Strain identifier

BacDive ID: 6564

Type strain: Yes

Species: Lacticaseibacillus zeae

Strain history: CIP <- 1988, DSM, Lactobacillus rhamnosus <- ATCC <- USRR: strain RIA 482 Lactobacterium zeae

NCBI tax ID(s): 57037 (species)

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General

@ref: 8608

BacDive-ID: 6564

DSM-Number: 20178

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

description: Lacticaseibacillus zeae DSM 20178 is a facultative anaerobe, mesophilic, rod-shaped bacterium that was isolated from corn steep liquor.

NCBI tax id

  • NCBI tax id: 57037
  • Matching level: species

strain history

@refhistory
8608<- ATCC <- RIA (Lactobacterium zeae)
67770ATCC 15820 <-- RIA 482.
67771<- CCUG <- DSM <- ATCC <- RIA 482, `Lactobacterium zeae`
124024CIP <- 1988, DSM, Lactobacillus rhamnosus <- ATCC <- USRR: strain RIA 482 Lactobacterium zeae

doi: 10.13145/bacdive6564.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lacticaseibacillus
  • species: Lacticaseibacillus zeae
  • full scientific name: Lacticaseibacillus zeae (Dicks et al. 1996 ex Kuznetsov 1959) Liu and Gu 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus zeae

@ref: 8608

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lacticaseibacillus

species: Lacticaseibacillus zeae

full scientific name: Lacticaseibacillus zeae (Dicks et al. 1996) Liu and Gu 2020

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stain
67771rod-shapedno
67771positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8608MRS 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
40580MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
124024CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
8608positivegrowth37mesophilic
40580positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: facultative anaerobe

murein

  • @ref: 8608
  • 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
68371L-arabitol-builds acid from18403
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371galactitol-builds acid from16813
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
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754

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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
124024--------------------

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8608-----+----++++-+--+---++++++---++-+-------+-+-----
8608---+-+----++++-+-+/-+---++++++++-++-+----+--+-++-++-
124024-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample type
8608corn steep liquor
52785Corn steep liquor
67771From corn steep ilquor
124024Food, Corn steep liquor

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Beverage
#Engineered#Food production#Fermented
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_113.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_88;97_93;98_102;99_113&stattab=map
  • Last taxonomy: Lactobacillaceae
  • 16S sequence: AB008213
  • Sequence Identity:
  • Total samples: 44444
  • soil counts: 1801
  • aquatic counts: 2397
  • animal counts: 39363
  • plant counts: 883

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
86081Risk group (German classification)
1240241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus zeae gene for 16S rRNA, partial sequence, strain: YIT 0278 (= ATCC 15820)AB0082131559ena57037
20218Lactobacillus zeae ATCC 15820 16S ribosomal RNA gene, partial sequenceAF429522507ena57037
20218Lactobacillus zeae strain ATCC 15820 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF429609538ena57037
20218Lactobacillus zeae strain ATCC 15820 16S ribosomal RNA gene, partial sequenceAY196979518ena57037
20218Lactobacillus zeae gene for 16S ribosomal RNA, partial sequenceD865161522ena57037
20218Lactobacillus zeae genes for 16S rRNA, 16S-23S internal transcribed spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain:JCM 11302AB237514577ena57037
20218Lactobacillus zeae genes for 16S rRNA, 16S-23S internal transcribed spacer, 23S rRNA, partial sequence, strain:JCM 11302AB237515364ena57037
20218Lactobacillus zeae gene for 16S rRNA, partial sequence, strain: JCM 11302AB289313643ena57037

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus zeae DSM 20178 = KCTC 38041423816.3wgspatric1423816
66792Lactobacillus zeae KCTC 38041046597.4wgspatric1423816
66792Lactobacillus zeae KCTC 38042513237379draftimg1423816
66792Lactobacillus zeae DSM 201782667528132draftimg1423816
67770Lacticaseibacillus zeae DSM 20178 = KCTC 3804GCA_001433745scaffoldncbi1423816
67771Lacticaseibacillus zeae DSM 20178 = KCTC 3804GCA_000260435contigncbi1423816

GC content

@refGC-contentmethod
860848.0
6777048high performance liquid chromatography (HPLC)
6777148.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.365yes
gram-positiveyes96.332yes
anaerobicno95.536yes
halophileyes80.433no
spore-formingno89.389no
glucose-utilyes90.899no
thermophileno97.898no
aerobicno93.047yes
flagellatedno98.273yes
glucose-fermentyes90.799no

