Strain identifier

BacDive ID: 6548

Type strain: Yes

Species: Lacticaseibacillus paracasei

Strain Designation: RO94

Strain history: CIP <- 1993, F. Gasser, Inst. Pasteur, Paris, France <- NCDO, Lactobacillus casei

NCBI tax ID(s): 525337 (strain), 1597 (species)

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General

@ref: 2263

BacDive-ID: 6548

DSM-Number: 5622

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

description: Lacticaseibacillus paracasei RO94 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from Milk products.

NCBI tax id

NCBI tax idMatching level
1597species
525337strain

strain history

@refhistory
2263<- NCDO <- NIRD, RO94 (Lactobacillus casei)
67770NCFB 151 <-- NIRD.
121547CIP <- 1993, F. Gasser, Inst. Pasteur, Paris, France <- NCDO, Lactobacillus casei

doi: 10.13145/bacdive6548.20230509.8.1

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 paracasei
  • full scientific name: Lacticaseibacillus paracasei (Collins et al. 1989) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus paracasei

@ref: 2263

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lacticaseibacillus

species: Lacticaseibacillus paracasei subsp. paracasei

full scientific name: Lacticaseibacillus paracasei subsp. paracasei (Collins et al. 1989) Zheng et al. 2020

strain designation: RO94

type strain: yes

Morphology

cell morphology

  • @ref: 121547
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2263MRS 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
34920MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121547CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
2263positivegrowth30mesophilic
34920positivegrowth30mesophilic
50901positivegrowth30mesophilic
50901positivegrowth37mesophilic
67770positivegrowth30mesophilic
121547positivegrowth15-37
121547nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
50901anaerobe
50901microaerophile
121547facultative anaerobe

murein

  • @ref: 2263
  • 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
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
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-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
121547nitrate-reduction17632
121547nitrite-reduction16301
121547nitrate+respiration17632

antibiotic resistance

  • @ref: 121547
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

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
121547oxidase-
121547alcohol dehydrogenase-1.1.1.1
121547catalase-1.11.1.6
121547lysine decarboxylase-4.1.1.18
121547ornithine 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
121547-+++-+++--++---++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
2263-----+----++++----+---+-++++++-++-+----++-+-------
2263-----+----++++----+---+-++++-+--+-+-----+-+-------
2263-----+----++++----+---+-++++++--+-+----++-+-------
2263-----+----++++----+---+-++++-+--+-+-----+-+-------
2263-----+----++++----+---+-++++-+-++-+----++-+----+--
2263-----+----++++----+---+-++++++-++-+----++-+----+--
121547----+----++++----+---+-++++++/---+/--+/------+/--+/-----+/---
2263-----+----++++----+---+-++++++-++-+----++-+-------

Isolation, sampling and environmental information

isolation

@refsample type
50901Milk products
67770Milk products

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Dairy product
#Host Body Product#Fluids#Milk

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: LC096209
  • Sequence Identity:
  • Total samples: 44444
  • soil counts: 1801
  • aquatic counts: 2397
  • animal counts: 39363
  • plant counts: 883

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
2263yes, in single cases1Risk group (German classification)
1215471Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus paracasei strain ATCC 25302 16S ribosomal RNA gene, partial sequenceHQ4231651441ena1597
20218Lactobacillus paracasei subsp. paracasei strain CECT 4022 16S ribosomal RNA gene, partial sequenceAY196966525ena47714
20218Lactobacillus paracasei subsp. paracasei genes for 16S rRNA, 16S-23S internal transcribed spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain:JCM 8130AB237506572ena47714
20218Lactobacillus paracasei subsp. paracasei genes for 16S rRNA, 16S-23S internal transcribed spacer, 23S rRNA, partial sequence, strain:JCM 8130AB237507364ena47714
20218Lactobacillus paracasei subsp. paracasei gene for 16S rRNA, partial sequence, strain: JCM 8130AB289225670ena47714
20218Lactobacillus paracasei subsp. paracasei gene for 16S rRNA, partial sequenceD792121522ena47714
20218Lactobacillus paracasei subsp. paracasei gene for 16S rRNA, partial sequence, strain: NBRC 15889AB6260541495ena47714
20218Lactobacillus casei gene for 16S rRNA, partial sequence, strain: YIT 0209 (= NCDO 151)AB0082051561ena1582
67770Lactobacillus paracasei subsp. paracasei gene for 16S ribosomal RNA, partial sequence, strain: JCM 8130LC0962091511ena47714

