Name: Profundibacterium mesophilum KAUST100406-0324
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133848

Type strain:

Species: Profundibacterium mesophilum

Strain Designation: KAUST100406-0324

Culture col. no.: JCM 17872, NRRL B-59665

Strain history: P. Y. Lai KAUST100406-0324.

NCBI tax ID(s): 1258573 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Profundibacterium mesophilum KAUST100406-0324 is an aerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

coccus-shaped
Gram-negative
motile
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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	"Profundibacterium"
	Species	"Profundibacterium mesophilum"
	Full Scientific Name (LPSN)	Profundibacterium mesophilum corrig. Lai 2012

	Synonym	"Profundibacterium* mesophila"*
	Synonym	**Profundibacterium mesophilum**

Information on morphological and physiological properties Morphology

[Ref.: #30668]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %97.5
[Ref.: #125438]	Gram stain	negative Confidence in %97.5

[Ref.: #30668]	Cell length	0.2 µm

[Ref.: #30668]	Cell width	0.2 µm

[Ref.: #30668]	Cell shape	coccus-shaped

[Ref.: #30668]	Motility	yes

[Ref.: #30668]	Flagellum arrangement	gliding

[Ref.: #30668]

Pigment production

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30668]	growth	15-25 °C
[Ref.: #30668]	optimum	22.5 °C
[Ref.: #67770]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #30668]			optimum	7.5
[Ref.: #30668]			growth	6-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30668]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	aerobe Confidence in %90.6

[Ref.: #30668]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %94.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30668]		NaCl		optimum	4	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30668]	arginine ChEBI	+	carbon source
[Ref.: #30668]	citrate ChEBI	+	carbon source
[Ref.: #30668]	galactose ChEBI	+	carbon source
[Ref.: #30668]	glucose ChEBI	+	carbon source
[Ref.: #30668]	glutamate ChEBI	+	carbon source
[Ref.: #30668]	glycerol ChEBI	+	carbon source
[Ref.: #30668]	propionate ChEBI	+	carbon source
[Ref.: #30668]	pyruvate ChEBI	+	carbon source
[Ref.: #30668]	succinate ChEBI	+	carbon source
[Ref.: #30668]	xylose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30668]	acid phosphatase	+	3.1.3.2
[Ref.: #30668]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30668]	catalase	+	1.11.1.6
[Ref.: #30668]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #30668]	Sample type/isolated from	marine sediment

[Ref.: #67770]	Sample type/isolated from	Sea-floor sediment collected from the Red Sea
[Ref.: #67770]	Country	Saudi Arabia
[Ref.: #67770]	Country ISO 3 Code	SAU
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JF776971 (>99% sequence identity) for Profundibacterium mesophilum subclade from Microbeatlas

Aquatic Samples	284
Soil Samples	56
Animal Samples	10
Plant Samples	1
Total Samples	351

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.: #30668]	Profundibacterium mesophilum KAUST100406-0324 16S ribosomal RNA gene, partial sequence	JF776971	1436	GenBank ENA	1037889 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Profundibacterium mesophilum KAUST100406-0324	GCA_009835145	contig	GenBank ENA	1037889 tax ID	*
[Ref.: #66792]	Profundibacterium mesophilum KAUST100406-0324	1037889.3	wgs	PATRIC	1037889 tax ID	*

[Ref.: #30668]	GC-content	64 mol%
[Ref.: #67770]	GC-content	64 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: Profundibacterium mesophilum KAUST100406-0324 PATRIC: 1037889.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.5	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.508	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	84.837	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	82.64	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.358	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	54.237	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Profundibacterium mesophilum KAUST100406-0324 NCBI: GCA_009835145
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	94.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	53.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	90.6

Availability in culture collections External links

[Ref.: #30668]

Culture collection no.

JCM 17872, NRRL B-59665

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia.	Lai PY, Miao L, Lee OO, Liu LL, Zhou XJ, Xu Y, Al-Suwailem A, Qian PY	Int J Syst Evol Microbiol	10.1099/ijs.0.041525-0	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 )

#30668

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 #26999 (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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João 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.: MicrobeAtlas 1.0 beta .

#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 .

#26999

IJSEM 1007 2013 ( DOI 10.1099/ijs.0.041525-0 , PubMed 22685108 )

* These data were automatically processed and therefore are not curated

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