Name: Pseudomonas profundi M5
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158812

Type strain:

Species: Pseudomonas profundi

Strain Designation: M5

Culture col. no.: CCTCC AB 2017186, KCTC 62119, CICC 24308

NCBI tax ID(s): 1981513 (species)

Section

Pseudomonas profundi M5 is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from deep-sea water sample.

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Pseudomonas*
	Species	**Pseudomonas profundi**
	Full Scientific Name (LPSN)	Pseudomonas profundi Sun et al. 2018

Synonym

Neopseudomonas profundi

Information on morphological and physiological properties Morphology

[Ref.: #65576]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #65576]	Cell length	1.8-2 µm

[Ref.: #65576]	Cell width	0.6-0.7 µm

[Ref.: #65576]	Cell shape	rod-shaped

[Ref.: #65576]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.612

[Ref.: #65576]	Flagellum arrangement	polar

[Ref.: #65576]	Colony size	0.5-1 mm
[Ref.: #65576]	Colony color	creamy
[Ref.: #65576]	Colony shape	circular
[Ref.: #65576]	Incubation period	3 days
[Ref.: #65576]	Cultivation medium used	MA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65576]

Culture medium

Marine agar (MA)

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Culture medium growth

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Culture medium

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #65576]			growth	4-40 °C
[Ref.: #65576]			optimum	25 °C

[Ref.: #65576]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #65576]			optimum	9
[Ref.: #65576]			growth	7-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65576]

Oxygen tolerance

obligate aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #65576]

Halophily / tolerance level

slightly halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65576]		NaCl		growth	0-10	%
[Ref.: #65576]		NaCl		optimum	1-2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65576]	(S)-lactate ChEBI	+	carbon source
[Ref.: #65576]	acetate ChEBI	+	carbon source
[Ref.: #65576]	adipate ChEBI	-	assimilation
[Ref.: #65576]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #65576]	bromosuccinate ChEBI	+	carbon source
[Ref.: #65576]	D-glucose ChEBI	-	assimilation
[Ref.: #65576]	D-mannitol ChEBI	-	assimilation
[Ref.: #65576]	D-mannose ChEBI	-	assimilation
[Ref.: #65576]	decanoate ChEBI	-	assimilation
[Ref.: #65576]	esculin ChEBI	-	hydrolysis
[Ref.: #65576]	gelatin ChEBI	-	hydrolysis
[Ref.: #65576]	gluconate ChEBI	-	assimilation
[Ref.: #65576]	glucose ChEBI	-	fermentation
[Ref.: #65576]	L-arabinose ChEBI	-	assimilation
[Ref.: #65576]	L-glutamate ChEBI	+	carbon source
[Ref.: #65576]	L-malate ChEBI	+	carbon source
[Ref.: #65576]	malate ChEBI	-	assimilation
[Ref.: #65576]	maltose ChEBI	-	assimilation
[Ref.: #65576]	N-acetylglucosamine ChEBI	-	assimilation
[Ref.: #65576]	nitrate ChEBI	+	reduction
[Ref.: #65576]	phenylacetate ChEBI	-	assimilation
[Ref.: #65576]	propionate ChEBI	+	carbon source
[Ref.: #65576]	sodium citrate ChEBI	-	assimilation
[Ref.: #65576]	starch ChEBI	-	hydrolysis
[Ref.: #65576]	tween 20 ChEBI	+	hydrolysis
[Ref.: #65576]	tween 40 ChEBI	+	carbon source
[Ref.: #65576]	tween 60 ChEBI	+	hydrolysis
[Ref.: #65576]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65576]	amikacin ChEBI	yes	30	µg (disc)
[Ref.: #65576]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #65576]	aztreonam ChEBI	yes	30	µg (disc)
[Ref.: #65576]	cefalotin ChEBI	yes	30	µg (disc)
[Ref.: #65576]	cefazolin ChEBI	yes	30	µg (disc)
[Ref.: #65576]	cefepime ChEBI	yes	30	µg (disc)
[Ref.: #65576]	cefoperazone ChEBI	yes	75	µg (disc)
[Ref.: #65576]	cefotaxime ChEBI	yes	30	µg (disc)
[Ref.: #65576]	cefoxitin ChEBI	yes	30	µg (disc)
[Ref.: #65576]	ceftazidime ChEBI	yes	30	µg (disc)
[Ref.: #65576]	ceftriaxone ChEBI	yes	30	µg (disc)
[Ref.: #65576]	cefuroxime ChEBI	yes	30	µg (disc)
[Ref.: #65576]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #65576]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #65576]	clarithromycin ChEBI	yes	15	µg (disc)
[Ref.: #65576]	clindamycin ChEBI	yes	2	µg (disc)
[Ref.: #65576]	clindamycin ChEBI				yes	2	µg (disc)
[Ref.: #65576]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #65576]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #65576]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #65576]	levofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #65576]	minocycline ChEBI	yes	30	µg (disc)
[Ref.: #65576]	nitrofurantoin ChEBI	yes	300	µg (disc)
[Ref.: #65576]	norfloxacin ChEBI	yes	10	µg (disc)
[Ref.: #65576]	ofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #65576]	oxacillin ChEBI				yes	1	µg (disc)
[Ref.: #65576]	penicillin g ChEBI	yes	10	µg (disc)
[Ref.: #65576]	piperacillin ChEBI	yes	100	µg (disc)
[Ref.: #65576]	polymyxin b ChEBI	yes	30	µg (disc)
[Ref.: #65576]	spectinomycin ChEBI	yes	100	µg (disc)
[Ref.: #65576]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #65576]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #65576]	tobramycin ChEBI	yes	10	µg (disc)
[Ref.: #65576]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65576]		hydrogen sulfide ChEBI	yes
[Ref.: #65576]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #65576]	acid phosphatase	-	3.1.3.2
[Ref.: #65576]	alkaline phosphatase	+	3.1.3.1
[Ref.: #65576]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #65576]	alpha-fucosidase	-	3.2.1.51
[Ref.: #65576]	alpha-galactosidase	-	3.2.1.22
[Ref.: #65576]	alpha-glucosidase	-	3.2.1.20
[Ref.: #65576]	alpha-mannosidase	-	3.2.1.24
[Ref.: #65576]	arginine dihydrolase	-	3.5.3.6
[Ref.: #65576]	beta-galactosidase	-	3.2.1.23
[Ref.: #65576]	beta-glucosidase	-	3.2.1.21
[Ref.: #65576]	beta-glucuronidase	-	3.2.1.31
[Ref.: #65576]	catalase	+	1.11.1.6
[Ref.: #65576]	cystine arylamidase	-	3.4.11.3
[Ref.: #65576]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65576]	esterase (C 4)	+
[Ref.: #65576]	esterase Lipase (C 8)	+
[Ref.: #65576]	leucine arylamidase	+	3.4.11.1
[Ref.: #65576]	lipase (C 14)	-
[Ref.: #65576]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #65576]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #65576]	trypsin	-	3.4.21.4
[Ref.: #65576]	urease	-	3.5.1.5
[Ref.: #65576]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #65576]	Sample type/isolated from	deep-sea water sample
[Ref.: #65576]	Sampling date	2016-09
[Ref.: #65576]	Geographic location (country and/or sea, region)	Mariana Trench
[Ref.: #65576]	Country	Pacific Ocean
[Ref.: #65576]	Geographic location	11.3859°/142.4840°
[Ref.: #65576]	Enrichment culture	MA
[Ref.: #65576]	Enrichment culture duration	14 days
[Ref.: #65576]	Enrichment culture temperature	4 ̊C
[Ref.: #65576]	Isolation/enrichment procedure	standard dilution-plating method, purification repeated three times
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

