Strain identifier

BacDive ID: 6624

Type strain: Yes

Species: Levilactobacillus hammesii

Strain Designation: LP38

Strain history: CIP <- 2004, M. Korakli, Munich Tech. Univ., Freising, Germany: strain LP38

NCBI tax ID(s): 1423753 (strain), 267633 (species)

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General

@ref: 6418

BacDive-ID: 6624

DSM-Number: 16381

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

description: Levilactobacillus hammesii LP38 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from wheat sourdough.

NCBI tax id

NCBI tax idMatching level
267633species
1423753strain

strain history

@refhistory
6418<- M. Korakli, TMW <- R. Valcheva; LP38
382742004, M. Korakli, Freising, Germany: strain LP38
67770CIP 108387 <-- M. Korakli LP38.
119831CIP <- 2004, M. Korakli, Munich Tech. Univ., Freising, Germany: strain LP38

doi: 10.13145/bacdive6624.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Levilactobacillus
  • species: Levilactobacillus hammesii
  • full scientific name: Levilactobacillus hammesii (Valcheva et al. 2005) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus hammesii

@ref: 6418

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Levilactobacillus

species: Levilactobacillus hammesii

full scientific name: Levilactobacillus hammesii (Valcheva et al. 2005) Zheng et al. 2020

strain designation: LP38

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31323positive3 µm0.5 µmrod-shapedno
69480no98.007
69480positive100
119831positiverod-shapedno

colony morphology

  • @ref: 59150
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6418MRS MEDIUM (DSMZ Medium 11)yeshttps://mediadive.dsmz.de/medium/11Name: MRS MEDIUM (DSMZ Medium 11; with strain-specific modifications) Composition: Glucose 20.0 g/l Maltose 10.0 g/l Meat extract 10.0 g/l Casein peptone 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
38274MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
119831CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
6418positivegrowth30mesophilic
31323positivegrowth15-45
31323positiveoptimum32.5mesophilic
38274positivegrowth30mesophilic
59150positivegrowth30mesophilic
67770positivegrowth30mesophilic
119831positivegrowth15-37
119831nogrowth10psychrophilic
119831nogrowth45thermophilic

culture pH

@refabilitytypepH
31323positivegrowth4.7-7.2
31323positiveoptimum5.95

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6418microaerophile
31323facultative anaerobe
59150anaerobe
119831microaerophile

spore formation

@refspore formationconfidence
31323no
69481no100
69480no99.997

halophily

@refsaltgrowthtested relationconcentration
31323NaClpositivegrowth<6.6 %
31323NaClpositiveoptimum1 %

murein

  • @ref: 6418
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

observation

  • @ref: 31323
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3132322599arabinose+carbon source
3132317057cellobiose+carbon source
3132328757fructose+carbon source
3132328260galactose+carbon source
3132317234glucose+carbon source
3132317306maltose+carbon source
3132329864mannitol+carbon source
3132337684mannose+carbon source
31323506227N-acetylglucosamine+carbon source
3132327082trehalose+carbon source
3132318222xylose+carbon source
313234853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11983117632nitrate-reduction
11983116301nitrite-reduction
11983117632nitrate+respiration

antibiotic resistance

  • @ref: 119831
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119831
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 119831
  • 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
119831oxidase-
119831alcohol dehydrogenase-1.1.1.1
119831catalase-1.11.1.6
119831lysine decarboxylase-4.1.1.18
119831ornithine decarboxylase-4.1.1.17
119831urease-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
119831-+++-+++-+++-++-+---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6418----+++--+-+----------------+---------------------
119831---+++--+-++---------+--+/---+----------------+/--+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6418wheat sourdoughPays des la LoireFranceFRAEurope
59150Wheat sourdoughPays de la LoireFranceFRAEurope2001
67770French sourdough
119831Food, Wheat sourdoughPays de la LoireFranceFRAEurope2001

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6777.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_484;97_553;98_1175;99_6777&stattab=map
  • Last taxonomy: Levilactobacillus
  • 16S sequence: LC519851
  • Sequence Identity:
  • Total samples: 921
  • soil counts: 117
  • aquatic counts: 119
  • animal counts: 507
  • plant counts: 178

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64181Risk group (German classification)
1198311Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus hammesii strain CIP 108387 16S-23S ribosomal RNA intergenic spacer and 23S ribosomal RNA gene, partial sequenceEU161595795ena267633
6418Lactobacillus hammesii partial 16S rRNA gene, strain TMW 1.1236AJ6322191549ena267633
67770Lactobacillus hammesii JCM 16170 gene for 16S rRNA, partial sequenceLC5198511505ena267633

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus hammesii DSM 163811423753.3wgspatric1423753
66792Levilactobacillus hammesii DSM 163812700989150draftimg1423753
67770Levilactobacillus hammesii DSM 16381GCA_001434395scaffoldncbi1423753

GC content

@refGC-content
641852.6
6777049.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.288yes
gram-positiveyes96.249no
anaerobicno90.26no
halophileyes89.755no
spore-formingno94.118no
glucose-utilyes93.025no
thermophileno99.446yes
aerobicno95.022no
flagellatedno98.747no
glucose-fermentyes84.077no

External links

@ref: 6418

culture collection no.: DSM 16381, CIP 108387, TMW 1.1236, CCUG 51325, JCM 16170, BCRC 80779, LMG 23074

straininfo link

  • @ref: 76098
  • straininfo: 138007

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774659Lactobacillus hammesii sp. nov., isolated from French sourdough.Valcheva R, Korakli M, Onno B, Prevost H, Ivanova I, Ehrmann MA, Dousset X, Ganzle MG, Vogel RFInt J Syst Evol Microbiol10.1099/ijs.0.63311-02005Bread/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Sequence Analysis, DNA, Triticum/*microbiologyGenetics
Phylogeny18599706Lactobacillus senmaizukei sp. nov., isolated from Japanese pickle.Hiraga K, Ueno Y, Sukontasing S, Tanasupawat S, Oda KInt J Syst Evol Microbiol10.1099/ijs.0.65677-02008*Food Microbiology, Japan, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsBiotechnology
Phylogeny19933585Lactobacillus paucivorans sp. nov., isolated from a brewery environment.Ehrmann MA, Preissler P, Danne M, Vogel RFInt J Syst Evol Microbiol10.1099/ijs.0.018077-02009Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, *Food Industry, Lactobacillus/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny23475345Lactobacillus yonginensis sp. nov., a lactic acid bacterium with ginsenoside converting activity isolated from Kimchi.Yi EJ, Yang JE, Lee JM, Park Y, Park SY, Shin HS, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijs.0.045799-02013Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Ginsenosides/*metabolism, Lactic Acid, Lactobacillus/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNABiotechnology
Phylogeny35834933Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili.Zhang Z, Wang Y, Dong Y, Xiang F, Zhang Y, Zhang H, Sun Y, Guo ZSyst Appl Microbiol10.1016/j.syapm.2022.1263442022Bacterial Typing Techniques, Base Composition, Carbon, *Cardiolipins, Catalase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycolipids, Nucleic Acid Hybridization, *Pentoses, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, gamma-Aminobutyric Acid/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6418Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16381)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16381
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
31323Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127638
38274Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6003
59150Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51325)https://www.ccug.se/strain?id=51325
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
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
76098Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138007.1StrainInfo: A central database for resolving microbial strain identifiers
119831Curators of the CIPCollection of Institut Pasteur (CIP 108387)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108387