Strain identifier

BacDive ID: 7748

Type strain: Yes

Species: Micrococcus lylae

Strain Designation: JL 178

Strain history: CIP <- 1981, CCM <- W.E. Kloos: strain JL 178

NCBI tax ID(s): 1349773 (strain), 1273 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8593

BacDive-ID: 7748

DSM-Number: 20315

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, pigmented

description: Micrococcus lylae JL 178 is an aerobe, mesophilic bacterium that has a white pigmentation and was isolated from human skin.

NCBI tax id

NCBI tax idMatching level
1273species
1349773strain

strain history

@refhistory
8593<- K.H. Schleifer <- W.E. Kloss, JL 178
67770LMG 14218 <-- CCM 2693 <-- W. E. Kloos JL 178.
120723CIP <- 1981, CCM <- W.E. Kloos: strain JL 178

doi: 10.13145/bacdive7748.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Micrococcus
  • species: Micrococcus lylae
  • full scientific name: Micrococcus lylae Kloos et al. 1974 (Approved Lists 1980)

@ref: 8593

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Micrococcus

species: Micrococcus lylae

full scientific name: Micrococcus lylae Kloos et al. 1974 emend. Wieser et al. 2002 emend. Nouioui et al. 2018

strain designation: JL 178

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.524
69480100positive
120723nopositivecoccus-shaped

pigmentation

  • @ref: 22934
  • production: yes
  • name: white

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8593CORYNEBACTERIUM AGAR (DSMZ Medium 53)yeshttps://mediadive.dsmz.de/medium/53Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water
37625MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120723CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120723CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8593positivegrowth37mesophilic
37625positivegrowth30mesophilic
51330positivegrowth30-37mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
22934positivemaximum10alkaliphile
22934nogrowth6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51330aerobe
120723obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

murein

  • @ref: 8593
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
22934161933-hydroxybenzoate+growth
22934305664-aminobutyrate-growth
22934178794-hydroxybenzoate+growth
2293430089acetate+growth
2293417128adipate-growth
2293415963ribitol-growth
2293478208azelaate-growth
22934casein-hydrolysis
2293416383cis-aconitate-growth
2293416947citrate+growth
2293415824D-fructose+growth
2293417634D-glucose+growth
2293417306maltose+growth
2293416899D-mannitol-growth
2293416024D-mannose-growth
2293417924D-sorbitol-growth
2293465327D-xylose-growth
22934370543-hydroxybutyrate+growth
2293424996lactate+growth
2293429806fumarate+growth
2293424265gluconate-growth
2293417859glutarate-growth
2293417240itaconate-growth
2293416977L-alanine-growth
2293429991L-aspartate+growth
2293415971L-histidine+growth
2293415603L-leucine+growth
2293415589L-malate-growth
2293415729L-ornithine-growth
2293417295L-phenylalanine-growth
2293417203L-proline-growth
2293462345L-rhamnose-growth
2293417115L-serine-growth
2293416828L-tryptophan-growth
2293468428maltitol+growth
2293436986mesaconate-growth
2293417268myo-inositol-growth
22934506227N-acetyl-D-glucosamine-growth
22934309162-oxoglutarate-growth
2293418401phenylacetate-growth
2293417272propionate-growth
2293417148putrescine-growth
2293415361pyruvate+growth
2293476282suberate-growth
2293417992sucrose+growth
2293415708trans-aconitate-growth
2293427082trehalose+growth
2293453424tween 20+hydrolysis
2293453426tween 80+hydrolysis
2293416199urea-hydrolysis
2293416958beta-alanine-growth
12072317632nitrate-reduction
12072316301nitrite-reduction
6837516199urea-hydrolysis
6837529016arginine-hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose-fermentation
6837515824D-fructose-fermentation
6837516024D-mannose-fermentation
6837517306maltose-fermentation
6837517716lactose-fermentation
6837527082trehalose-fermentation
6837516899D-mannitol-fermentation
6837516634raffinose-fermentation
6837516988D-ribose-fermentation
6837517057cellobiose-fermentation
6837517632nitrate-reduction
6837517992sucrose-fermentation
6837559640N-acetylglucosamine-fermentation
6837532528turanose-fermentation
6837522599arabinose-fermentation

