Strain identifier

BacDive ID: 131462

Type strain: Yes

Species: Lysinibacter cavernae

Strain Designation: CC5-806

Strain history: <- C.-H. Sun, Chinese Acad. Med. Sciences & Peking Union Medical College; CC5-806 <- L. Tuo

NCBI tax ID(s): 1640652 (species)

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General

@ref: 22689

BacDive-ID: 131462

DSM-Number: 27960

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

description: Lysinibacter cavernae CC5-806 is a mesophilic bacterium that was isolated from soil from a wild karst cave.

NCBI tax id

  • NCBI tax id: 1640652
  • Matching level: species

strain history

  • @ref: 22689
  • history: <- C.-H. Sun, Chinese Acad. Med. Sciences & Peking Union Medical College; CC5-806 <- L. Tuo

doi: 10.13145/bacdive131462.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Lysinibacter
  • species: Lysinibacter cavernae
  • full scientific name: Lysinibacter cavernae Tuo et al. 2015

@ref: 22689

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Lysinibacter

species: Lysinibacter cavernae

full scientific name: Lysinibacter cavernae Tuo et al. 2015

strain designation: CC5-806

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 22689
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

  • @ref: 22689
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Isolation, sampling and environmental information

isolation

  • @ref: 22689
  • sample type: soil from a wild karst cave
  • geographic location: Chongqing, Wulong region (29° 29' 42'' N 107° 54' 32'' E)
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 29.495
  • longitude: 107.909

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_76277.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_133;97_20679;98_53352;99_76277&stattab=map
  • Last taxonomy: Lysinibacter cavernae subclade
  • 16S sequence: KP411613
  • Sequence Identity:
  • Total samples: 173
  • soil counts: 11
  • aquatic counts: 42
  • animal counts: 5
  • plant counts: 115

Safety information

risk assessment

  • @ref: 22689
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22689
  • description: Lysinibacter cavernae strain CC5-806 16S ribosomal RNA gene, partial sequence
  • accession: KP411613
  • length: 1482
  • database: ena
  • NCBI tax ID: 1640652

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lysinibacter cavernae DSM 27960GCA_011758565contigncbi1640652
66792Lysinibacter cavernae strain DSM 279601640652.3wgspatric1640652
66792Lysinibacter cavernae DSM 279602820970551draftimg1640652

GC content

  • @ref: 22689
  • GC-content: 62.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.259no
gram-positiveyes88.624no
anaerobicno99.381no
aerobicyes88.425no
halophileno85.5no
spore-formingno93.275no
glucose-utilyes84.604no
flagellatedno97.301no
thermophileno99.632no
glucose-fermentno83.508no

External links

@ref: 22689

culture collection no.: DSM 27960, CGMCC 1.14983, KCTC 39762

straininfo link

  • @ref: 89881
  • straininfo: 396763

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26296577Lysinibacter cavernae gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a karst cave.Tuo L, Guo L, Liu SW, Liu JM, Zhang YQ, Jiang ZK, Liu XF, Chen L, Zu J, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0004152015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Phylogeny31691050Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment.Zhuo Y, Jin CZ, Jin FJ, Li T, Kang DH, Oh HM, Lee HG, Jin LAntonie Van Leeuwenhoek10.1007/s10482-019-01347-82019Fresh Water/*microbiology, Genome, Viral, Genomics/methods, Geologic Sediments/*microbiology, Mycobacteriaceae/*classification/genetics/*isolation & purification, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Water MicrobiologyGenetics

Reference

@idauthorstitledoi/urlcatalogue
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
22689Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27960Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27960)
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
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/
89881Reimer, 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-ID396763.1