Name: Massilia lurida D5
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133930

Type strain:

Species: Massilia lurida

Strain Designation: D5

Culture col. no.: CGMCC 1.10822, KCTC 23880

NCBI tax ID(s): 1036180 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Massilia lurida D5 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	*Massilia*
	Species	**Massilia lurida**
	Full Scientific Name (LPSN)	Massilia lurida Luo et al. 2013

Synonym

Pseudoduganella lurida

Information on morphological and physiological properties Morphology

[Ref.: #30901]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %97
[Ref.: #125439]	Gram stain	negative Confidence in %99.3

[Ref.: #30901]	Cell length	2.1 µm

[Ref.: #30901]	Cell width	0.75 µm

[Ref.: #30901]	Cell shape	rod-shaped

[Ref.: #30901]	Motility	yes

[Ref.: #30901]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #30901]			growth	10-37 °C
[Ref.: #30901]			optimum	29 °C

	pH	Kind of pH		pH
[Ref.: #30901]			optimum	7
[Ref.: #30901]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30901]	Oxygen tolerance	aerobe
[Ref.: #125438]	Oxygen tolerance	aerobe Confidence in %90.669
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %98.9

[Ref.: #30901]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %97.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30901]		NaCl		growth	0-0.5	%

[Ref.: #30901]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30901]	arabinose ChEBI	+	carbon source
[Ref.: #30901]	cellobiose ChEBI	+	carbon source
[Ref.: #30901]	esculin ChEBI	+	hydrolysis
[Ref.: #30901]	fructose ChEBI	+	carbon source
[Ref.: #30901]	glucose ChEBI	+	carbon source
[Ref.: #30901]	glycerol ChEBI	+	carbon source
[Ref.: #30901]	lactose ChEBI	+	carbon source
[Ref.: #30901]	malate ChEBI	+	carbon source
[Ref.: #30901]	maltose ChEBI	+	carbon source
[Ref.: #30901]	mannose ChEBI	+	carbon source
[Ref.: #30901]	melibiose ChEBI	+	carbon source
[Ref.: #30901]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30901]	rhamnose ChEBI	+	carbon source
[Ref.: #30901]	salicin ChEBI	+	carbon source
[Ref.: #30901]	trehalose ChEBI	+	carbon source
[Ref.: #30901]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30901]	acid phosphatase	+	3.1.3.2
[Ref.: #30901]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30901]	catalase	+	1.11.1.6
[Ref.: #30901]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30901]	gelatinase	+
[Ref.: #30901]	urease	+	3.5.1.5

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

[Ref.: #30901]	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.: #30901]	Massilia lurida strain D5 16S ribosomal RNA gene, partial sequence	HQ839786	1486	GenBank ENA	1036180 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoduganella lurida CGMCC 1.10822	GCA_007830455	contig	GenBank ENA	1036180 tax ID	*
[Ref.: #66792]	Massilia lurida strain CGMCC 1.10822	1036180.3	wgs	PATRIC	1036180 tax ID	*
[Ref.: #66792]	Massilia lurida CGMCC 1.10822	2596583599	draft	JGI IMG/M	1036180 tax ID	*

[Ref.: #30901]

GC-content

65.9 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: Massilia lurida strain CGMCC 1.10822 PATRIC: 1036180.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.419	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	81.457	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	90.669	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.5	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	81.775	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoduganella lurida CGMCC 1.10822 NCBI: GCA_007830455
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	77.4
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.7

Availability in culture collections External links

[Ref.: #30901]

Culture collection no.

CGMCC 1.10822, KCTC 23880

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia buxea sp. nov., isolated from a rock surface.	Sun LN, Yang ED, Cui DX, Ni YW, Wang YB, Sun DD, Wang WY	Int J Syst Evol Microbiol	10.1099/ijsem.0.002301	2017	*
Phylogeny	Massilia lurida sp. nov., isolated from soil.	Luo X, Xie Q, Wang J, Pang H, Fan J, Zhang J	Int J Syst Evol Microbiol	10.1099/ijs.0.047068-0	2012	*

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 )

#30901

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 #27231 (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 .

#27231

IJSEM 2118 2013 ( DOI 10.1099/ijs.0.047068-0 , PubMed 23087170 )

* These data were automatically processed and therefore are not curated

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Massilia lurida strain CGMCC 1.10822

Pseudoduganella lurida CGMCC 1.10822

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