Strain identifier

BacDive ID: 6407

Type strain: Yes

Species: Ligilactobacillus agilis

Strain Designation: 262

Strain history: CIP <- 1985, DSMZ <- N. Weiss: strain 262

NCBI tax ID(s): 1423718 (strain), 1601 (species)

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

@ref: 8858

BacDive-ID: 6407

DSM-Number: 20509

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, lactate production

description: Ligilactobacillus agilis 262 is an anaerobe, mesophilic bacterium that produces lactate and was isolated from municipal sewage.

NCBI tax id

NCBI tax idMatching level
1423718strain
1601species

strain history

@refhistory
8858<- N. Weiss, 262
67770DSM 20509 <-- N. Weiss 262.
116161CIP <- 1985, DSMZ <- N. Weiss: strain 262

doi: 10.13145/bacdive6407.20230509.8.1

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 agilis
  • full scientific name: Ligilactobacillus agilis (Weiss et al. 1982) Zheng et al. 2020
  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus agilis

@ref: 8858

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus agilis

full scientific name: Ligilactobacillus agilis (Weiss et al. 1982) Zheng et al. 2020

strain designation: 262

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8858MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232)yeshttps://mediadive.dsmz.de/medium/232Name: MRS MEDIUM WITH CYSTEINE (DSMZ Medium 232) 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)2 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
34906MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116161CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8858positivegrowth37mesophilic
34906positivegrowth37mesophilic
50605positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8858anaerobe
8858microaerophile

compound production

  • @ref: 8858
  • compound: (L+) lactic acid

murein

  • @ref: 8858
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8858-----+/-----++++----+---+++++++++++--+---+----------
116161-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
8858municipal sewage
50605Municipal sewage
67770Municipal sewage
116161Environment, Municipal sewageMünchenGermanyDEUEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_6918.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_3250;97_3988;98_5089;99_6918&stattab=map
  • Last taxonomy: Ligilactobacillus agilis subclade
  • 16S sequence: LC065041
  • Sequence Identity:
  • Total samples: 41290
  • soil counts: 1642
  • aquatic counts: 1961
  • animal counts: 36795
  • plant counts: 892

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88581Risk group (German classification)
1161611Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus agilis strain DSM 20509 16S ribosomal RNA gene, partial sequenceM588031511ena1601
20218Lactobacillus agilis gene for 16S rRNA, partial sequence, strain: JCM 1187AB5969451485ena1601
67770Lactobacillus agilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1187LC0650411462ena1601

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus agilis DSM 205091423718.3wgspatric1423718
66792Ligilactobacillus agilis DSM 205092667527581draftimg1423718
67770Ligilactobacillus agilis DSM 20509GCA_001436215scaffoldncbi1423718

GC content

@refGC-contentmethod
885843.6
6777041
6777041.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes53.049no
gram-positiveyes94.259no
anaerobicno85.715no
halophileyes85.529no
spore-formingno89.936no
glucose-utilyes92.208no
thermophileno97.98yes
aerobicno97.629yes
flagellatedno88.762no
glucose-fermentyes91.68no

External links

@ref: 8858

culture collection no.: DSM 20509, NCIB 11716, CCUG 31450, JCM 1187, BCRC 12931, CECT 4131, CIP 101264, KCTC 3606, LMG 9186, NCFB 2744, NCIMB 11716, NRIC 1642, NRRL B-14856, NCDO 2744

straininfo link

  • @ref: 75880
  • straininfo: 3201

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8858Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20509)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20509
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
34906Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12820
50605Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 31450)https://www.ccug.se/strain?id=31450
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
75880Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3201.1StrainInfo: A central database for resolving microbial strain identifiers
116161Curators of the CIPCollection of Institut Pasteur (CIP 101264)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20101264