Name: Sphingomonas metalli 9O-5
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140852

Type strain:

Species: Sphingomonas metalli

Strain Designation: 9O-5

Culture col. no.: CGMCC 1.15330, KCTC 42759

NCBI tax ID(s): 1779358 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Sphingomonas metalli 9O-5 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from lead-zinc ore sampled from an abondened lead-zinc mine.

colony-forming
Gram-negative
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	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingomonas*
	Species	**Sphingomonas metalli**
	Full Scientific Name (LPSN)	Sphingomonas metalli Feng et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43663]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.542

[Ref.: #43663]	Cell length	1-1.5 µm

[Ref.: #43663]	Cell width	0.7-0.9 µm

[Ref.: #43663]	Cell shape	rod-shaped

[Ref.: #43663]	Motility	no

[Ref.: #43663]	Colony size	1-2 mm
[Ref.: #43663]	Colony color	Orange
[Ref.: #43663]	Colony shape	circular
[Ref.: #43663]	Incubation period	3 days
[Ref.: #43663]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43663]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43663]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #43663]			growth	15-37 °C
[Ref.: #43663]			optimum	25-30 °C

	pH	Kind of pH		pH
[Ref.: #43663]			optimum	7
[Ref.: #43663]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43663]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.2

[Ref.: #43663]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.449
[Ref.: #125439]	Ability of spore formation	no Confidence in %91.1

[Ref.: #43663]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43663]		NaCl		growth	0-1	%(w/v)
[Ref.: #43663]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43663]	2-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #43663]	2-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #43663]	2-oxobutanoate ChEBI	-	assimilation
[Ref.: #43663]	2-oxoglutarate ChEBI	+	assimilation
[Ref.: #43663]	4-hydroxyphenylacetic acid ChEBI	-	assimilation
[Ref.: #43663]	acetate ChEBI	-	assimilation
[Ref.: #43663]	acetoacetate ChEBI	-	assimilation
[Ref.: #43663]	adipate ChEBI	-	assimilation
[Ref.: #43663]	bromosuccinate ChEBI	-	assimilation
[Ref.: #43663]	cellobiose ChEBI	+	assimilation
[Ref.: #43663]	citrate ChEBI	-	assimilation
[Ref.: #43663]	D-fructose ChEBI	+	assimilation
[Ref.: #43663]	D-fructose 6-phosphate ChEBI	+	assimilation
[Ref.: #43663]	D-fucose ChEBI	+	assimilation
[Ref.: #43663]	D-galactose ChEBI	+	assimilation
[Ref.: #43663]	D-galacturonic acid ChEBI	-	assimilation
[Ref.: #43663]	D-gluconate ChEBI	+	assimilation
[Ref.: #43663]	D-glucose ChEBI	+	assimilation
[Ref.: #43663]	D-glucose 6-phosphate ChEBI	+	assimilation
[Ref.: #43663]	D-glucuronate ChEBI	+	assimilation
[Ref.: #43663]	D-malate ChEBI	+	assimilation
[Ref.: #43663]	D-mannitol ChEBI	-	assimilation
[Ref.: #43663]	D-mannose ChEBI	+	assimilation
[Ref.: #43663]	D-saccharate ChEBI	+	assimilation
[Ref.: #43663]	D-serine ChEBI	-	assimilation
[Ref.: #43663]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43663]	decanoate ChEBI	-	assimilation
[Ref.: #43663]	dextrin ChEBI	+	assimilation
[Ref.: #43663]	esculin ChEBI	+	hydrolysis
[Ref.: #43663]	formate ChEBI	+	assimilation
[Ref.: #43663]	galactarate ChEBI	+	assimilation
[Ref.: #43663]	gamma-aminobutyric acid ChEBI	-	assimilation
[Ref.: #43663]	gelatin ChEBI	+	hydrolysis
[Ref.: #43663]	gentiobiose ChEBI	+	assimilation
[Ref.: #43663]	glucose ChEBI	-	builds acid from
[Ref.: #43663]	glycine-proline ChEBI	+	assimilation
[Ref.: #43663]	inosine ChEBI	+	assimilation
[Ref.: #43663]	L-arabinose ChEBI	+	assimilation
[Ref.: #43663]	L-arginine ChEBI	-	assimilation
[Ref.: #43663]	L-fucose ChEBI	+	assimilation
[Ref.: #43663]	L-histidine ChEBI	-	assimilation
[Ref.: #43663]	L-malate ChEBI	+	assimilation
[Ref.: #43663]	L-serine ChEBI	+	assimilation
[Ref.: #43663]	maltose ChEBI	+	assimilation
[Ref.: #43663]	methyl pyruvate ChEBI	-	assimilation
[Ref.: #43663]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #43663]	nitrate ChEBI	-	reduction
[Ref.: #43663]	pectin ChEBI	-	assimilation
[Ref.: #43663]	phenylacetate ChEBI	-	assimilation
[Ref.: #43663]	potassium gluconate ChEBI	+	assimilation
[Ref.: #43663]	propionate ChEBI	-	assimilation
[Ref.: #43663]	quinate ChEBI	+	assimilation
[Ref.: #43663]	raffinose ChEBI	-	assimilation
[Ref.: #43663]	salicin ChEBI	+	assimilation
[Ref.: #43663]	stachyose ChEBI	-	assimilation
[Ref.: #43663]	starch ChEBI	-	hydrolysis
[Ref.: #43663]	trehalose ChEBI	+	assimilation
[Ref.: #43663]	tween 40 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43663]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43663]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43663]	beta-galactosidase	+	3.2.1.23
[Ref.: #43663]	catalase	+	1.11.1.6
[Ref.: #43663]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43663]	urease	-	3.5.1.5

