Strain identifier

BacDive ID: 13824

Type strain: Yes

Species: Rhodobacter megalophilus

Strain Designation: JA194

Strain history: Arunasri, K. JNT University

NCBI tax ID(s): 418630 (subspecies)

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General

@ref: 7795

BacDive-ID: 13824

DSM-Number: 18937

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, Gram-negative, ovoid-shaped

description: Rhodobacter megalophilus JA194 is an anaerobe, Gram-negative, ovoid-shaped bacterium that was isolated from soil sample collected from Suraj tal near Sarchu .

NCBI tax id

  • NCBI tax id: 418630
  • Matching level: subspecies

strain history

@refhistory
7795<- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA194 <- K. Arunasri
67770Ch. Sasikala JA194.
67772Arunasri, K. JNT University

doi: 10.13145/bacdive13824.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Rhodobacter
  • species: Rhodobacter megalophilus
  • full scientific name: Rhodobacter megalophilus Arunasri et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Luteovulum sphaeroides subsp. megalophilum

@ref: 7795

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rhodobacter

species: Rhodobacter megalophilus

full scientific name: Rhodobacter megalophilus Arunasri et al. 2008

strain designation: JA194

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32531negative1.5-2 µm1.2-1.5 µmovoid-shapedno
125438negative98.482
125439negative98.3

pigmentation

  • @ref: 32531
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperature
32531positivegrowth05-40
32531positiveoptimum30-35
67770positivegrowth30
67772positiveminimum5
67772positiveoptimum30
67772positivemaximum40

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7795anaerobe
32531aerobe
125439aerobe93.1

spore formation

@refspore formationconfidence
32531no
125439no95.9

observation

  • @ref: 32531
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3253130089acetate+carbon source
3253135391aspartate+carbon source
3253116947citrate+carbon source
3253116236ethanol+carbon source
3253115740formate+carbon source
3253128757fructose+carbon source
3253129987glutamate+carbon source
3253117754glycerol+carbon source
3253125115malate+carbon source
3253117272propionate+carbon source
3253130911sorbitol+carbon source
3253131011valerate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling datelatitudelongitude
7795soil sample collected from Suraj tal near Sarchu (34° 17' N 77° 58' E, 11 975 feet above sea level)Indian Himalayas, between Jammu and KashmirIndiaINDAsia
67770Soil of the Indian Himalaya
67772Soil of the Indian HimalayaLadakhIndiaINDAsia200634.283377.9167

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1809.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1024;97_1194;98_1430;99_1809&stattab=map
  • Last taxonomy: Luteovulum
  • 16S sequence: AM421024
  • Sequence Identity:
  • Total samples: 17229
  • soil counts: 1540
  • aquatic counts: 10335
  • animal counts: 4862
  • plant counts: 492

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77951Risk group (German classification)
677721

Sequence information

16S sequences

  • @ref: 7795
  • description: Rhodobacter aflagellatum partial 16S rRNA gene, type strain JA194T
  • accession: AM421024
  • length: 1406
  • database: nuccore
  • NCBI tax ID: 418630

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodobacter megalophilus strain DSM 18937418630.3wgspatric418630
66792Luteovulum sphaeroides megalophilum DSM 189372681813553draftimg418630
67772[Luteovulum] sphaeroides subsp. megalophilum DSM 18937GCA_900188265scaffoldncbi418630

GC content

@refGC-contentmethod
779566.67high performance liquid chromatography (HPLC)
3253166.67

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.482no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no72.946no
125438spore-formingspore-formingAbility to form endo- or exosporesno80.907yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes65.023no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno98.092yes
125438motile2+flagellatedAbility to perform flagellated movementyes70.808no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno95.9
125439BacteriaNetmotilityAbility to perform movementyes58.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe93.1

External links

@ref: 7795

culture collection no.: DSM 18937, JCM 14598, KCTC 5602, UCCCB23

literature

  • topic: Phylogeny
  • Pubmed-ID: 18676458
  • title: Rhodobacter megalophilus sp. nov., a phototroph from the Indian Himalayas possessing a wide temperature range for growth.
  • authors: Arunasri K, Venkata Ramana V, Sproer C, Sasikala Ch, Ramana ChV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65642-0
  • year: 2008
  • mesh: *Altitude, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fourier Analysis, Genes, rRNA, Genotype, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, *Phototrophic Processes, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/genetics/*growth & development/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Temperature
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7795Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18937)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18937
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
32531Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2874928776041
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/
67772Curators of the UCCCBhttps://ucccb.uc.pt/
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1