromatography (HPLC)
6777038.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.591yes
gram-positiveyes95.176yes
anaerobicno90.125no
halophileyes86.851no
spore-formingno93.684yes
glucose-utilyes92.54no
thermophileno97.939no
aerobicno98.086yes
flagellatedno98.197yes
glucose-fermentyes91.967no

External links

@ref: 6537

culture collection no.: DSM 16634, CIP 108913, JCM 16172, NCIMB 14359

straininfo link

  • @ref: 76120
  • straininfo: 292425

literature

  • topic: Phylogeny
  • Pubmed-ID: 16825652
  • title: Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces.
  • authors: Osawa R, Fujisawa T, Pukall R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64147-0
  • year: 2006
  • mesh: Animals, Bacterial Infections/*microbiology/*veterinary, Base Composition, Carbohydrate Metabolism, Carboxylic Ester Hydrolases/*biosynthesis, Cell Wall/chemistry, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Genes, rRNA, Lactobacillus/*classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, Murinae/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6537Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16634)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16634
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
31735Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128011
38184Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6596
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
76120Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292425.1StrainInfo: A central database for resolving microbial strain identifiers
116423Curators of the CIPCollection of Institut Pasteur (CIP 108913)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108913