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

[Ref.: #43663]	Sample type/isolated from	lead-zinc ore sampled from an abondened lead-zinc mine
[Ref.: #43663]	Geographic location (country and/or sea, region)	Meizhou, Guangdong Province
[Ref.: #43663]	Country	China
[Ref.: #43663]	Country ISO 3 Code	CHN
[Ref.: #43663]	Continent	Asia
[Ref.: #43663]	Geographic location	24.3620°/116.2760°
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Geologic

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.: #43663]	Sphingomonas metalli strain 9O-5 16S ribosomal RNA gene, partial sequence	KU053645		GenBank ENA

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingomonas metalli CGMCC 1.15330	GCA_014641735	contig	GenBank ENA	1779358 tax ID	*
[Ref.: #66792]	Sphingomonas metalli strain CGMCC 1.15330	1779358.3	wgs	PATRIC	1779358 tax ID	*

[Ref.: #43663]

GC-content

69.1 mol%

high performance liquid chromatography (HPLC)

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: Sphingomonas metalli strain CGMCC 1.15330 PATRIC: 1779358.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.542	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.061	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.449	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	87.043	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.353	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	73.796	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas metalli CGMCC 1.15330 NCBI: GCA_014641735
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	91.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	50.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	82.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.2

Availability in culture collections External links

[Ref.: #43663]

Culture collection no.

CGMCC 1.15330, KCTC 42759

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas metalli sp. nov., isolated from an abandoned lead-zinc mine.	Feng GD, Yang SZ, Xiong X, Li HP, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000989	2016	*

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 )

#43663

Guang-Da Feng, Song-Zhen Yang, Xiong Xiong, Hua-Ping Li, Hong-Hui Zhu: Sphingomonas metalli sp. nov., isolated from an abandoned lead–zinc mine. IJSEM 66: 2046 - 2051 2016 ( DOI 10.1099/ijsem.0.000989 , PubMed 26908362 )

#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 .

* These data were automatically processed and therefore are not curated

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Sphingomonas metalli strain CGMCC 1.15330

Sphingomonas metalli CGMCC 1.15330

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