Archive BacDiveID:10.13145/bacdive133466.20250331.9.3

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BacDive ID 133466

Type strain

Strain Designation 908087

Culture col. no. CGMCC 1.7285 JCM 15534 908087

NCBI tax ID(s) 519453

Links

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For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 29079

BacDive-ID: 133466

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, rod-shaped

description: Pseudidiomarina tainanensis 908087 is an aerobe, Gram-negative, motile bacterium that was isolated from seawater.

NCBI tax id

NCBI tax id: 519453
Matching level: species

strain history

@ref: 67770
history: X.-W. Xu 908087.

doi: 10.13145/bacdive133466.20250331.9.3

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Alteromonadales
family: Idiomarinaceae
genus: Pseudidiomarina
species: Pseudidiomarina tainanensis
full scientific name: Pseudidiomarina tainanensis Jean et al. 2009
synonyms
@ref synonym
20215 Idiomarina tainanensis
20215 Pseudidiomarina maritima
20215 Idiomarina maritima

@ref	synonym
20215	Idiomarina tainanensis
20215	Pseudidiomarina maritima
20215	Idiomarina maritima

@ref: 29079

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Idiomarinaceae

genus: Pseudidiomarina

species: Pseudidiomarina maritima

strain designation: 908087

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29079	negative	1.75 µm	0.5 µm	rod-shaped	yes
125438	negative					98.744

pigmentation

@ref: 29079
production: no

Culture and growth conditions

culture temp

@ref	growth	type	temperature
29079	positive	growth	10-45
29079	positive	optimum	37
67770	positive	growth	30

culture pH

@ref	ability	type	pH	PH range
29079	positive	growth	6.5-10.0	alkaliphile
29079	positive	optimum	8.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
29079	aerobe
125439	obligate aerobe	99.7

spore formation

@ref: 125438
spore formation: no
confidence: 93.563

halophily

@ref	salt	growth	tested relation	concentration
29079	NaCl	positive	growth	0.5-15 %
29079	NaCl	positive	optimum	3 %

observation

@ref: 67770
observation: quinones: Q-8

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29079	53424	tween 20	+	carbon source
29079	53426	tween 80	+	carbon source

enzymes

@ref	value	activity	ec
29079	catalase	+	1.11.1.6
29079	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref	sample type	country	origin.country	continent
29079	seawater
67770	Coastal seawater sample collected from the East China Sea	China	CHN	Asia

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic
Cat3: #Marine

taxonmaps

@ref: 69479
File name: preview.99_26495.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_197;96_3743;97_4602;98_5910;99_26495&stattab=map
Last taxonomy: Pseudidiomarina
16S sequence: EU600203
Sequence Identity:
Total samples: 522
soil counts: 13
aquatic counts: 337
animal counts: 168
plant counts: 4

Sequence information

16S sequences

@ref: 29079
description: Pseudidiomarina maritima strain 908087 16S ribosomal RNA gene, partial sequence
accession: EU600203
length: 1507
database: nuccore
NCBI tax ID: 519453

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Idiomarina maritima strain CGMCC 1.7285	519453.3	wgs	patric	519453
66792	Idiomarina maritima CGMCC 1.7285	2617270903	draft	img	519453
67770	Pseudidiomarina maritima CGMCC 1.7285	GCA_900115255	contig	ncbi	519453

GC content

@ref	GC-content	method
29079	45.2
67770	45.2	high performance liquid chromatography (HPLC)
67770	47.4	genome sequence analysis

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	no	98.744	yes
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	96.606	yes
125438	spore-forming	spore-forming	Ability to form endo- or exospores	no	93.563	no
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	81.014	yes
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	no	97.475	no
125438	motile2+	flagellated	Ability to perform flagellated movement	no	54.491	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	no	85.7
125439	BacteriaNet	motility	Ability to perform movement	yes	65.1
125439	BacteriaNet	gram_stain	Reaction to gram-staining	negative	80.3
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	obligate aerobe	99.7

External links

@ref: 29079

culture collection no.: CGMCC 1.7285, JCM 15534

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19502309	Pseudidiomarina donghaiensis sp. nov. and Pseudidiomarina maritima sp. nov., isolated from the East China Sea.	Wu YH, Shen YQ, Xu XW, Wang CS, Oren A, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.005702-0	2009	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gammaproteobacteria/classification/genetics/isolation & purification/physiology, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Species Specificity	Genetics
Phylogeny	23223816	Idiomarina indica sp. nov., isolated from seawater.	Song L, Ren F, Huang Y, Dai X, Zhou Y	Int J Syst Evol Microbiol	10.1099/ijs.0.046789-0	2012	Alteromonadaceae/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis	Genetics
Phylogeny	25078320	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	Aerobiosis, Alteromonadaceae/classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature	Genetics
Phylogeny	31486762	Pseudidiomarina maritima Wu et al. 2009 is a later heterotypic synonym of Pseudidiomarina tainanensis Jean et al. 2009 and emended description of the species.	Liu Y, Lai Q, Shao Z, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003678	2019	Alteromonadaceae/classification/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Transcriptome
Phylogeny	31697639	Pseudidiomarina gelatinasegens sp. nov., isolated from surface sediment of the Terra Nova Bay, Antarctica.	Li A, Zhang M, Xu S, Chen M, Yao Q, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003760	2020	Alteromonadaceae/classification/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, Bays, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Glycolipids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry	Transcriptome

Reference

@id	authors	title	doi/url	ID_cross_reference	pubmed
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	10.1099/ijsem.0.004332
29079	Barberan A, Caceres Velazquez H, Jones S, Fierer N.	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	10.1128/mSphere.00237-17	25509	28776041
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)	https://diaspora-project.de/progress.html#genomes
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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	https://microbeatlas.org/
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets	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	https://github.com/GenomeNet/deepG

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Archive

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

pigmentation

Culture and growth conditions

culture temp

culture pH

Physiology and metabolism

oxygen tolerance

spore formation

halophily

observation

metabolite utilization

enzymes

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

literature

Reference

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