Strain identifier

BacDive ID: 6708

Type strain: Yes

Species: Legionella gormanii

Strain Designation: LS-13

Variant: Isotype of BacDive ID 6709

Strain history: CIP <- 1996, C. Tram, Inst. Pasteur, Paris, France <- ATCC <- G.K. Morris: strain LS-13 <- G. Gorman

NCBI tax ID(s): 464 (species)

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General

@ref: 6544

BacDive-ID: 6708

DSM-Number: 16641

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

description: Legionella gormanii LS-13 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from soil from a creek bank.

NCBI tax id

  • NCBI tax id: 464
  • Matching level: species

strain history

@refhistory
6544<- ATCC; ATCC 33297 <- G. K. Morris; <- G. W. Gorman; LS-13
119712CIP <- 1996, C. Tram, Inst. Pasteur, Paris, France <- ATCC <- G.K. Morris: strain LS-13 <- G. Gorman

doi: 10.13145/bacdive6708.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Legionellales
  • family: Legionellaceae
  • genus: Legionella
  • species: Legionella gormanii
  • full scientific name: Legionella gormanii Morris et al. 1980

  • synonyms

    • @ref: 20215
    • synonym: Fluoribacter gormanii

@ref: 6544

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Legionellales

family: Legionellaceae

genus: Legionella

species: Legionella gormanii

full scientific name: Legionella gormanii Morris et al. 1980

strain designation: LS-13

variant: Isotype of BacDive ID 6709

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119712negativerod-shapedno
125439negative99.8
125438negative99.494

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6544BCYE-AGAR (DSMZ Medium 585)yeshttps://mediadive.dsmz.de/medium/585Name: BCYE AGAR (DSMZ Medium 585) Composition: OXOID Legionella CYE-Agar base
38670MEDIUM 23 - for Afipia and LegionellayesDistilled water make up to (1000.000 ml);Legionella agar (37.000 g);Legionella - enrichment mixture (10.000 ml)
119712CIP Medium 23yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=23

culture temp

@refgrowthtypetemperature
6544positivegrowth37
38670positivegrowth37
119712positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6544microaerophile
125439obligate aerobe98.7

spore formation

@refspore formationconfidence
125439no99.7
125438no91.067

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11971217632nitrate-reduction
11971216301nitrite-reduction

metabolite production

  • @ref: 119712
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
6544catalase+1.11.1.6
6544cytochrome-c oxidase-1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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
119712oxidase-
119712catalase+1.11.1.6
119712urease-3.5.1.5
68382alpha-galactosidase-3.2.1.22

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119712-+++-++---++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6544soil from a creek bankAtlanta, GeorgiaUSAUSANorth America
119712Environment, Soil from a creek bankAtlanta, GeorgiaUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_80116.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_35;96_70;97_584;98_923;99_80116&stattab=map
  • Last taxonomy: Legionella
  • 16S sequence: Z32639
  • Sequence Identity:
  • Total samples: 12
  • soil counts: 2
  • aquatic counts: 9
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65442Risk group (German classification)
1197121Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Fluoribacter gormanii strain MDC1609 16S ribosomal RNA gene, partial sequenceJF720383522nuccore464
6544L.gormanii (LS-13) gene for 16S ribosomal RNAZ326391450nuccore464

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fluoribacter gormanii NCTC11401GCA_900450965contigncbi464
66792Fluoribacter gormanii ATCC 33297GCA_001648685scaffoldncbi464
66792Fluoribacter gormanii strain ATCC 33297464.6wgspatric464
66792Fluoribacter gormanii strain LS-13464.5wgspatric464
66792Fluoribacter gormanii strain NCTC11401464.13wgspatric464
66792Fluoribacter gormanii NCTC 114012839705416draftimg464

GC content

  • @ref: 6544
  • GC-content: 40.7

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99.494no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.228yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no78.592yes
125438spore-formingspore-formingAbility to form endo- or exosporesno91.067no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes66.85no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.7
125439BacteriaNetmotilityAbility to perform movementyes61.3
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.7

