Strain identifier

BacDive ID: 6422

Type strain: Yes

Species: Lentilactobacillus buchneri

Strain history: CIP <- 1987, NCIB <- 1950, ATCC <- C.S. Pederson <- R.S. Breed <- F.L. Mickle, Lactobacillus lycopersici

NCBI tax ID(s): 1581 (species)

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General

@ref: 8488

BacDive-ID: 6422

DSM-Number: 20057

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

description: Lentilactobacillus buchneri DSM 20057 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from tomato pulp.

NCBI tax id

  • NCBI tax id: 1581
  • Matching level: species

strain history

@refhistory
8488<- ATCC <- C.S. Pederson <- R.S. Breed <- F.L. Mickle (Lactobacillus lycopersici)
67770ATCC 4005 <-- C. S. Pederson <-- R. S. Breed <-- F. L. Mickle ("Lactobacillus lycopersici").
117067CIP <- 1987, NCIB <- 1950, ATCC <- C.S. Pederson <- R.S. Breed <- F.L. Mickle, Lactobacillus lycopersici

doi: 10.13145/bacdive6422.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lentilactobacillus
  • species: Lentilactobacillus buchneri
  • full scientific name: Lentilactobacillus buchneri (Henneberg 1903) Zheng et al. 2020

  • synonyms

    @refsynonym
    20215Lactobacillus buchneri
    20215Bacillus buchneri

@ref: 8488

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lentilactobacillus

species: Lentilactobacillus buchneri subsp. buchneri

full scientific name: Lentilactobacillus buchneri subsp. buchneri (Henneberg 1903) Liu and Gu 2020

type strain: yes

Morphology

cell morphology

  • @ref: 117067
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8488MRS 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
35472MEDIUM 41- for Lactobacillus, Leuconostoc, Weissella, Pediococcus, Sporolactobacillus inulinusyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp broth (55.000 g)
117067CIP Medium 41yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=41

culture temp

@refgrowthtypetemperaturerange
8488positivegrowth37mesophilic
35472positivegrowth30mesophilic
47424positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117067
  • oxygen tolerance: facultative anaerobe

murein

  • @ref: 8488
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
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-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose+builds acid from6731
68371trehalose-builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
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
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
117067nitrate-reduction17632
117067nitrite-reduction16301

metabolite production

  • @ref: 117067
  • Chebi-ID: 35581
  • metabolite: indole
  • production: 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
117067oxidase-
117067catalase-1.11.1.6
117067urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
117067---+-+++--+-+++++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8488----+++---+++------------+--+-++-++---------------
8488----+++---+++--------+---+--++++--++----+---------
8488----+++---+++--------+---+/---+-++--++----+------+-+
8488----+++---+++-----+--+---+--++++--++----+------+-+

Isolation, sampling and environmental information

isolation

@refsample type
8488tomato pulp
47424Tomato pulp
67770Tomato pulp
117067Food, Tomato pulp

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3539.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_367;97_831;98_967;99_3539&stattab=map
  • Last taxonomy: Lentilactobacillus
  • 16S sequence: LC064887
  • Sequence Identity:
  • Total samples: 4525
  • soil counts: 442
  • aquatic counts: 432
  • animal counts: 3255
  • plant counts: 396

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
84881Risk group (German classification)
1170671Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus buchneri gene for 16S rRNA, partial sequence, strain: YIT 0077AB4293681567ena1581
20218Lactobacillus buchneri ATCC 4005 16S ribosomal RNA gene, partial sequenceAF429499505ena1581
20218Lactobacillus buchneri strain ATCC 4005 16S ribosomal RNA gene, partial sequence; 16S-23S intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF429586545ena1581
20218Lactobacillus buchneri 16S-23S ribosomal RNA intergenic spacer, complete sequenceAY821850222ena1581
20218Lactobacillus buchneri gene for 16S ribosomal RNA, partial sequenceD31682196ena1581
20218Lactobacillus buchneri 16S ribosomal RNAM588111521ena1581
20218Lactobacillus buchneri gene for 16S ribosomal RNA, partial sequenceAB2050551542ena1581
20218Lactobacillus buchneri gene for 16S rRNA, partial sequence, strain: JCM 1115AB289055677ena1581
20218Lactobacillus buchneri strain LMG 6892 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceEU161616806ena1581
20218L.buchneri 16S rRNA geneX611391382ena1581
67770Lactobacillus buchneri gene for 16S ribosomal RNA, partial sequence, strain: JCM 1115LC0648871475ena1581

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lentilactobacillus buchneri ATCC 4005GCA_018314255completencbi1581
66792Lentilactobacillus buchneri ATCC 4005GCA_009495475scaffoldncbi1581
66792Lentilactobacillus buchneri NBRC 107764GCA_007992235contigncbi1581
66792Lactobacillus buchneri DSM 200571423728.3wgspatric1423728
66792Lactobacillus buchneri strain ATCC 40051581.57wgspatric1581
66792Lactobacillus buchneri strain ATCC 40051581.44wgspatric1581
66792Lactobacillus buchneri strain NBRC 1077641581.54wgspatric1581
66792Lentilactobacillus buchneri strain ATCC 40051581.76completepatric1581
66792Lentilactobacillus buchneri DSM 200572700989132draftimg1423728
67770Lentilactobacillus buchneri DSM 20057GCA_001434735contigncbi1423728
67770Lentilactobacillus buchneri ATCC 4005GCA_004354745scaffoldncbi1581