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.: #65576]	16S rRNA gene sequence	KY988340		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudomonas profundi M5	GCA_008638305	scaffold	GenBank	1981513 tax ID	*

[Ref.: #65576]

GC-content

62.4 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pseudomonas profundi M5 NCBI: GCA_008638305.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudomonas profundi M5 NCBI: GCA_008638305.1
[Ref.: #69480]	motile	yes	91.557	no
[Ref.: #69480]	flagellated	yes	88.743	yes
[Ref.: #69480]	gram-positive	no	98.552	no
[Ref.: #69480]	anaerobic	no	97.501	yes
[Ref.: #69480]	aerobic	yes	88.031	no
[Ref.: #69480]	halophile	yes	52.118	no
[Ref.: #69480]	spore-forming	no	94.856	no
[Ref.: #69480]	thermophile	no	99.583	yes
[Ref.: #69480]	glucose-util	no	52.303	no
[Ref.: #69480]	glucose-ferment	no	91.044	no

Availability in culture collections External links

[Ref.: #65576]

Culture collection no.

CCTCC AB 2017186, KCTC 62119, CICC 24308

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudomonas profundi sp. nov., isolated from deep-sea water.	Sun J, Wang W, Ying Y, Zhu X, Liu J, Hao J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002748	2018	*

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 )

#65576

Jingjing Sun, Wei Wang, Yu Ying, Xiangjie Zhu, Junzhong Liu and Jianhua Hao: Pseudomonas profundi sp. nov., isolated from deep-sea water. IJSEM 68: 1776 - 1780 2018 ( DOI 10.1099/ijsem.0.002748 , PubMed 29620498 )

#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) .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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