Strain identifier

BacDive ID: 6575

Type strain: Yes

Species: Limosilactobacillus panis

Strain Designation: 1

Strain history: CIP <- 2008, CCUG <- 1997, B.G. Wiese, Hanover Univ., Hanover, Germany: strain 37482

NCBI tax ID(s): 1423782 (strain), 47493 (species)

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General

@ref: 2209

BacDive-ID: 6575

DSM-Number: 6035

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

description: Limosilactobacillus panis 1 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from sourdough.

NCBI tax id

NCBI tax idMatching level
47493species
1423782strain

strain history

@refhistory
2209<- F. Olms <- W. Strohmar; 1
67770DSM 6035 <-- F. Olms <-- W. Strohmar.
121530CIP <- 2008, CCUG <- 1997, B.G. Wiese, Hanover Univ., Hanover, Germany: strain 37482

doi: 10.13145/bacdive6575.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Limosilactobacillus
  • species: Limosilactobacillus panis
  • full scientific name: Limosilactobacillus panis (Wiese et al. 1996) Zheng et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Lactobacillus panis

@ref: 2209

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Limosilactobacillus

species: Limosilactobacillus panis

full scientific name: Limosilactobacillus panis (Wiese et al. 1996) Zheng et al. 2020

strain designation: 1

type strain: yes

Morphology

cell morphology

  • @ref: 121530
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2209LACTOBACILLUS MEDIUM IV (DSMZ Medium 859)yeshttps://mediadive.dsmz.de/medium/859Name: LACTOBACILLUS MEDIUM IV (DSMZ Medium 859) Composition: Tryptone 10.0 g/l Na-acetate x 3 H2O 5.0 g/l Yeast extract 5.0 g/l Maltose 4.0 g/l Glucose 4.0 g/l Meat extract 3.0 g/l K2HPO4 x 3 H2O 2.6 g/l (NH4)2 citrate 2.0 g/l L-Cysteine HCl x H2O 0.5 g/l MgSO4 x 7 H2O 0.1 g/l MnSO4 x 4 H2O 0.05 g/l Tween 80 Distilled water
40074MEDIUM 40- for Lactobacillus and LeuconostocyesDistilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
121530CIP Medium 40yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=40

culture temp

@refgrowthtypetemperaturerange
2209positivegrowth37mesophilic
40074positivegrowth37mesophilic
67770positivegrowth37mesophilic
121530positivegrowth25-45
121530nogrowth15psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 53692
  • oxygen tolerance: anaerobe

murein

  • @ref: 2209
  • 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-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
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
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
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121530nitrate-reduction17632
121530nitrite-reduction16301
121530nitrate+respiration17632
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose+fermentation16024
68380raffinose+fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897
68381arginine-hydrolysis29016
68381D-ribose-builds acid from16988
68381D-mannitol-builds acid from16899
68381sorbitol-builds acid from30911
68381lactose-builds acid from17716
68381trehalose-builds acid from27082
68381raffinose-builds acid from16634
68381sucrose-builds acid from17992
68381L-arabinose-builds acid from30849
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin-builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose-builds acid from17306
68381melibiose-builds acid from28053
68381melezitose-builds acid from6731
68381methyl beta-D-glucopyranoside-builds acid from320055
68381D-tagatose-builds acid from16443
68381urea-hydrolysis16199

metabolite production

@refChebi-IDmetaboliteproduction
12153035581indoleno
6838035581indoleno
6838115688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin+
6838035581indole-
12153015688acetoin-

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
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase+3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase-
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68379catalase-1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
121530alcohol dehydrogenase-1.1.1.1
121530catalase-1.11.1.6
121530lysine decarboxylase-4.1.1.18
121530ornithine decarboxylase-4.1.1.17
121530urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
53692-----++-+------------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
53692-++--++---+-++-++---
121530-+++------++++-++---

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
2209----------+++---------------+-+----+--------------
2209-------------------------+------------------------
53692-----+-------------------+--+---------------------
121530---+++--+++++----+--+---+--++++---+----+------+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
53692--++-++---++---------+-------

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
53692-+--++----------+-+-------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
2209sourdoughGermanyDEUEurope
53692Rye sourdoughGermanyDEUEurope
67770Rye sourdough
121530Rye sourdoughGermanyDEUEuropeHanover1996

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_61999.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_45;96_1693;97_2027;98_2492;99_61999&stattab=map
  • Last taxonomy: Limosilactobacillus panis
  • 16S sequence: X94230
  • Sequence Identity:
  • Total samples: 2131
  • soil counts: 42
  • aquatic counts: 106
  • animal counts: 1909
  • plant counts: 74

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
22091Risk group (German classification)
1215301Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Lactobacillus panis gene for 16S rRNA, partial sequence, strain: JCM 11053AB289208637ena47493
20218Lactobacillus panis 23S rRNA gene and 16S-23S IGS, strain DSM 6035AJ616012689ena47493
20218Lactobacillus panis strain DSM 6035 16S-23S ribosomal RNA large intergenic spacer, tRNA-Ile, and tRNA-Ala genes, complete sequenceAY839300405ena47493
20218Lactobacillus panis strain DSM 6035 16S-23S ribosomal RNA small intergenic spacer, complete sequenceAY839301222ena47493
2209L.panis 16S ribosomal RNAX942301490ena47493
67770Lactobacillus panis gene for 16S ribosomal RNA, partial sequence, strain: JCM 11053LC1455601508ena47493

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus panis DSM 60351423782.3wgspatric1423782
66792Lactobacillus panis DSM 60351423782.4wgspatric1423782
66792Limosilactobacillus panis DSM 60352700989156draftimg1423782
66792Limosilactobacillus panis DSM 60352630968969draftimg1423782
67770Limosilactobacillus panis DSM 6035GCA_001435935scaffoldncbi1423782
67770Limosilactobacillus panis DSM 6035GCA_001027985contigncbi1423782

GC content

@refGC-contentmethod
220948.3high performance liquid chromatography (HPLC)
6777048.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.608no
gram-positiveyes97.441no
anaerobicno72.806no
halophileyes86.807no
spore-formingno94.457no
thermophileno98.863yes
glucose-utilyes89.628no
aerobicno97.308yes
flagellatedno98.78no
glucose-fermentyes86.119yes

External links

@ref: 2209

culture collection no.: DSM 6035, JCM 11053, CCUG 37482, CIP 109875

straininfo link

  • @ref: 76049
  • straininfo: 48056

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8934903Lactobacillus panis sp. nov., from sourdough with a long fermentation period.Wiese BG, Strohmar W, Rainey FA, Diekmann HInt J Syst Bacteriol10.1099/00207713-46-2-4491996Base Sequence, Bread/*microbiology, DNA, Bacterial/analysis, Electrophoresis, Polyacrylamide Gel, Fermentation, Lactobacillus/classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, Plasmids, RNA, Ribosomal, 16S/analysis, Time FactorsEnzymology
Phylogeny12807222Strain DSM 6035 is the type strain of Lactobacillus panis (Wiese et al. 1996). Opinion 72.Judicial Commission Of The International Committee On Systematics Of ProkaryotesInt J Syst Evol Microbiol10.1099/ijs.0.02495-02003Lactobacillus/*classification, *Terminology as Topic
Genetics26205855Draft Genome Sequence of Lactobacillus panis DSM 6035T, First Isolated from Sourdough.Zhu Y, Fang D, Shi D, Li A, Lv L, Yan R, Yao J, Hua D, Hu X, Guo F, Wu W, Guo J, Chen Y, Jiang X, Chen X, Li LGenome Announc10.1128/genomeA.00778-152015Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2209Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6035)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6035
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
40074Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7669
53692Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37482)https://www.ccug.se/strain?id=37482
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
68379Automatically annotated from API Coryne
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
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
76049Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48056.1StrainInfo: A central database for resolving microbial strain identifiers
121530Curators of the CIPCollection of Institut Pasteur (CIP 109875)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109875