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lacticaseibacillus paracasei subsp. paracasei JCM 8130GCA_000829035completencbi47714
66792Lacticaseibacillus paracasei subsp. paracasei NBRC 15889GCA_007989125contigncbi47714
66792Lactobacillus paracasei subsp. paracasei ATCC 25302525337.3wgspatric525337
66792Lactobacillus paracasei subsp. paracasei DSM 56221423829.3wgspatric525337
66792Lactobacillus paracasei subsp. paracasei JCM 81301226298.3completepatric525337
66792Lactobacillus paracasei subsp. paracasei JCM 81301226298.10plasmidpatric525337
66792Lactobacillus paracasei subsp. paracasei JCM 81301226298.9plasmidpatric525337
66792Lactobacillus paracasei subsp. paracasei strain ATCC 2530247714.15wgspatric47714
66792Lactobacillus paracasei subsp. paracasei strain NBRC 1588947714.17wgspatric47714
66792Lactobacillus paracasei paracasei JCM 81302912347755completeimg1226298
66792Lacticaseibacillus paracasei paracasei DSM 56222667528038draftimg1423829
66792Lacticaseibacillus paracasei subsp. paracasei ATCC 25302643886051draftimg525337
67770Lacticaseibacillus paracasei subsp. paracasei ATCC 25302 = DSM 5622 = JCM 8130GCA_000159495scaffoldncbi525337
67770Lacticaseibacillus paracasei subsp. paracasei ATCC 25302 = DSM 5622 = JCM 8130GCA_001436385contigncbi525337
67770Lacticaseibacillus paracasei subsp. paracasei ATCC 25302GCA_004354655scaffoldncbi47714

GC content

  • @ref: 67770
  • GC-content: 46.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.945no
gram-positiveyes95.702no
anaerobicno95.248no
aerobicno95.191yes
halophileyes74.49no
spore-formingno90.493no
thermophileno97.201yes
glucose-utilyes90.748no
flagellatedno97.851no
glucose-fermentyes89.066no

External links

@ref: 2263

culture collection no.: DSM 5622, ATCC 25302, NCDO 151, CCUG 32212, LMG 13087, JCM 8130, CIP 103918, NBRC 15889, AS 1.2826, BCRC 12248, CECT 4022, IFO 15889, KCTC 3510, NCFB 151, NRIC 0950