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is sensitive: yes
  • sensitivity conc.: 1.8 µg

metabolite production

  • @ref: 120723
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
22934urease-3.5.1.5
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
68375beta-glucuronidase-3.2.1.31
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase+
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease-3.5.1.5
120723oxidase+
120723catalase+1.11.1.6
120723urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120723-+---+--++-----+----

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
8593---------------+/--+-+/-------

Isolation, sampling and environmental information

isolation

@refsample type
8593human skin
51330Human skin
67770Human skin
120723Human, Skin

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_4186.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_453;97_519;98_3158;99_4186&stattab=map
  • Last taxonomy: Micrococcus lylae subclade
  • 16S sequence: X80750
  • Sequence Identity:
  • Total samples: 8162
  • soil counts: 901
  • aquatic counts: 819
  • animal counts: 6055
  • plant counts: 387

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
85931Risk group (German classification)
1207231Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: M.lylae 16S rDNA
  • accession: X80750
  • length: 1472
  • database: ena
  • NCBI tax ID: 1273

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micrococcus lylae NBRC 153551349773.3wgspatric1349773
66792Micrococcus lylae strain BCRC 121511273.6wgspatric1273
66792Micrococcus lylae NBRC 153552731957609draftimg1349773
67770Micrococcus lylae NBRC 15355GCA_001570885contigncbi1349773
67770Micrococcus lylae BCRC 12151GCA_004563975scaffoldncbi1273

GC content

@refGC-contentmethod
859367.1
6777067.1thermal denaturation, midpoint method (Tm)
6777071.3genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno75no
motileno95.286no
gram-positiveyes92.246no
anaerobicno98.963yes
halophileyes51.651no
spore-formingno94.203no
glucose-utilyes82.923yes
flagellatedno96.992no
thermophileno96.162yes
aerobicyes94.117yes
glucose-fermentno89.893yes

External links

@ref: 8593

culture collection no.: DSM 20315, ATCC 27566, CCM 2693, CCUG 33027, NCTC 11037, JCM 11572, BCRC 12151, CGMCC 1.2300, CIP 81.70, IAM 13002, IFO 15355, KCTC 3517, LMG 14218, NBRC 15355, NCAIM B.02054, NCIMB 14422, VKM Ac-2240, VKM B-1815

straininfo link

  • @ref: 77191
  • straininfo: 9307

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931177Emended descriptions of the genus Micrococcus, Micrococcus luteus (Cohn 1872) and Micrococcus lylae (Kloos et al. 1974).Wieser M, Denner EB, Kampfer P, Schumann P, Tindall B, Steiner U, Vybiral D, Lubitz W, Maszenan AM, Patel BK, Seviour RJ, Radax C, Busse HJInt J Syst Evol Microbiol10.1099/00207713-52-2-6292002Air Microbiology, Art, Benzoquinones/analysis, Micrococcus/*classification/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Paleontology, Peptidoglycan/analysis, RNA, Bacterial/chemistry, RNA, Ribosomal, 16S/chemistry, Sequence Homology, Nucleic Acid, Sewage/microbiology, Species Specificity, Spectroscopy, Fourier Transform InfraredGenetics
Phylogeny17220443Micrococcus flavus sp. nov., isolated from activated sludge in a bioreactor.Liu XY, Wang BJ, Jiang CY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.64489-02007Base Composition, Bioreactors/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Micrococcus/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8593Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20315)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20315
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
22934Monika Wieser, Ewald B M Denner, Peter Kämpfer, Peter Schumann, Brian Tindall, Ulrike Steiner, Dietmar Vybiral, Werner Lubitz, A M Maszenan, B K C Patel, Robert J Seviour, Christian Radax, Hans-Jürgen Busse10.1099/00207713-52-2-629Emended descriptions of the genus Micrococcus, Micrococcus luteus (Cohn 1872) and Micrococcus lylae (Kloos et al. 1974).IJSEM 52: 629-637 200211931177
37625Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11235
51330Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33027)https://www.ccug.se/strain?id=33027
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/
68375Automatically annotated from API ID32STA
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
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)
77191Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9307.1StrainInfo: A central database for resolving microbial strain identifiers
120723Curators of the CIPCollection of Institut Pasteur (CIP 81.70)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.70