Strain identifier

BacDive ID: 6417

Type strain: Yes

Species: Ligilactobacillus araffinosus

Strain Designation: ML2

Strain history: CIP <- 1988, DSM <- T. Mitsuoka: strain ML2

NCBI tax ID(s): 1423820 (strain), 147809 (species)

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General

@ref: 8873

BacDive-ID: 6417

DSM-Number: 20653

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

description: Ligilactobacillus araffinosus ML2 is an anaerobe, mesophilic bacterium that was isolated from intestine of chicken.

NCBI tax id

NCBI tax idMatching level
147809species
1423820strain

strain history

@refhistory
8873<- T. Mitsuoka, ML2
67770T. Fujisawa ML 2.
116469CIP <- 1988, DSM <- T. Mitsuoka: strain ML2

doi: 10.13145/bacdive6417.20230509.8.1

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 araffinosus
  • full scientific name: Ligilactobacillus araffinosus (Fujisawa et al. 1986) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus aviarius subsp. araffinosus

@ref: 8873

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus araffinosus

full scientific name: Ligilactobacillus araffinosus (Fujisawa et al. 1986) Zheng et al. 2020

strain designation: ML2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.467
69480100positive
116469nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8873BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water
8873MRS 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
40538MEDIUM 43 - for Lactobacillus hamsteri and Lactobacillus ruminisyesDistilled water make up to (900.000 ml);Man Rogosa Sharp broth (55.000 g);Cysteine hydrochloride 5 % solution - M0172 (100.000 ml)
116469CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
8873positivegrowth37mesophilic
40538positivegrowth37mesophilic
50914positivegrowth37mesophilic
67770positivegrowth37mesophilic
116469positivegrowth37mesophilic
116469nogrowth15psychrophilic
116469nogrowth25mesophilic
116469nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8873anaerobe
50914anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.974

murein

  • @ref: 8873
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

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
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116469nitrate-reduction17632
116469nitrite-reduction16301
116469nitrate+respiration17632

metabolite production

  • @ref: 116469
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 116469
  • 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
116469oxidase-
116469alcohol dehydrogenase+1.1.1.1
116469catalase-1.11.1.6
116469lysine decarboxylase-4.1.1.18
116469ornithine decarboxylase-4.1.1.17
116469urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    50914C14:0614
    50914C16:036.716
    50914C18:010.818
    50914C16:1 ω7c5.315.819
    50914C18:1 ω7c /12t/9t18.417.824
    50914C18:1 ω9c11.617.769
    50914C18:2 ω6,9c/C18:0 ANTE11.317.724
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116469-+--------++--++----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8873-----------+++--------------+--++-----------------
116469-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8873intestine of chicken
50914Chicken duodenum
67770Chicken duodenum
116469Animal, Intestinal content, healthy chicken

isolation source categories

Cat1Cat2Cat3
#Host#Birds#Chicken
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_4454.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_2227;97_2697;98_3347;99_4454&stattab=map
  • Last taxonomy: Ligilactobacillus
  • 16S sequence: JX986976
  • Sequence Identity:
  • Total samples: 26439
  • soil counts: 1429
  • aquatic counts: 1732
  • animal counts: 22696
  • plant counts: 582

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88731Risk group (German classification)
1164691Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus aviarius subsp. araffinosus gene for 16S rRNA, partial sequence, strain: JCM 5667AB289043680ena147809
20218Lactobacillus aviarius subsp. araffinosus strain LMG 23560 16S ribosomal RNA gene, partial sequenceJX9869761515ena147809
67770Lactobacillus aviarius subsp. araffinosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5667LC0718261496ena147809

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus aviarius subsp. araffinosus DSM 206531423820.4wgspatric1423820
66792Ligilactobacillus aviarius araffinosus DSM 206532660238151draftimg1423820
67770Ligilactobacillus araffinosus DSM 20653GCA_001435375scaffoldncbi1423820

GC content

  • @ref: 8873
  • GC-content: 41.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.557no
gram-positiveyes95.291no
anaerobicno66.216yes
halophileyes86.529no
spore-formingno96.607no
thermophileno99.124no
glucose-utilyes92.33no
aerobicno96.512yes
flagellatedno98.828no
glucose-fermentyes89.165no

External links

@ref: 8873

culture collection no.: CCUG 32231, JCM 5667, DSM 20653, ATCC 43235, CIP 103145, LMG 23560, NCFB 2785

straininfo link

  • @ref: 75892
  • straininfo: 265419

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8873Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20653)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20653
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
40538Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14910
50914Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32231)https://www.ccug.se/strain?id=32231
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
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
75892Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265419.1StrainInfo: A central database for resolving microbial strain identifiers
116469Curators of the CIPCollection of Institut Pasteur (CIP 103145)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103145