Name: Pseudidiomarina marina PIM1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133427

Type strain:

Species: Pseudidiomarina marina

Strain Designation: PIM1

Culture col. no.: BCRC 17749, JCM 15083

Strain history: W. Y. Shieh PIM1.

NCBI tax ID(s): 502366 (species)

SI-ID 360524

BCRC 17749, JCM 15083

Special Collections

Section

Pseudidiomarina marina PIM1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

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	*Gammaproteobacteria*
	Order	*Alteromonadales*
	Family	*Idiomarinaceae*
	Genus	*Pseudidiomarina*
	Species	**Pseudidiomarina marina**
	Full Scientific Name (LPSN)	Pseudidiomarina marina Jean et al. 2009

Synonym

Idiomarina marina

Information on morphological and physiological properties Morphology

[Ref.: #28905]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.744

[Ref.: #28905]	Cell length	2.75 µm

[Ref.: #28905]	Cell width	0.7 µm

[Ref.: #28905]	Cell shape	rod-shaped

[Ref.: #28905]	Motility	no

[Ref.: #28905]

Pigment production

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #28905]	growth	10-42 °C
[Ref.: #28905]	optimum	32.5 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #28905]			optimum	7.5
[Ref.: #28905]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28905]

Oxygen tolerance

aerobe

[Ref.: #28905]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %91.938

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28905]		NaCl		growth	0.5-15	%
[Ref.: #28905]		NaCl		optimum	3.5	%

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28905]		gelatin ChEBI	+	carbon source
[Ref.: #28905]		leucine ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #28905]	acid phosphatase	+	3.1.3.2
[Ref.: #28905]	alkaline phosphatase	+	3.1.3.1
[Ref.: #28905]	catalase	+	1.11.1.6
[Ref.: #28905]	cytochrome oxidase	+	1.9.3.1
[Ref.: #28905]	gelatinase	+

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

[Ref.: #28905]	Sample type/isolated from	seawater

[Ref.: #67770]	Sample type/isolated from	Shallow coastal seawater of An-Ping Harbour
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tainan
[Ref.: #67770]	Country	Taiwan, Province of China
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU423908 (>99% sequence identity) for Pseudidiomarina marina from Microbeatlas

Aquatic Samples	80
Soil Samples	9
Animal Samples	19
Plant Samples	5
Total Samples	113

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.: #28905]	Pseudidiomarina marina strain PIM1 16S ribosomal RNA gene, partial sequence	EU423908	1465	GenBank ENA	502366 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudidiomarina marina PIM1	GCA_003987045	contig	GenBank ENA	502366 tax ID

[Ref.: #28905]	GC-content	46.6 mol%
[Ref.: #67770]	GC-content	47.17 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	46.6 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudidiomarina marina PIM1 NCBI: GCA_003987045.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.744	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.333	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.671	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.938	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.958	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	52.491	no

Availability in culture collections External links

[Ref.: #28905]

Culture collection no.

BCRC 17749, JCM 15083

[Ref.: #91432]

SI-ID 360524

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudidiomarina marina sp. nov. and Pseudidiomarina tainanensis sp. nov. and reclassification of Idiomarina homiensis and Idiomarina salinarum as Pseudidiomarina homiensis comb. nov. and Pseudidiomarina salinarum comb. nov., respectively.	Jean WD, Leu TY, Lee CY, Chu TJ, Lin SY, Shieh WY	Int J Syst Evol Microbiol	10.1099/ijs.0.001180-0	2009	*
Phylogeny	Idiomarina andamanensis sp. nov., an alkalitolerant bacterium isolated from Andaman Sea water.	Zachariah S, Das SK	Antonie Van Leeuwenhoek	10.1007/s10482-017-0908-5	2017	*
Phylogeny	Comparative analysis of 16S rRNA signature sequences of the genus Idiomarina and Idiomarina woesei sp. nov., a novel marine bacterium isolated from the Andaman Sea.	Poddar A, Lepcha RT, Mukherjee D, Bhattacharyya D, Das SK	Res Microbiol	10.1016/j.resmic.2014.07.008	2014	*

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 )

#28905

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 #25344 (see below)

#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 .

#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) .

#91432

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID360524.1 )

#25344

IJSEM 53 2009 ( DOI 10.1099/ijs.0.001180-0 , PubMed 19126723 )

* These data were automatically processed and therefore are not curated

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