Strain identifier

BacDive ID: 23327

Type strain: Yes

Species: Melghirimyces profundicolus

Strain history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 11153

NCBI tax ID(s): 1242148 (species)

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

@ref: 18938

BacDive-ID: 23327

DSM-Number: 45787

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

description: Melghirimyces profundicolus DSM 45787 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 1242148
  • Matching level: species

strain history

  • @ref: 18938
  • history: <- J. Li, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 11153

doi: 10.13145/bacdive23327.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Thermoactinomycetaceae
  • genus: Melghirimyces
  • species: Melghirimyces profundicolus
  • full scientific name: Melghirimyces profundicolus Li et al. 2013

@ref: 18938

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Thermoactinomycetaceae

genus: Melghirimyces

species: Melghirimyces profundicolus

full scientific name: Melghirimyces profundicolus Li et al. 2013

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
31102positive
69480positive100

pigmentation

  • @ref: 31102
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerangeconfidence
31102positivegrowth37-65
31102positiveoptimum52.5thermophilic
69480thermophilic97.407

culture pH

@refabilitytypepHPH range
31102positivegrowth4.0-8.0acidophile
31102positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31102
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31102yes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
31102NaClpositivegrowth0-12 %
31102NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31102581435-dehydro-D-gluconate+carbon source
3110228757fructose+carbon source
3110233942ribose+carbon source

enzymes

@refvalueactivityec
31102acid phosphatase+3.1.3.2
31102alkaline phosphatase+3.1.3.1
31102cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 18938
  • sample type: deep-sea sediment
  • geographic location: (80° 03.099' E 01° 03.300' N) at a depth of 4593 m
  • country: Indian Ocean
  • continent: Asia
  • latitude: 1.05
  • longitude: 80.05

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Safety information

risk assessment

  • @ref: 18938
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18938
  • description: Melghirimyces profundicolus strain SCSIO 11153 16S ribosomal RNA gene, partial sequence
  • accession: JX555981
  • length: 1427
  • database: ena
  • NCBI tax ID: 1242148

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Melghirimyces profundicolus DSM 45787GCA_003054245scaffoldncbi1242148
66792Melghirimyces profundicolus strain DSM 457871242148.3wgspatric1242148
66792Melghirimyces profundicolus DSM 457872734482286draftimg1242148

GC content

@refGC-contentmethod
1893852.6high performance liquid chromatography (HPLC)
3110252.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno93.731no
gram-positiveyes88.128yes
anaerobicno98.184yes
halophileno68.213no
spore-formingyes93.774no
glucose-utilyes92.224no
aerobicyes96.022no
thermophileyes99.019yes
motileno78.264no
glucose-fermentno92.045no

External links

@ref: 18938

culture collection no.: DSM 45787, CCTCC AA 2012007, NBRC 109068, SCSIO 11153

literature

  • topic: Phylogeny
  • Pubmed-ID: 23912721
  • title: Melghirimyces profundicolus sp. nov., isolated from a deep-sea sediment.
  • authors: Li J, Qin S, You ZQ, Long LJ, Tian XP, Wang FZ, Zhang S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.052175-0
  • year: 2013
  • mesh: Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18938Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45787)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45787
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
31102Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2743128776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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