Strain identifier

BacDive ID: 140349

Type strain: Yes

Species: Micrococcoides hystricis

Strain Designation: TSL3

Strain history: <- A. Tóth, National Agricultural Res. and Innovation Center, Dept. of Appl and Environmental Microbiol., Budapest, Hungary; TSL3

NCBI tax ID(s): 1572761 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 42956

BacDive-ID: 140349

DSM-Number: 29785

keywords: 16S sequence, Bacteria, aerobe, Gram-positive, coccus-shaped, colony-forming

description: Micrococcoides hystricis TSL3 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from feces of Hystrix cristata.

NCBI tax id

  • NCBI tax id: 1572761
  • Matching level: species

strain history

  • @ref: 42956
  • history: <- A. Tóth, National Agricultural Res. and Innovation Center, Dept. of Appl and Environmental Microbiol., Budapest, Hungary; TSL3

doi: 10.13145/bacdive140349.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Micrococcoides
  • species: Micrococcoides hystricis
  • full scientific name: Micrococcoides hystricis Tóth et al. 2017

@ref: 42956

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Micrococcaceae

genus: Micrococcoides

species: Micrococcoides hystricis

full scientific name: Micrococcoides hystricis Tóth et al. 2017

strain designation: TSL3

type strain: yes

Morphology

cell morphology

  • @ref: 43846
  • gram stain: positive
  • cell length: 0.9-1.1 µm
  • cell width: 0.7 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 43846
  • colony color: cream
  • colony shape: circular
  • medium used: TSA medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43846LB (Luria-Bertani) MEDIUMyes
43846Nutrient mediumno
43846Tryptic soy agaryes
43846TSA mediumyes
42956TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43846positivegrowth4-50
43846positiveoptimum20-37
42956positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43846positivegrowth7.0-11.0alkaliphile
43846positiveoptimum9.0-10.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43846
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43846
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43846NaClpositivegrowth1-8 %(w/v)
43846NaClpositiveoptimum1-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
438463557154-nitrophenyl beta-D-galactopyranoside-builds acid from
4384617128adipate-builds acid from
4384616899D-mannitol-builds acid from
4384616024D-mannose-builds acid from
4384617992sucrose-builds acid from
438464853esculin-builds acid from
43846esculin ferric citrate-builds acid from
438465291gelatin-builds acid from
4384625115malate-builds acid from
4384617306maltose-builds acid from
43846maltose hydrate-builds acid from
43846506227N-acetylglucosamine-builds acid from
4384653258sodium citrate-builds acid from
4384627082trehalose-builds acid from
4384632528turanose-builds acid from
43846casein-hydrolysis
4384617634D-glucose+assimilation
4384618401phenylacetate+assimilation
4384616828L-tryptophan+builds acid from
4384618401phenylacetate+builds acid from
4384617634D-glucose+fermentation
4384628017starch+hydrolysis

metabolite production

  • @ref: 43846
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
43846catalase+1.11.1.6
43846cytochrome oxidase+1.9.3.1
43846esterase (C 4)+
43846esterase Lipase (C 8)+
43846leucine arylamidase+3.4.11.1
43846trypsin+3.4.21.4
43846acid phosphatase+3.1.3.2
43846naphthol-AS-BI-phosphohydrolase+
43846alkaline phosphatase-3.1.3.1
43846valine arylamidase-
43846alpha-glucosidase-3.2.1.20

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43846C15:0 anteiso54.4
    43846C17:0 anteiso4.8
    43846C14:01.8
    43846C16:05
    43846C14:0 iso3.9
    43846C16:0 iso18.2
    43846C15:0 iso9.7
  • type of FA analysis: whole cell analysis
  • incubation medium: Luria-Bertani agar
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 1
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA40 4.10
  • system: MIS MIDI
  • instrument: Agilent 6850 gas chromatograph
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentsampling dateenrichment cultureenrichment culture durationenrichment culture temperature
42956feces of Hystrix cristataHystrix cristataBudapest Zoo and Botanical GardenHungaryHUNEurope
43846faeces of porcupine Hystrix indica from Budapest Zoo and Botanical GardenBudapestHungaryHUNEurope2013Luria-Bertani agar3 days37

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Rodentia (Other)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 42956
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42956
  • description: Micrococcoides hystricis strain TSL3 16S ribosomal RNA gene, partial sequence
  • accession: KP144782
  • length: 1427
  • database: ena
  • NCBI tax ID: 1572761

GC content

@refGC-contentmethod
4384658.4genome sequence analysis
4295658.4sequence analysis

External links

@ref: 42956

culture collection no.: DSM 29785, NCAIM B.02604

straininfo link

  • @ref: 96648
  • straininfo: 406678

literature

  • topic: Phylogeny
  • Pubmed-ID: 28853684
  • title: Micrococcoides hystricis gen. nov., sp. nov., a novel member of the family Micrococcaceae, phylum Actinobacteria.
  • authors: Toth A, Baka E, Bata-Vidacs I, Luzics S, Kosztik J, Toth E, Keki Z, Schumann P, Tancsics A, Nagy I, Sos E, Kukolya J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002018
  • year: 2017
  • mesh: Animals, Animals, Zoo/microbiology, Arthrobacter/classification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Glycolipids/chemistry, Hungary, Micrococcaceae/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Porcupines/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
42956Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29785Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29785)
43846Ákos Tóth, Erzsébet Baka, Ildikó Bata-Vidács, Szabina Luzics, Judit Kosztik, Erika Tóth, Zsuzsa Kéki, Peter Schumann, András Táncsics, István Nagy, Endre Sós, József KukolyaMicrococcoides hystricis gen. nov., sp. nov., a novel member of the family Micrococcaceae, phylum Actinobacteria10.1099/ijsem.0.002018IJSEM 67: 2758-2765 201728853684
96648Reimer, 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-ID406678.1