External links

@ref: 6544

culture collection no.: DSM 16641, ATCC 33297, CCUG 12267, CIP 104724, NCTC 11401

straininfo link

  • @ref: 76182
  • straininfo: 40452

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology10817705The Legionella (Fluoribacter) gormanii metallo-beta-lactamase: a new member of the highly divergent lineage of molecular-subclass B3 beta-lactamases.Boschi L, Mercuri PS, Riccio ML, Amicosante G, Galleni M, Frere JM, Rossolini GMAntimicrob Agents Chemother10.1128/AAC.44.6.1538-1543.20002000Amino Acid Sequence, Base Sequence, Cloning, Molecular, *Genes, Bacterial, Legionella/enzymology/*genetics, Molecular Sequence Data, Sequence Alignment, beta-Lactamases/*genetics/metabolismGenetics
Enzymology11257043Biochemical characterization of the FEZ-1 metallo-beta-lactamase of Legionella gormanii ATCC 33297T produced in Escherichia coli.Mercuri PS, Bouillenne F, Boschi L, Lamotte-Brasseur J, Amicosante G, Devreese B, van Beeumen J, Frere JM, Rossolini GM, Galleni MAntimicrob Agents Chemother10.1128/AAC.45.4.1254-1262.20012001Amino Acid Sequence, Binding Sites, Cephalosporin Resistance, Chelating Agents/pharmacology, Escherichia coli/genetics, Genes, Bacterial, Hydrogen-Ion Concentration, Kinetics, Legionella/*enzymology/*genetics, Models, Molecular, Molecular Sequence Data, Sequence Homology, Amino Acid, Transfection, Zinc/analysis, beta-Lactamases/*chemistry/*genetics/metabolismGenetics
Enzymology11709332Characterization of OXA-29 from Legionella (Fluoribacter) gormanii: molecular class D beta-lactamase with unusual properties.Franceschini N, Boschi L, Pollini S, Herman R, Perilli M, Galleni M, Frere JM, Amicosante G, Rossolini GMAntimicrob Agents Chemother10.1128/AAC.45.12.3509-3516.20012001Amino Acid Sequence, Anti-Bacterial Agents/pharmacology, *Bacterial Proteins, Chelating Agents/pharmacology, Chromatography, Gel, Cloning, Molecular, DNA, Recombinant/genetics, Edetic Acid/pharmacology, Electrophoresis, Polyacrylamide Gel, Escherichia coli/enzymology/genetics, Genes, Bacterial, Kinetics, Legionella/*enzymology/genetics, Microbial Sensitivity Tests, Molecular Sequence Data, Spectrometry, Mass, Electrospray Ionization, Sulfhydryl Compounds/chemistry, beta-Lactamases/*genetics/*metabolismGenetics
Genetics12205057Sequence and genome context analysis of a new molecular class D beta-lactamase gene from Legionella pneumophila.Avison MB, Simm AMJ Antimicrob Chemother10.1093/jac/dkf1352002Amino Acid Sequence, Base Sequence, Chromosomes, Bacterial/genetics, Cloning, Molecular, Genes, Bacterial/*genetics, *Genome, Bacterial, Legionella pneumophila/enzymology/*genetics, Molecular Sequence Data, Penicillinase/*genetics, Phylogeny, Polymerase Chain Reaction, Sequence Alignment, beta-Lactamases/geneticsEnzymology
28352254Distribution of Secretion Systems in the Genus Legionella and Its Correlation with Pathogenicity.Qin T, Zhou H, Ren H, Liu WFront Microbiol10.3389/fmicb.2017.003882017

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6544Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16641)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16641
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
38670Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16664
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)
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
76182Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40452.1StrainInfo: A central database for resolving microbial strain identifiers
119712Curators of the CIPCollection of Institut Pasteur (CIP 104724)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104724
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