Strain identifier

BacDive ID: 12589

Type strain: Yes

Species: Myceligenerans crystallogenes

Strain Designation: CD12E2-27

Strain history: I. Groth CD12E2-27 (=HKI 0369).

NCBI tax ID(s): 316335 (species)

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General

@ref: 6781

BacDive-ID: 12589

DSM-Number: 17134

keywords: 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, rod-shaped

description: Myceligenerans crystallogenes CD12E2-27 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from tufa, Catacomb Domitilla.

NCBI tax id

  • NCBI tax id: 316335
  • Matching level: species

strain history

@refhistory
6781<- I. Groth <- C.H. Weigel
67770I. Groth CD12E2-27 (=HKI 0369).

doi: 10.13145/bacdive12589.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Myceligenerans
  • species: Myceligenerans crystallogenes
  • full scientific name: Myceligenerans crystallogenes Groth et al. 2006

@ref: 6781

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Myceligenerans

species: Myceligenerans crystallogenes

full scientific name: Myceligenerans crystallogenes Groth et al. 2006

strain designation: CD12E2-27

type strain: yes

Morphology

cell morphology

  • @ref: 31535
  • gram stain: positive
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 31535
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6781TRYPTICASE 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
6781TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
6781positivegrowth28
31535positivegrowth10-40
31535positiveoptimum28
67770positivegrowth28

culture pH

@refabilitytypepHPH range
31535positivegrowth06-09alkaliphile
31535positiveoptimum06-09

Physiology and metabolism

oxygen tolerance

  • @ref: 31535
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31535
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31535NaClpositivegrowth0-5 %
31535NaClpositiveoptimum0-5 %

observation

@refobservation
31535aggregates in chains
67770quinones: MK-9(H8), MK-9(H4), MK-9(H6), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3153528260galactose+carbon source
3153517234glucose+carbon source
3153537684mannose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6781tufa, Catacomb DomitillaRomeItalyITAEurope
67770Tufa from the catacomb of DomitillaRomeItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Environmental#Terrestrial#Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_38330.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_28;96_17545;97_21606;98_28126;99_38330&stattab=map
  • Last taxonomy: Myceligenerans crystallogenes subclade
  • 16S sequence: FR733716
  • Sequence Identity:
  • Total samples: 68
  • soil counts: 18
  • aquatic counts: 8
  • animal counts: 40
  • plant counts: 2

Safety information

risk assessment

  • @ref: 6781
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Myceligenerans crystallogenes partial 16S rRNA gene, type strain DSM17134TFR7337161469nuccore316335
6781Myceligenerans crystallogenes strain CD12E2-27 16S ribosomal RNA gene, partial sequenceAY9281811044nuccore316335

GC content

@refGC-contentmethod
678172.3
3153572
6777072.3high performance liquid chromatography (HPLC)

External links

@ref: 6781

culture collection no.: DSM 17134, HKI 0369, NCIMB 14061, VTT E-032285, JCM 14326, NBRC 110697

straininfo link

  • @ref: 81803
  • straininfo: 289865

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403899Myceligenerans crystallogenes sp. nov., isolated from Roman catacombs.Groth I, Schumann P, Schutze B, Gonzalez JM, Laiz L, Suihko ML, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.63756-02006Actinobacteria/chemistry/*classification/isolation & purification/physiology, Archaeology, Bacterial Typing Techniques, Base Composition, Base Sequence, Biodegradation, Environmental, Molecular Sequence Data, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rome, Sequence Homology, Nucleic Acid, Soil Microbiology, Species Specificity, Xylans/metabolismGenetics
Phylogeny20511461Myceligenerans halotolerans sp. nov., an actinomycete isolated from a salt lake, and emended description of the genus Myceligenerans.Wang Y, Tang SK, Li Z, Lou K, Mao PH, Jin X, Klenk HP, Zhang LX, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.024091-02010Actinomycetales/*classification/genetics/growth & development/*isolation & purification, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysis, *Water MicrobiologyGenetics
Phylogeny23224437Myceligenerans salitolerans sp. nov., a halotolerant actinomycete isolated from a salt lake in Xinjiang, China.Guan TW, Wu N, Tang SK, Che ZM, Chen XGExtremophiles10.1007/s00792-012-0502-82012Actinobacteria/*genetics/*isolation & purification/*metabolism, Base Sequence, China, Membrane Lipids/chemistry/metabolism, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyMetabolism
Phylogeny25667397Myceligenerans cantabricum sp. nov., a barotolerant actinobacterium isolated from a deep cold-water coral.Sarmiento-Vizcaino A, Gonzalez V, Brana AF, Molina A, Acuna JL, Garcia LA, Blanco GInt J Syst Evol Microbiol10.1099/ijs.0.0001072015Actinomycetales/*classification/genetics/isolation & purification, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31532356Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern.Zhang LY, Fang BZ, Jiao JY, Zhang XT, Liu L, Meng XL, Ming H, Nie GX, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0036822019Actinobacteria/*classification/isolation & purification, Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6781Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17134)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17134
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
31535Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127828
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
81803Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289865.1StrainInfo: A central database for resolving microbial strain identifiers