Strain identifier

BacDive ID: 132969

Type strain: Yes

Species: Apibacter mensalis

Strain Designation: R-53146

Strain history: <- P. Vandamme, Lab. Microbiology, Ghent Univ., Belgium; R-53146

NCBI tax ID(s): 1586267 (species)

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General

@ref: 24757

BacDive-ID: 132969

DSM-Number: 100903

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Apibacter mensalis R-53146 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from gut of a Bombus lapidarius bumblebee.

NCBI tax id

  • NCBI tax id: 1586267
  • Matching level: species

strain history

  • @ref: 24757
  • history: <- P. Vandamme, Lab. Microbiology, Ghent Univ., Belgium; R-53146

doi: 10.13145/bacdive132969.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Weeksellaceae
  • genus: Apibacter
  • species: Apibacter mensalis
  • full scientific name: Apibacter mensalis Praet et al. 2016

@ref: 24757

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Apibacter

species: Apibacter mensalis

full scientific name: Apibacter mensalis Praet et al. 2016

strain designation: R-53146

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43992negative3.0-5.0 µm1 µmrod-shapedno
69480negative99.992

colony morphology

  • @ref: 43992
  • colony size: 1 mm
  • colony color: colourless
  • colony shape: circular
  • incubation period: 2 days
  • medium used: All culture agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43992All culture agaryes
43992Basal mediumno
43992Columbia blood agaryes
43992MacConkey agarno
24757COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperaturerange
43992positiveoptimum37mesophilic
43992nogrowth20psychrophilic
43992nogrowth28mesophilic
43992nogrowth45thermophilic
24757positivegrowth37mesophilic

culture pH

@refabilitytypepH
43992positiveoptimum7
43992nogrowth9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43992anaerobe
43992microaerotolerant

spore formation

@refspore formationconfidence
69481no100
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4399217128adipate-assimilation
4399227689decanoate-assimilation
4399217634D-glucose-assimilation
4399216899D-mannitol-assimilation
4399216024D-mannose-assimilation
4399230849L-arabinose-assimilation
4399225115malate-assimilation
4399217306maltose-assimilation
43992506227N-acetylglucosamine-assimilation
4399218401phenylacetate-assimilation
4399232032potassium gluconate-assimilation
4399253258sodium citrate-assimilation
43992casein-hydrolysis
439925291gelatin-hydrolysis
4399228017starch-hydrolysis
4399217234glucose+fermentation
439924853esculin+hydrolysis
4399217632nitrate+reduction

enzymes

@refvalueactivityec
43992catalase+1.11.1.6
43992cytochrome oxidase+1.9.3.1
43992alkaline phosphatase+3.1.3.1
43992acid phosphatase+3.1.3.2
43992esterase (C 4)+
43992esterase Lipase (C 8)+
43992leucine arylamidase+3.4.11.1
43992valine arylamidase+
43992cystine arylamidase+3.4.11.3
43992trypsin+3.4.21.4
43992naphthol-AS-BI-phosphohydrolase+
43992beta-glucosidase+3.2.1.21
43992lipase (C 14)-
43992alpha-chymotrypsin-3.4.21.1
43992alpha-galactosidase-3.2.1.22
43992beta-galactosidase-3.2.1.23
43992beta-glucuronidase-3.2.1.31
43992alpha-glucosidase-3.2.1.20
43992N-acetyl-beta-glucosaminidase-3.2.1.52
43992alpha-mannosidase-3.2.1.24
43992alpha-fucosidase-3.2.1.51
43992urease-3.5.1.5
43992arginine dihydrolase-3.5.3.6
43992gelatinase-
43992tryptophanase-4.1.99.1
43992amylase-
43992DNase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43992C16:014.7
    43992C15:0 iso16.92
    43992C17:0 iso 3OH24.25
  • type of FA analysis: whole cell analysis
  • incubation medium: All culture agar
  • agar/liquid: agar
  • incubation temperature: 37
  • incubation time: 2
  • software version: Sherlock 5.0
  • library/peak naming table: TSBA50
  • system: MIS MIDI
  • instrument: Agilent 6890N gas chromatograph

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture durationenrichment culture temperature
24757gut of a Bombus lapidarius bumblebeeBombus lapidariusGhentBelgiumBELEurope
43992gut samples of Bombus lapidarius bumblebees caught in Ghent, BelgiumGhentBelgiumBELEurope2013-08All culture agar5 days37

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Gastrointestinal tract#Stomach
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_6412.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_570;96_3038;97_3733;98_4734;99_6412&stattab=map
  • Last taxonomy: Apibacter mensalis subclade
  • 16S sequence: LN713847
  • Sequence Identity:
  • Total samples: 472
  • soil counts: 6
  • aquatic counts: 28
  • animal counts: 422
  • plant counts: 16

Safety information

risk assessment

  • @ref: 24757
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24757
  • description: Bacteroidetes bacterium LMG 28357 partial 16S rRNA gene, strain LMG 28357
  • accession: LN713847
  • length: 1489
  • database: ena
  • NCBI tax ID: 1586267

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Apibacter mensalis R-53146GCA_900018365scaffoldncbi1586267
66792Apibacter mensalis R-53146GCA_001418685scaffoldncbi1586267
66792Apibacter mensalis R-531462615840617draftimg1586267

GC content

@refGC-contentmethod
4399230.4genome sequence analysis
2475730.4sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.165yes
flagellatedno96.052no
gram-positiveno97.965no
anaerobicno86.488no
aerobicno88.8no
halophileno84.295no
spore-formingno97.025no
glucose-fermentno73.174no
thermophileno95.809no
glucose-utilyes61.866yes

External links

@ref: 24757

culture collection no.: DSM 100903, LMG 28357

straininfo link

  • @ref: 91246
  • straininfo: 405846

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26813786Apibacter mensalis sp. nov.: a rare member of the bumblebee gut microbiota.Praet J, Aerts M, Brandt E, Meeus I, Smagghe G, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0009212016Animals, Bacterial Typing Techniques, Base Composition, Bees/*microbiology, Belgium, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Gastrointestinal Tract/*microbiology, Genes, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31661042Apibacter raozihei sp. nov. isolated from bat feces of Hipposideros and Taphozous spp.Huang Y, Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Huang Y, Ren Z, Zhu W, Liang H, Zhou P, Shi Z, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0038012020Animals, Bacterial Typing Techniques, Base Composition, China, Chiroptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Flavobacteriaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24757Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100903Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100903)
43992Jessy Praet, Maarten Aerts, Evie De Brandt, Ivan Meeus, Guy Smagghe, Peter VandammeApibacter mensalis sp. nov.: a rare member of the bumblebee gut microbiota10.1099/ijsem.0.000921IJSEM 66: 1645-1651 201626813786
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91246Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405846.1