GC content

@refGC-contentmethod
848844.8
6777045thermal denaturation, midpoint method (Tm)
6777044.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.826no
gram-positiveyes97.884no
anaerobicno94.479no
aerobicno94.199no
halophileyes94.889no
spore-formingno94.003no
thermophileno98.905no
glucose-utilyes88.57no
motileno95.992no
glucose-fermentyes86.983no

External links

@ref: 8488

culture collection no.: DSM 20057, ATCC 4005, CCM 1819, NCDO 110, NCIB 8007, CCUG 21532, JCM 1115, BCRC 14066, CECT 4111, CIP 103023, KCTC 3784, LMG 6892, NBRC 107764, NCFB 110, NCIMB 8007, NRIC 1040, NRRL B-1837, VKM B-1599, VTT E-93445, IMET 10692

straininfo link

  • @ref: 75897
  • straininfo: 264238

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Pathogenicity2632048Superoxide dismutase activity in some strains of lactobacilli: induction by manganese.Gonzalez SN, Apella MC, Romero N, Pesce de Ruiz Holgado AA, Oliver GChem Pharm Bull (Tokyo)10.1248/cpb.37.30261989Enzyme Induction/drug effects, Lactobacillus/*enzymology, Manganese/*pharmacology, Superoxide Dismutase/*biosynthesisEnzymology
Phylogeny2733612Comparative characterization of spirosomes isolated from Lactobacillus brevis, Lactobacillus fermentum, and Lactobacillus buchneri.Nomura S, Masuda K, Kawata TMicrobiol Immunol10.1111/j.1348-0421.1989.tb01494.x1989Amino Acids, Bacterial Proteins/analysis/*isolation & purification/ultrastructure, Chemical Phenomena, Chemistry, Electrophoresis, Polyacrylamide Gel, Lactobacillus/classification/*ultrastructure, Organelles/analysis/immunology/ultrastructure, Peptide Mapping, Protoplasts/*analysis/ultrastructure, Species SpecificityEnzymology
Enzymology3030360Carbamate kinase of Lactobacillus buchneri NCDO110. I. Purification and properties.Manca de Nadra MC, Nadra Chaud CA, Pesce de Ruiz Holgado A, Oliver GBiotechnol Appl Biochem1986Chromatography, Ion Exchange, Culture Media, Electrophoresis, Polyacrylamide Gel, Hydrogen-Ion Concentration, Lactobacillus/*enzymology, Molecular Weight, Phosphotransferases/analysis/*isolation & purification, *Phosphotransferases (Carboxyl Group Acceptor)Cultivation
Enzymology3036180Carbamate kinase of Lactobacillus buchneri NCDO110. II. Kinetic studies and reaction mechanism.Manca de Nadra MC, Pesce de Ruiz Holgado AA, Oliver GBiotechnol Appl Biochem1987Adenosine Diphosphate/pharmacology, Kinetics, Lactobacillus/*enzymology, Magnesium, Phosphotransferases/*metabolism, *Phosphotransferases (Carboxyl Group Acceptor)Metabolism
Metabolism3139054Arginine dihydrolase pathway in Lactobacillus buchneri: a review.Manca de Nadra MC, Pesce de Ruiz Holgado AA, Oliver GBiochimie10.1016/0300-9084(88)90209-x1988Hydrolases/*metabolism, Lactobacillus/*enzymologyEnzymology
Enzymology24039265Identification, purification, and characterization of a novel amino acid racemase, isoleucine 2-epimerase, from Lactobacillus species.Mutaguchi Y, Ohmori T, Wakamatsu T, Doi K, Ohshima TJ Bacteriol10.1128/JB.00709-132013Amino Acid Isomerases/chemistry/genetics/isolation & purification/*metabolism, Cloning, Molecular, Coenzymes/metabolism, Escherichia coli/genetics, Gene Expression, Isoleucine/*metabolism, Kinetics, Lactobacillus/*enzymology/genetics, Molecular Sequence Data, Molecular Weight, Protein Multimerization, Protein Subunits, Pyridoxal Phosphate/metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification, Sequence Analysis, DNA, Sequence Analysis, Protein, Substrate SpecificityMetabolism
30038603A Novel PLP-Dependent Alanine/Serine Racemase From the Hyperthermophilic Archaeon Pyrococcus horikoshii OT-3.Kawakami R, Ohshida T, Sakuraba H, Ohshima TFront Microbiol10.3389/fmicb.2018.014812018
Genetics31775607Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage.Nethery MA, Henriksen ED, Daughtry KV, Johanningsmeier SD, Barrangou RBMC Genomics10.1186/s12864-019-6274-02019Computational Biology/methods, Evolution, Molecular, Fermentation, *Food Microbiology, *Genome, Bacterial, *Genomics/methods, Lactobacillus/classification/*genetics/*isolation & purification, Molecular Sequence Annotation, Phylogeny, Whole Genome SequencingPhylogeny
Phylogeny32250236Lactobacillus buchneri subsp. silagei subsp. nov., isolated from rice grain silage.Tanizawa Y, Kobayashi H, Nomura M, Sakamoto M, Arita M, Nakamura Y, Ohkuma M, Tohno MInt J Syst Evol Microbiol10.1099/ijsem.0.0041382020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Edible Grain/microbiology, Fatty Acids/chemistry, Genes, Bacterial, Japan, Lactobacillus/*classification/isolation & purification, Nucleic Acid Hybridization, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Silage/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8488Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20057)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20057
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
35472Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14774
47424Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 21532)https://www.ccug.se/strain?id=21532
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
75897Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264238.1StrainInfo: A central database for resolving microbial strain identifiers
117067Curators of the CIPCollection of Institut Pasteur (CIP 103023)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103023