Strain identifier

BacDive ID: 4982

Type strain: Yes

Species: Leminorella richardii

Strain Designation: BE2-2083

Strain history: CIP <- 1989, NCTC <- 1986, ATCC <- F. Brenner: strain BE2-2083

NCBI tax ID(s): 1354266 (strain), 158841 (species)

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General

@ref: 5577

BacDive-ID: 4982

DSM-Number: 14849

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, oval-shaped

description: Leminorella richardii BE2-2083 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from faeces of female with diarrhea on corticosteroid therapy.

NCBI tax id

NCBI tax idMatching level
1354266strain
158841species

strain history

@refhistory
5577<- ATCC <- F. W. Brenner, CDC, Atlanta, USA
67770DSM 14849 <-- ATCC 33998 <-- F. W. Brenner; CDC, USA; BE2-2083.
122234CIP <- 1989, NCTC <- 1986, ATCC <- F. Brenner: strain BE2-2083

doi: 10.13145/bacdive4982.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Budviciaceae
  • genus: Leminorella
  • species: Leminorella richardii
  • full scientific name: Leminorella richardii Hickman-Brenner et al. 1985

@ref: 5577

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Budviciaceae

genus: Leminorella

species: Leminorella richardii

full scientific name: Leminorella richardii Hickman-Brenner et al. 1985

strain designation: BE2-2083

type strain: yes

Morphology

cell morphology

@refgram staincell shapeconfidence
122234negativeoval-shaped
125438negative99
125439negative93.3

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5577NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
40620MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122234CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
122234CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
5577positivegrowth37
40620positivegrowth30
67770positivegrowth37
122234positivegrowth10-37
122234nogrowth5
122234nogrowth41

Physiology and metabolism

oxygen tolerance

  • @ref: 122234
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 125438
  • spore formation: no
  • confidence: 94.696

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837430911sorbitol-builds acid from
6837417268myo-inositol-builds acid from
6837417057cellobiose-builds acid from
6837462345L-rhamnose-builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose-builds acid from
6837417634D-glucose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837418024D-galacturonic acid-builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837418403L-arabitol-builds acid from
6837416199urea-hydrolysis
6837425094lysine-degradation
6837418257ornithine-degradation
12223429864mannitol-fermentation
12223416947citrate-carbon source
12223417234glucose+fermentation
12223417716lactose-fermentation
12223417632nitrate+reduction
12223416301nitrite-reduction
12223415792malonate-assimilation
122234132112sodium thiosulfate+builds gas from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837430849L-arabinose+builds acid from
6837417992sucrose-builds acid from
6837427897tryptophan-energy source
6837415792malonate-assimilation
6837417306maltose-builds acid from
6837416899D-mannitol-builds acid from
6837429016arginine-hydrolysis
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
6837117716lactose-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
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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117113erythritol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
12223435581indoleno

metabolite tests

  • @ref: 68374
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51
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
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122234oxidase-
122234beta-galactosidase+3.2.1.23
122234alcohol dehydrogenase-1.1.1.1
122234gelatinase-
122234catalase+1.11.1.6
122234lysine decarboxylase-4.1.1.18
122234ornithine decarboxylase-4.1.1.17
122234tryptophan deaminase-
122234urease-3.5.1.5
68374beta-galactosidase-3.2.1.23
68374urease-3.5.1.5
68374ornithine decarboxylase-4.1.1.17
68382beta-galactosidase-3.2.1.23
68382leucine arylamidase+3.4.11.1
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase-3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase-3.2.1.21
68374lipase-
68374lysine decarboxylase-4.1.1.18
68374arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122234-++--+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122234+/--+/-+/-+/-+/-----+/-----------+/-------------------------+/-+/-+/-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
47225--------+----------+-+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122234-+-----------------+++---------+-----------+-+++++-+-++-+--++--------------+---++--------+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
5577faeces of female with diarrhea on corticosteroid therapyTexasUSAUSANorth America
47225Human feces,7-month-old female,gastroenteritis1987
67770Stool of female with diarrhea on corticosteroid therapyTexasUSAUSANorth America
122234Human, Female with diarrhoea on corticosteroid, stoolTexasUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Female

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
5577yes, in single cases1Risk group (German classification)
1222341Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Leminorella richardii partial 16S rRNA gene, strain BE2-2083
  • accession: HF558368
  • length: 1516
  • database: nuccore
  • NCBI tax ID: 158841

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leminorella richardii NCTC12151GCA_900478135completencbi158841
66792Leminorella richardii strain NCTC12151158841.3completepatric158841
66792Leminorella richardii NCTC 121512887760073completeimg158841

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno99no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no88.8yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no72.351yes
125438spore-formingspore-formingAbility to form endo- or exosporesno94.696no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99.413yes
125438motile2+flagellatedAbility to perform flagellated movementno68.034no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno89.4
125439BacteriaNetmotilityAbility to perform movementyes82.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative93.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe89.1

External links

@ref: 5577

culture collection no.: CCUG 20910, NCTC 12151, LMG 7911, JCM 5905, DSM 14849, ATCC 33998, CDC 978-82, JCM 31908, CCM 4004, CIP 103360, CDC 0978-82

straininfo link

  • @ref: 74478
  • straininfo: 13713

literature

  • topic: Phylogeny
  • Pubmed-ID: 3972991
  • title: Leminorella, a new genus of Enterobacteriaceae: identification of Leminorella grimontii sp. nov. and Leminorella richardii sp. nov. found in clinical specimens.
  • authors: Hickman-Brenner FW, Vohra MP, Huntley-Carter GP, Fanning GR, Lowery VA 3rd, Brenner DJ, Farmer JJ 3rd
  • journal: J Clin Microbiol
  • DOI: 10.1128/jcm.21.2.234-239.1985
  • year: 1985
  • mesh: DNA, Bacterial/analysis, Enterobacteriaceae/*classification/isolation & purification/metabolism, Humans, Nucleic Acid Hybridization, Terminology as Topic
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5577Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14849)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14849
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
40620Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15149
47225Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 20910)https://www.ccug.se/strain?id=20910
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
68374Automatically annotated from API ID32E
68382Automatically annotated from API zym
74478Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13713.1StrainInfo: A central database for resolving microbial strain identifiers
122234Curators of the CIPCollection of Institut Pasteur (CIP 103360)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103360
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