External links

@ref: 8608

culture collection no.: DSM 20178, ATCC 15820, RIA 482, CCUG 35515, KCTC 3804, JCM 11302, BCRC 17942, LMG 17315, NCIMB 9537, CIP 103253, NCIB 9537

straininfo link

  • @ref: 76036
  • straininfo: 264339

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8573516Reclassification of Lactobacillus casei subsp. casei ATCC 393 and Lactobacillus rhamnosus ATCC 15820 as Lactobacillus zeae nom. rev., designation of ATCC 334 as the neotype of L. casei subsp. casei, and rejection of the name Lactobacillus paracasei.Dicks LM, Du Plessis EM, Dellaglio F, Lauer EInt J Syst Bacteriol10.1099/00207713-46-1-3371996Base Sequence, DNA Primers, DNA, Bacterial/genetics, Lactobacillus/*classification/genetics, Lactobacillus casei/*classification/genetics, Molecular Sequence Data, Phylogeny, Polymorphism, Genetic, Random Amplified Polymorphic DNA TechniqueGenetics
Metabolism10772153Citrate utilization by homo- and heterofermentative lactobacilli.Medina de Figueroa R, Alvarez F, Pesce de Ruiz Holgado A, Oliver G, Sesma FMicrobiol Res10.1016/S0944-5013(00)80005-12000Acetoin/metabolism, *Bacterial Proteins, Biological Transport, Carrier Proteins/genetics/metabolism, Citrates/*metabolism, Culture Media, Diacetyl/metabolism, Fermentation, Genes, Bacterial, Glucose/metabolism, Lactobacillus/genetics/growth & development/*metabolism, SymportersCultivation
Phylogeny11760954Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group.Felis GE, Dellaglio F, Mizzi L, Torriani SInt J Syst Evol Microbiol10.1099/00207713-51-6-21132001DNA, Bacterial/genetics, Lactobacillus casei/*classification/genetics, Molecular Sequence Data, Phylogeny, Rec A Recombinases/*genetics, *Sequence Analysis, DNA, Species SpecificityTranscriptome
Phylogeny12656154Significant differences between Lactobacillus casei subsp. casei ATCC 393T and a commonly used plasmid-cured derivative revealed by a polyphasic study.Acedo-Felix E, Perez-Martinez GInt J Syst Evol Microbiol10.1099/ijs.0.02325-02003Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Lactobacillus casei/*classification/*genetics, Molecular Sequence Data, Phenotype, Plasmids/genetics, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Ribotyping, Species SpecificityGenetics
Phylogeny16094870DNA-based classification and sequence heterogeneities in the 16S rRNA genes of Lactobacillus casei/paracasei and related species.Vasquez A, Molin G, Pettersson B, Antonsson M, Ahrne SSyst Appl Microbiol10.1016/j.syapm.2005.02.0112005Base Sequence, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis, Electrophoresis, Agar Gel/methods, Genes, rRNA, *Genetic Variation, Humans, Lactobacillus/*classification/genetics, Lactobacillus casei/*classification/genetics, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, Prohibitins, RNA, Ribosomal, 16S/*genetics, Restriction Mapping, *Ribotyping, Sequence Analysis, DNAEnzymology
Pathogenicity21059159Protective effect of Lactobacillus casei strain Shirota against lethal infection with multi-drug resistant Salmonella enterica serovar Typhimurium DT104 in mice.Asahara T, Shimizu K, Takada T, Kado S, Yuki N, Morotomi M, Tanaka R, Nomoto KJ Appl Microbiol10.1111/j.1365-2672.2010.04884.x2010Acetic Acid/pharmacology, Animals, Disease Models, Animal, Drug Resistance, Multiple, Bacterial, Lactobacillus, *Lactobacillus casei, Male, Mice, Mice, Inbred BALB C, Probiotics/pharmacology/*therapeutic use, Salmonella Infections, Animal/pathology/*prevention & control, *Salmonella typhimurium/drug effects/growth & development
Genetics21868802Draft genome sequence of Lactobacillus zeae KCTC 3804.Kim DW, Choi SH, Kang A, Nam SH, Kim DS, Kim RN, Kim A, Park HSJ Bacteriol10.1128/JB.05602-112011Animals, Base Composition, Cattle, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Lactobacillus/*genetics/isolation & purification, Milk/microbiology, Molecular Sequence Data, *Sequence Analysis, DNATranscriptome
Phylogeny32421490Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae.Huang CH, Chen CC, Liou JS, Lee AY, Blom J, Lin YC, Huang L, Watanabe KInt J Syst Evol Microbiol10.1099/ijsem.0.0039692020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Lactobacillus/*classification, Lactobacillus casei/*classification, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8608Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20178)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20178
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
40580Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15030
52785Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35515)https://www.ccug.se/strain?id=35515
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
76036Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264339.1StrainInfo: A central database for resolving microbial strain identifiers
124024Curators of the CIPCollection of Institut Pasteur (CIP 103253)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103253