Pseudidiomarina sediminum (DSM 21906, CICC 10319, LMG 24046)

Name: Pseudidiomarina sediminum (DSM 21906, CICC 10319, LMG 24046)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6237

Type strain

Strain Designation c121

Culture col. no. DSM 21906 CICC 10319 LMG 24046 c121

NCBI tax ID(s) 1122124 431675

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Pseudidiomarina sediminum c121 is a facultative anaerobe, mesophilic, Gram-negative prokaryote that was isolated from coastal sediment.

Gram-negative rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 298148

LMG 24046,DSM 21906,KCTC 22743

@ref 20215

Last LPSN update 2025-12-16 09:48:16

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Alteromonadales

Family Idiomarinaceae

Genus Pseudidiomarina

Species Pseudidiomarina sediminum

Full scientific name Pseudidiomarina sediminum Hu and Li 2007

Synonyms (1)

Idiomarina sediminum

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
32253	negative	1.5 µm	0.3 µm	rod-shaped
125439	negative
125438	negative

Pigmentation

32253

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15901	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15901	positive	growth	28	mesophilic
32253	positive	growth	13-42
32253	positive	optimum	35	mesophilic

Culture pH

@ref	Ability	Type	PH
32253	positive	optimum	8.5
32253	positive	growth	6.3-10.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
32253	facultative anaerobe
125439	obligate aerobe

Spore formation

@ref	Spore formation
32253
125439
125438

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32253	NaCl	positive	growth	0.5-15 %
32253	NaCl	positive	optimum	4.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32253	5291 ChEBI	gelatin	+	carbon source
32253	17306 ChEBI	maltose	+	carbon source
32253	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32253	cytochrome oxidase	+	1.9.3.1
32253	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Coast

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15901	coastal sediment	Luoyuan Bay, Fujian Province	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF212001 (>99% sequence identity) for Pseudidiomarina sediminum subclade from Microbeatlas

Aquatic Samples	57
Soil Samples	3
Animal Samples	32
Plant Samples
Total Samples	92

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15901	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM398726v1 assembly for Pseudidiomarina sediminum c121	contig	GCA_003987265	431675.4	431675	78.33
66792	ASM42316v1 assembly for Pseudidiomarina sediminum DSM 21906	scaffold	GCA_000423165	1122124.3	1122124	77

Genome browser: GCA_003987265

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15901	Pseudidiomarina sediminum strain c121 16S ribosomal RNA gene, partial sequence	EF212001	1455		1122124

GC content

@ref	GC-content (mol%)
15901	50.0
32253	50

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudidiomarina sediminum DSM 21906
NCBI: GCA_000423165

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	84.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudidiomarina sediminum DSM 21906 DSM 21906
NCBI: GCA_000423165.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.10	yes
125438	anaerobic	anaerobicⓘ	no	96.47	yes
125438	aerobic	aerobicⓘ	yes	66.84	yes
125438	spore-forming	spore-formingⓘ	no	94.49	yes
125438	thermophilic	thermophileⓘ	no	96.21	yes
125438	flagellated	motile2+ⓘ	no	73.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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
Phylogeny	Pseudidiomarina sediminum sp. nov., a marine bacterium isolated from coastal sediments of Luoyuan Bay in China.	Hu ZY, Li Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65199-0	2007

References

#15901	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21906
#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 )
#32253	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 #28494 (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) .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pseudidiomarina sediminum (DSM 21906, CICC 10319, LMG 24046)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003987265

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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