Strain identifier

BacDive ID: 2277

Type strain: Yes

Species: Isobaculum melis

Strain Designation: M577-94

Strain history: CIP <- 2002, CCUG <- M.D. Collins, IFR, London, UK <- G. Foster: strain m577-94

NCBI tax ID(s): 142588 (species)

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General

@ref: 5153

BacDive-ID: 2277

DSM-Number: 13760

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, spore-forming, mesophilic

description: Isobaculum melis M577-94 is a microaerophile, spore-forming, mesophilic bacterium that was isolated from small intestine of dead badger.

NCBI tax id

  • NCBI tax id: 142588
  • Matching level: species

strain history

@refhistory
5153<- M.D. Collins <- G. Foster; M577-94
120886CIP <- 2002, CCUG <- M.D. Collins, IFR, London, UK <- G. Foster: strain m577-94

doi: 10.13145/bacdive2277.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Isobaculum
  • species: Isobaculum melis
  • full scientific name: Isobaculum melis Collins et al. 2002

@ref: 5153

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Isobaculum

species: Isobaculum melis

full scientific name: Isobaculum melis Collins et al. 2002

strain designation: M577-94

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.126
69480100positive
120886nopositiverod-shaped

colony morphology

  • @ref: 120886

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5153COLUMBIA 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
5153PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
33781MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120886CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
5153positivegrowth37mesophilic
33781positivegrowth37mesophilic
53790positivegrowth37mesophilic
120886positivegrowth10-37
120886nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
53790microaerophile
120886facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480no99.966

murein

  • @ref: 5153
  • murein short key: A11.24
  • type: A3alpha L-Lys-L-Thr-Gly

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
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
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-fructose-builds acid from15824
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120886esculin+hydrolysis4853
120886nitrate-reduction17632
120886nitrite-reduction16301
120886nitrate+respiration17632

antibiotic resistance

  • @ref: 120886
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite tests

  • @ref: 120886
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
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
120886oxidase-
120886alcohol dehydrogenase-1.1.1.1
120886catalase-1.11.1.6
120886lysine decarboxylase-4.1.1.18
120886ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120886--++------++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120886----------+/--+/---------+/---+/-+/---+/---------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5153small intestine of dead badgerUnited KingdomGBREurope
53790Badger
120886Small intestine of dead badgerUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host#Other#Decomposing animal
#Host#Mammals
#Host Body-Site#Gastrointestinal tract#Small intestine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
51531Risk group (German classification)
1208861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5153
  • description: Isobaculum melis 16S rRNA gene, isolate CCUG 37660T
  • accession: AJ302648
  • length: 1515
  • database: ena
  • NCBI tax ID: 142588

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Isobaculum melis DSM 13760GCA_900111355scaffoldncbi142588
66792Isobaculum melis strain DSM 13760142588.3wgspatric142588
66792Isobaculum melis DSM 137602634166323draftimg142588

GC content

  • @ref: 5153
  • GC-content: 39
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno96.491no
flagellatedno97.964no
gram-positiveyes94.313no
anaerobicno91.873yes
aerobicno95.519yes
halophileyes81.417no
spore-formingno84.644no
glucose-fermentyes70.285no
thermophileno99.785no
glucose-utilyes88.092no

External links

@ref: 5153

culture collection no.: DSM 13760, CCUG 37660, CIP 107375

straininfo link

  • @ref: 71835
  • straininfo: 87823

literature

  • topic: Phylogeny
  • Pubmed-ID: 11837304
  • title: Isobaculum melis gen. nov., sp. nov., a Carnobacterium-like organism isolated from the intestine of a badger.
  • authors: Collins MD, Hutson RA, Foster G, Falsen E, Weiss N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-52-1-207
  • year: 2002
  • mesh: Anaerobiosis, Animals, Bacterial Typing Techniques, Carnivora/*microbiology, DNA, Ribosomal/analysis, Gram-Positive Rods/*classification/genetics/*isolation & purification, Intestines/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5153Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13760)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13760
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
33781Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4803
53790Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37660)https://www.ccug.se/strain?id=37660
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71835Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87823.1StrainInfo: A central database for resolving microbial strain identifiers
120886Curators of the CIPCollection of Institut Pasteur (CIP 107375)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107375