Name: Duganella sacchari Sac-22
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133833

Type strain:

Species: Duganella sacchari

Strain Designation: Sac-22

Culture col. no.: KCTC 22381, NCIMB 14475

NCBI tax ID(s): 551987 (species)

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Oxalobacteraceae*
	Genus	*Duganella*
	Species	**Duganella sacchari**
	Full Scientific Name (LPSN)	Duganella sacchari Madhaiyan et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30627]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.7
[Ref.: #125438]	Gram stain	negative Confidence in %98.5

[Ref.: #30627]	Cell length	1.45 µm

[Ref.: #30627]	Cell width	0.385 µm

[Ref.: #30627]	Cell shape	rod-shaped

[Ref.: #30627]	Motility	yes
[Ref.: #125439]	Motility	yes Confidence in %92.2

[Ref.: #30627]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #30627]			growth	20-37 °C
[Ref.: #30627]			optimum	28 °C

	pH	Kind of pH		pH
[Ref.: #30627]			optimum	7.2
[Ref.: #30627]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30627]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %91.8

[Ref.: #30627]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %99.5

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30627]		NaCl		growth	0-1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30627]	cellobiose ChEBI	+	carbon source
[Ref.: #30627]	ethanol ChEBI	+	carbon source
[Ref.: #30627]	galactose ChEBI	+	carbon source
[Ref.: #30627]	galacturonate ChEBI	+	carbon source
[Ref.: #30627]	glucosamine ChEBI	+	carbon source
[Ref.: #30627]	glucose ChEBI	+	carbon source
[Ref.: #30627]	histidine ChEBI	+	carbon source
[Ref.: #30627]	lactate ChEBI	+	carbon source
[Ref.: #30627]	maltose ChEBI	+	carbon source
[Ref.: #30627]	mannitol ChEBI	+	carbon source
[Ref.: #30627]	mannose ChEBI	+	carbon source
[Ref.: #30627]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #30627]	proline ChEBI	+	carbon source
[Ref.: #30627]	succinate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30627]		catalase	+	1.11.1.6
[Ref.: #30627]		cytochrome oxidase	+	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #30627]	Sample type/isolated from	soil
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #30627]	Duganella sacchari strain Sac-22 16S ribosomal RNA gene, partial sequence	EU672806	1408	GenBank ENA	551987 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Duganella sacchari Sac-22	GCA_900143065	scaffold	GenBank ENA	551987 tax ID	*
[Ref.: #66792]	Duganella sacchari Sac-22	2651870174	draft	JGI IMG/M	551987 tax ID	*

[Ref.: #30627]

GC-content

56.4 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Duganella sacchari Sac-22 NCBI: GCA_900143065.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.5	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.484	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	89.055	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	85.167	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	83.615	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Duganella sacchari Sac-22 NCBI: GCA_900143065
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	92.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	91.8

Availability in culture collections External links

[Ref.: #30627]

Culture collection no.

KCTC 22381, NCIMB 14475

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Duganella callida sp. nov., a novel addition to the Duganella genus, isolated from the soil of a cultivated maize field.	Raths R, Peta V, Bucking H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004599	2020	*
Phylogeny	Duganella 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 MY	Antonie Van Leeuwenhoek	10.1007/s10482-020-01422-5	2020	*
Phylogeny	Duganella 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 JS	Int J Syst Evol Microbiol	10.1099/ijs.0.040584-0	2012	*
Phylogeny	Duganella 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 M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004355	2020	*
Phylogeny	Duganella 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 M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004234	2020	*
Phylogeny	Duganella ginsengisoli sp. nov., isolated from ginseng soil.	Zhang J, Kim YJ, Hoang VA, Lan Nguyen N, Wang C, Kang JP, Wang D, Yang DC	Int J Syst Evol Microbiol	10.1099/ijsem.0.000669	2015	*

References

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#30627

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26958 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

#26958

IJSEM 1126 2013 ( DOI 10.1099/ijs.0.040584-0 , PubMed 22753524 )

* These data were automatically processed and therefore are not curated

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