Strain identifier

BacDive ID: 6580

Type strain: Yes

Species: Lactobacillus iners

Strain history: CIP <- 1999, CCUG <- 1991, K. Lincoln, PHLS, Göteborg, Sweden

NCBI tax ID(s): 525328 (strain), 147802 (species)

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General

@ref: 4998

BacDive-ID: 6580

DSM-Number: 13335

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

description: Lactobacillus iners DSM 13335 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human urine.

NCBI tax id

NCBI tax idMatching level
147802species
525328strain

strain history

@refhistory
4998<- CCUG <- K. Lincoln
67770CIP 105923 <-- CCUG 28746 <-- K. Lincoln.
120099CIP <- 1999, CCUG <- 1991, K. Lincoln, PHLS, Göteborg, Sweden

doi: 10.13145/bacdive6580.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Lactobacillaceae
  • genus: Lactobacillus
  • species: Lactobacillus iners
  • full scientific name: Lactobacillus iners Falsen et al. 1999

@ref: 4998

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Lactobacillaceae

genus: Lactobacillus

species: Lactobacillus iners

full scientific name: Lactobacillus iners Falsen et al. 1999

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
120099positiverod-shapedno
125438no95.125
125438positive93.005

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4998BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water
39393MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120099CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
4998positivegrowth37
39393positivegrowth37
49364positivegrowth37
67770positivegrowth37
120099positivegrowth25-37
120099nogrowth15
120099nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
4998anaerobe
49364anaerobe
49364microaerophile
125439microaerophile96.2

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 91.882

murein

  • @ref: 4998
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838016024D-mannose+fermentation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
1200994853esculin-hydrolysis
120099606565hippurate+hydrolysis
12009917632nitrate-reduction
12009916301nitrite-reduction
12009917632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6838027897tryptophan-energy source
6838017632nitrate-reduction
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-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
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+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
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

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
12009915688acetoin-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
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
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
120099oxidase-
120099alcohol dehydrogenase-1.1.1.1
120099catalase-1.11.1.6
120099lysine decarboxylase-4.1.1.18
120099ornithine decarboxylase-4.1.1.17
68380serine arylamidase+
68380tyrosine arylamidase+
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380glutamate decarboxylase-4.1.1.15
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase+3.4.11.1
68380L-arginine arylamidase+
68380alpha-fucosidase-3.2.1.51
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120099--++-+-----+---+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
4998-----------+----------+--+--+-------++------------
4998-----------+++--------+--+--++------++------------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
4998----++----+------+--++-++++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
4998human urineGöteborgSwedenSWEEurope
49364Human urine,36-yr-old womanGöteborgSwedenSWEEurope1991-07-05
67770Human urine
120099Human, UrineGöteborgSwedenSWEEurope1991

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Urine

taxonmaps

  • @ref: 69479
  • File name: preview.99_799.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_46;96_486;97_555;98_638;99_799&stattab=map
  • Last taxonomy: Lactobacillus iners subclade
  • 16S sequence: LC483559
  • Sequence Identity:
  • Total samples: 108742
  • soil counts: 4343
  • aquatic counts: 6944
  • animal counts: 95845
  • plant counts: 1610

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
4998yes, in single cases1Risk group (German classification)
1200991Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
4998Lactobacillus iners partial 16S rRNA gene, type strain CCUG 28746TY163291539nuccore525328
67770Lactobacillus iners gene for 16S ribosomal RNA, partial sequenceLC4835591506nuccore147802

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lactobacillus iners DSM 13335525328.13wgspatric525328
66792Lactobacillus iners DSM 13335525328.4wgspatric525328
66792Lactobacillus iners DSM 133352663763267draftimg525328
66792Lactobacillus iners DSM 13335645951832draftimg525328
67770Lactobacillus iners DSM 13335GCA_000160875scaffoldncbi525328
67770Lactobacillus iners DSM 13335GCA_001435015contigncbi525328

GC content

@refGC-contentmethod
499834.4thermal denaturation, midpoint method (Tm)
6777032.5genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes93.005no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no68.686no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.882no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no98.728yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.982yes
125438motile2+flagellatedAbility to perform flagellated movementno95.125no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno81.5
125439BacteriaNetmotilityAbility to perform movementno73.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive86
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile96.2

External links

@ref: 4998

culture collection no.: DSM 13335, CCUG 28746, CIP 105923, LMG 18914, NCIMB 13718, CCM 4943, JCM 12513

straininfo link

  • @ref: 76054
  • straininfo: 92543

literature

  • topic: Phylogeny
  • Pubmed-ID: 10028266
  • title: Phenotypic and phylogenetic characterization of a novel Lactobacillus species from human sources: description of Lactobacillus iners sp. nov.
  • authors: Falsen E, Pascual C, Sjoden B, Ohlen M, Collins MD
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-49-1-217
  • year: 1999
  • mesh: Base Sequence, Humans, Lactobacillus/*classification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/chemistry
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4998Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13335)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13335
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
39393Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17996
49364Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 28746)https://www.ccug.se/strain?id=28746
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
68380Automatically annotated from API rID32A
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
76054Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92543.1StrainInfo: A central database for resolving microbial strain identifiers
120099Curators of the CIPCollection of Institut Pasteur (CIP 105923)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105923
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1