straininfo link

  • @ref: 76019
  • straininfo: 7366

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1512565Cloning, sequencing and expression of the gene encoding the cell-envelope-associated proteinase from Lactobacillus paracasei subsp. paracasei NCDO 151.Holck A, Naes HJ Gen Microbiol10.1099/00221287-138-7-13531992Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Base Sequence, Blotting, Southern, Cell Membrane/*enzymology, Cloning, Molecular, DNA, Bacterial, Endopeptidases/*genetics/metabolism, Genes, Bacterial, Lactobacillus/*enzymology/genetics, Metalloendopeptidases/*genetics/metabolism, Molecular Sequence Data, Restriction Mapping, Sequence Homology, Nucleic AcidMetabolism
Enzymology1564442Purification and N-terminal amino acid sequence determination of the cell-wall-bound proteinase from Lactobacillus paracasei subsp. paracasei.Naes H, Nissen-Meyer JJ Gen Microbiol10.1099/00221287-138-2-3131992Amino Acid Sequence, Cell Wall/*enzymology, Chromatography, Gel, Chromatography, Ion Exchange, Electrophoresis, Polyacrylamide Gel, Endopeptidases/*chemistry/isolation & purification, Lactobacillus/*enzymology/ultrastructure, Molecular Sequence DataGenetics
Biotechnology2246138Lactobacilli isolated from sugary kefir grains capable of polysaccharide production and minicell formation.Pidoux M, Marshall VM, Zanoni P, Brooker BJ Appl Bacteriol10.1111/j.1365-2672.1990.tb01521.x1990Animals, DNA, Bacterial/analysis, *Food Microbiology, Hydrogen-Ion Concentration, Lactobacillus/*classification/genetics/growth & development/metabolism, Microscopy, Electron, *Milk, Nucleic Acid Hybridization, Phenotype, Polysaccharides, Bacterial/*biosynthesis, TemperaturePhylogeny
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
Phylogeny15630189Isolation and identification of lactic acid bacteria with effect of immune protection to Eschericia coli in mice.Ishida-Fujii K, Goto S, Kuboki H, Hirano S, Sakamoto M, Sato MBiofactors10.1002/biof.5522101312004Anaerobiosis, Animals, Escherichia coli/*immunology, Gram-Positive Bacterial Infections/*immunology, Lactobacillus/*growth & development/immunology, Male, Mice, Mice, Inbred ICR
Phylogeny22021580Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis).Volokhov DV, Amselle M, Beck BJ, Popham DL, Whittaker P, Wang H, Kerrigan E, Chizhikov VEInt J Syst Evol Microbiol10.1099/ijs.0.033852-02011Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/analysis, Feces/microbiology, Geese/*microbiology, Genes, Bacterial, Genotype, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Biotechnology22060654Accelerated production of dry fermented sausage.Blom H, Hagen BF, Pedersen BO, Holck AL, Axelsson L, Naes HMeat Sci10.1016/0309-1740(96)00068-x1996
Enzymology25533632Antibacterial activity of a cell wall hydrolase from Lactobacillus paracasei NRRL B-50314 produced by recombinant Bacillus megaterium.Liu S, Rich JO, Anderson AJ Ind Microbiol Biotechnol10.1007/s10295-014-1557-62014Amino Acid Sequence, Anti-Bacterial Agents/*pharmacology, Bacillus megaterium/*metabolism, Cell Wall/*enzymology, Chromatography, Liquid, Cloning, Molecular, Computational Biology, Gram-Positive Bacteria/drug effects, Hydrolases/biosynthesis/*pharmacology, Lactobacillus/*enzymology, Molecular Sequence Data, Plasmids, Recombinant Proteins/biosynthesis, Tandem Mass Spectrometry, Xylose/metabolismMetabolism
Pathogenicity28103748Stabilization of freeze-dried Lactobacillus paracasei subsp. paracasei JCM 8130(T) with the addition of disaccharides, polymers, and their mixtures.Teng D, Kawai K, Mikajiri S, Hagura YBiosci Biotechnol Biochem10.1080/09168451.2017.12798522017Animals, Cattle, Disaccharides/chemistry, *Food Microbiology, Freeze Drying, Humans, Lactobacillus paracasei/chemistry/*drug effects, Polysaccharides/pharmacology, Serum Albumin, Bovine/pharmacology, Sucrose/pharmacology, Temperature, Trehalose/pharmacology, Water/chemistryBiotechnology
Enzymology29915223Probiotic Lactobacillus paracasei A221 improves the functionality and bioavailability of kaempferol-glucoside in kale by its glucosidase activity.Shimojo Y, Ozawa Y, Toda T, Igami K, Shimizu TSci Rep10.1038/s41598-018-27532-92018Animals, Biological Availability, Brassica/*chemistry, Caco-2 Cells, Cell Line, Tumor, Glucosides/*pharmacokinetics, Humans, Kaempferols/*pharmacokinetics, Lactobacillus paracasei/*physiology, Male, Mice, Mice, Inbred C57BL, Plant Extracts/*pharmacokinetics, Probiotics/*pharmacologyPathogenicity
Phylogeny31534458In Vitro Evaluation of Probiotic Properties of Lactic Acid Bacteria Isolated from Some Traditionally Fermented Ethiopian Food Products.Mulaw G, Sisay Tessema T, Muleta D, Tesfaye AInt J Microbiol10.1155/2019/71795142019
Genetics32350548Whole-genome sequence and comparative genome analysis of Lactobacillus paracasei DTA93, a promising probiotic lactic acid bacterium.Tarrah A, Pakroo S, Corich V, Giacomini AArch Microbiol10.1007/s00203-020-01883-22020Feces/microbiology, Genome, Bacterial/*genetics, Genomics, Humans, Infant, Lactobacillus paracasei/*genetics/isolation & purification, Probiotics, Whole Genome SequencingPathogenicity
Phylogeny34134621Characterization of a bacterial strain Lactobacillus paracasei LP10266 recovered from an endocarditis patient in Shandong, China.Tang Q, Hao Y, Wang L, Lu C, Li M, Si Z, Wu X, Lu ZBMC Microbiol10.1186/s12866-021-02253-82021Biofilms, China, Endocarditis, Bacterial/*microbiology, Genome, Bacterial, Humans, Lactobacillus paracasei/classification/genetics/*isolation & purification/physiology, Male, Middle Aged, PhylogenyGenetics
Phylogeny34721319Comparison of 16S rRNA Gene Based Microbial Profiling Using Five Next-Generation Sequencers and Various Primers.Park C, Kim SB, Choi SH, Kim SFront Microbiol10.3389/fmicb.2021.7155002021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2263Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5622)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5622
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
34920Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15769
50901Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32212)https://www.ccug.se/strain?id=32212
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
76019Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7366.1StrainInfo: A central database for resolving microbial strain identifiers
121547Curators of the CIPCollection of Institut Pasteur (CIP 103918)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103918