Strain identifier

BacDive ID: 6605

Type strain: No

Species: Ligilactobacillus acidipiscis

Strain Designation: LMK3

Strain history: CIP <- 2000, CCUG <- P. Lawson, Reading, UK: strain LMK3, "Lactobacillus halloumi"

NCBI tax ID(s): 1046599 (strain), 89059 (species)

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General

@ref: 5868

BacDive-ID: 6605

DSM-Number: 15353

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

description: Ligilactobacillus acidipiscis LMK3 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from cheese, Halloumi.

NCBI tax id

NCBI tax idMatching level
89059species
1046599strain

strain history

@refhistory
5868<- CIP <- CCUG <- P.A. Lawson <- P. Papademas and R. Robinson; LMK3 (Lactobacillus halloumi)
67770CIP 106393 <-- CCUG 42961 <-- P. A. Lawson LMK3.
116005CIP <- 2000, CCUG <- P. Lawson, Reading, UK: strain LMK3, "Lactobacillus halloumi"

doi: 10.13145/bacdive6605.20230509.8.1

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 acidipiscis
  • full scientific name: Ligilactobacillus acidipiscis (Tanasupawat et al. 2000) Zheng et al. 2020

  • synonyms

    @refsynonym
    20215Lactobacillus acidipiscis
    20215Lactobacillus cypricasei

@ref: 5868

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Ligilactobacillus

species: Ligilactobacillus acidipiscis

full scientific name: Ligilactobacillus acidipiscis (Tanasupawat et al. 2000) Zheng et al. 2020

strain designation: LMK3

type strain: no

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116005positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5868MRS 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
38621MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
40592MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116005CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
5868positivegrowth37mesophilic
38621positivegrowth37mesophilic
40592positivegrowth30mesophilic
67770positivegrowth37mesophilic
116005positivegrowth22-37
116005nogrowth10psychrophilic
116005nogrowth15psychrophilic
116005nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116005
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.986

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
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose+builds acid from17057
68371esculin+builds acid from4853
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-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
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
116005nitrate-reduction17632
116005nitrite-reduction16301
116005nitrate+respiration17632

metabolite tests

  • @ref: 116005
  • 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
116005oxidase-
116005alcohol dehydrogenase-1.1.1.1
116005catalase-1.11.1.6
116005lysine decarboxylase-4.1.1.18
116005ornithine 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
116005-++--+++---+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116005----+----++++--------+-+/-++/-+----+------+----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5868cheese, HalloumiCyprusCYPEurope
55623Cheese,Halloumi
67770Halloumi cheese
116005Food, Cheese

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Food production
  • Cat3: #Dairy product

taxonmaps

  • @ref: 69479
  • File name: preview.99_1644.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_937;97_1090;98_1300;99_1644&stattab=map
  • Last taxonomy: Ligilactobacillus
  • 16S sequence: AJ251560
  • Sequence Identity:
  • Total samples: 24138
  • soil counts: 1132
  • aquatic counts: 706
  • animal counts: 21773
  • plant counts: 527

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58681Risk group (German classification)
1160051Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5868
  • description: Lactobacillus sp. LMK3 16S rRNA gene, strain LMK3
  • accession: AJ251560
  • length: 1456
  • database: ena
  • NCBI tax ID: 89059

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ligilactobacillus acidipiscis DSM 15353GCA_001436945scaffoldncbi89059
66792Ligilactobacillus acidipiscis KCTC 13900GCA_000260635contigncbi1046599
66792Lactobacillus acidipiscis KCTC 139001046599.3wgspatric1046599
66792Lactobacillus acidipiscis strain DSM 1535389059.3wgspatric89059
66792Ligilactobacillus acidipiscis KCTC 139002513237304draftimg1046599
66792Ligilactobacillus acidipiscis DSM 153532663763314draftimg89059

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileyes59.321no
flagellatedno86.312no
gram-positiveyes94.45no
anaerobicno87.7no
aerobicno93.936no
halophileyes91.057no
spore-formingno90.738no
thermophileno98.187yes
glucose-utilyes90.75no
glucose-fermentyes88.556no

External links

@ref: 5868

culture collection no.: DSM 15353, CCUG 42961, CIP 106393, ATCC BAA 288, JCM 11551, KCTC 13900, NBRC 102164

straininfo link

  • @ref: 76079
  • straininfo: 376997

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11211271Lactobacillus cypricasei sp. nov., isolated from Halloumi cheese.Lawson PA, Papademas P, Wacher C, Falsen E, Robinson R, Collins MDInt J Syst Evol Microbiol10.1099/00207713-51-1-452001Bacterial Typing Techniques, Carbohydrate Metabolism, Cheese/*microbiology, DNA, Ribosomal/analysis/genetics, Genes, rRNA, Lactobacillus/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny19783610Lactobacillus pobuzihii sp. nov., isolated from pobuzihi (fermented cummingcordia).Chen YS, Miyashita M, Suzuki KI, Sato H, Hsu JS, Yanagida FInt J Syst Evol Microbiol10.1099/ijs.0.016873-02009Carbohydrate Metabolism, Cordia/metabolism/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fermentation, Lactobacillus/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Genetics21742864Genome sequence of Lactobacillus cypricasei KCTC 13900.Kim DS, Choi SH, Kim DW, Kim RN, Nam SH, Kang A, Kim A, Park HSJ Bacteriol10.1128/JB.05659-112011Cheese/microbiology, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Lactobacillus/*genetics/isolation & purification, Molecular Sequence Data, *Sequence Analysis, DNATranscriptome
Genetics25501479Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade.Cousin FJ, Lynch SM, Harris HM, McCann A, Lynch DB, Neville BA, Irisawa T, Okada S, Endo A, O'Toole PWAppl Environ Microbiol10.1128/AEM.03594-142015Bacterial Proteins/genetics/metabolism, Flagellin/genetics/metabolism, Gene Expression Regulation, Bacterial, *Genome, Bacterial, Genomics, Lactobacillus/classification/*cytology/*genetics/metabolism, Operon, PhylogenyMetabolism
Genetics29942291Comparative Genomics of Lactobacillus acidipiscis ACA-DC 1533 Isolated From Traditional Greek Kopanisti Cheese Against Species Within the Lactobacillus salivarius Clade.Kazou M, Alexandraki V, Blom J, Pot B, Tsakalidou E, Papadimitriou KFront Microbiol10.3389/fmicb.2018.012442018Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5868Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15353)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15353
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
38621Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18518
40592Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18915
55623Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 42961)https://www.ccug.se/strain?id=42961
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
76079Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID376997.1StrainInfo: A central database for resolving microbial strain identifiers
116005Curators of the CIPCollection of Institut Pasteur (CIP 106393)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106393