Strain identifier

BacDive ID: 133833

Type strain: Yes

Species: Duganella sacchari

Strain Designation: Sac-22

NCBI tax ID(s): 551987 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 9.3 (current version)

General

@ref: 30627

BacDive-ID: 133833

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Duganella sacchari Sac-22 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 551987
  • Matching level: species

doi: 10.13145/bacdive133833.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Duganella
  • species: Duganella sacchari
  • full scientific name: Duganella sacchari Madhaiyan et al. 2013

@ref: 30627

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Duganella

species: Duganella sacchari

strain designation: Sac-22

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30627negative1.45 µm0.385 µmrod-shapedyes
125439negative99.7
125439yes92.2
125438negative98.5

pigmentation

  • @ref: 30627
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperature
30627positivegrowth20-37
30627positiveoptimum28

culture pH

@refabilitytypepH
30627positivegrowth06-08
30627positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30627aerobe
125439obligate aerobe91.8

spore formation

@refspore formationconfidence
30627no
125439no99.5

halophily

  • @ref: 30627
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3062717057cellobiose+carbon source
3062716236ethanol+carbon source
3062728260galactose+carbon source
3062724175galacturonate+carbon source
306275417glucosamine+carbon source
3062717234glucose+carbon source
3062727570histidine+carbon source
3062724996lactate+carbon source
3062717306maltose+carbon source
3062729864mannitol+carbon source
3062737684mannose+carbon source
3062726271proline+carbon source
3062751850methyl pyruvate+carbon source
3062730031succinate+carbon source

enzymes

@refvalueactivityec
30627catalase+1.11.1.6
30627cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 30627
  • sample type: soil

isolation source categories

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

Sequence information

16S sequences

  • @ref: 30627
  • description: Duganella sacchari strain Sac-22 16S ribosomal RNA gene, partial sequence
  • accession: EU672806
  • length: 1408
  • database: nuccore
  • NCBI tax ID: 551987

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Duganella sacchari Sac-22GCA_900143065scaffoldncbi551987
66792Duganella sacchari Sac-222651870174draftimg551987

GC content

  • @ref: 30627
  • GC-content: 56.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.484yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.055yes
125438spore-formingspore-formingAbility to form endo- or exosporesno85.167no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99yes
125438motile2+flagellatedAbility to perform flagellated movementyes83.615no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.5
125439BacteriaNetmotilityAbility to perform movementyes92.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe91.8

External links

@ref: 30627

culture collection no.: KCTC 22381, NCIMB 14475

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22753524Duganella sacchari sp. nov. and Duganella radicis sp. nov., two novel species isolated from rhizosphere of field-grown sugar cane.Madhaiyan M, Poonguzhali S, Saravanan VS, Hari K, Lee KC, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.040584-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines/analysis, Phosphatidylglycerols/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Saccharum/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analysisGenetics
Phylogeny26449233Duganella ginsengisoli sp. nov., isolated from ginseng soil.Zhang J, Kim YJ, Hoang VA, Lan Nguyen N, Wang C, Kang JP, Wang D, Yang DCInt J Syst Evol Microbiol10.1099/ijsem.0.0006692015Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Panax/*microbiology, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny32361957Duganella rivus sp. nov., Duganella fentianensis sp. nov., Duganella qianjiadongensis sp. nov. and Massilia guangdongensis sp. nov., isolated from subtropical streams in China and reclassification of all species within genus Pseudoduganella.Lu HB, Cai ZP, Yang YG, Xu MYAntonie Van Leeuwenhoek10.1007/s10482-020-01422-52020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genome, Bacterial, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/*isolation & purification/physiology, Phosphatidylethanolamines, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiologyGenetics
Phylogeny32459166Duganella alba sp. nov., Duganella aquatilis sp. nov., Duganella margarita sp. nov. and Duganella levis sp. nov., isolated from subtropical streams in China.Lu H, Deng T, Liu F, Wang Y, Yang X, Xu MInt J Syst Evol Microbiol10.1099/ijsem.0.0042342020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny32706332Duganella lactea sp. nov., Duganella guangzhouensis sp. nov., Duganella flavida sp. nov. and Massilia rivuli sp. nov., isolated from a subtropical stream in PR China and proposal to reclassify Duganella ginsengisoli as Massilia ginsengisoli comb. nov.Lu H, Deng T, Liu F, Wang Y, Yang X, Xu MInt J Syst Evol Microbiol10.1099/ijsem.0.0043552020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNATranscriptome
Phylogeny33269999Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field.Raths R, Peta V, Bucking HInt J Syst Evol Microbiol10.1099/ijsem.0.0045992020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, North Carolina, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Zea maysTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
30627Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172695828776041
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG