Perlucidibaca piscinae | Type strain | DSM 21586, KCCM 42363, NBRC 102354, IMCC 1704 | BacDiveID:8209

Strain identifier

BacDive ID: 8209

Type strain:

Species: Perlucidibaca piscinae

Culture col. no.: DSM 21586, KCCM 42363, NBRC 102354, IMCC 1704

Strain history: <- J.-C. Cho, Inha University, Incheon

NCBI tax ID(s): 1122951 (strain), 392589 (species)

SI-ID 399154

DSM 21586

Section

Perlucidibaca piscinae DSM 21586 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from eutrophic pond.

Gram-negative
motile
rod-shaped
facultative aerobe
mesophilic
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	*Moraxellaceae*
	Genus	*Perlucidibaca*
	Species	**Perlucidibaca piscinae**
	Full Scientific Name (LPSN)	Perlucidibaca piscinae Song et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32149]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.996

[Ref.: #32149]	Cell length	0.95 µm

[Ref.: #32149]	Cell width	0.6 µm

[Ref.: #32149]	Cell shape	rod-shaped

[Ref.: #32149]	Motility	yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

R2A MEDIUM (DSMZ Medium 830)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #15825]			growth	28 °C
[Ref.: #32149]			growth	08-37 °C
[Ref.: #32149]			optimum	30 °C

[Ref.: #15825]	Temperature range	mesophilic
[Ref.: #32149]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32149]			optimum	7
[Ref.: #32149]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

facultative aerobe

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

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32149]		NaCl		growth	0-1	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32149]		arabinose ChEBI	+	carbon source
[Ref.: #32149]		arginine ChEBI	+	carbon source
[Ref.: #32149]		citrate ChEBI	+	carbon source
[Ref.: #32149]		galactose ChEBI	+	carbon source
[Ref.: #32149]		gluconate ChEBI	+	carbon source
[Ref.: #32149]		glucosamine ChEBI	+	carbon source
[Ref.: #32149]		glucose ChEBI	+	carbon source
[Ref.: #32149]		glycerol ChEBI	+	carbon source
[Ref.: #32149]		glycine ChEBI	+	carbon source
[Ref.: #32149]		histidine ChEBI	+	carbon source
[Ref.: #32149]		itaconate ChEBI	+	carbon source
[Ref.: #32149]		L-arabitol ChEBI	+	carbon source
[Ref.: #32149]		malonate ChEBI	+	carbon source
[Ref.: #32149]		maltose ChEBI	+	carbon source
[Ref.: #32149]		mannitol ChEBI	+	carbon source
[Ref.: #32149]		mannose ChEBI	+	carbon source
[Ref.: #32149]		myo-inositol ChEBI	+	carbon source
[Ref.: #32149]		N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32149]		nitrate ChEBI	+	reduction
[Ref.: #32149]		ornithine ChEBI	+	carbon source
[Ref.: #32149]		pyruvate ChEBI	+	carbon source
[Ref.: #32149]		raffinose ChEBI	+	carbon source
[Ref.: #32149]		rhamnose ChEBI	+	carbon source
[Ref.: #32149]		ribose ChEBI	+	carbon source
[Ref.: #32149]		serine ChEBI	+	carbon source
[Ref.: #32149]		sorbitol ChEBI	+	carbon source
[Ref.: #32149]		sucrose ChEBI	+	carbon source
[Ref.: #32149]		trehalose ChEBI	+	carbon source
[Ref.: #32149]		xylitol ChEBI	+	carbon source
[Ref.: #32149]		xylose ChEBI	+	carbon source
		Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #32149]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #32149]		indole ChEBI	+

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32149]		alkaline phosphatase	+	3.1.3.1
[Ref.: #32149]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #15825]	Sample type/isolated from	eutrophic pond
[Ref.: #15825]	Geographic location (country and/or sea, region)	Incheon
[Ref.: #15825]	Country	Republic of Korea
[Ref.: #15825]	Country ISO 3 Code	KOR
[Ref.: #15825]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Pond (small)

What are isolation sources categories?

Global distribution of 16S sequence AB681750 (>99% sequence identity) for Perlucidibaca piscinae from Microbeatlas

Aquatic Samples	511
Soil Samples	74
Animal Samples	327
Plant Samples	8
Total Samples	920

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

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.: #15825]	Perlucidibaca piscinae strain IMCC1704 16S ribosomal RNA gene, partial sequence	DQ664237	1467	ENA	392589 tax ID
[Ref.: #20218]	Perlucidibaca piscinae gene for 16S rRNA, partial sequence, strain: NBRC 102354	AB681750	1450	ENA	392589 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Perlucidibaca piscinae DSM 21586	GCA_000420045	contig	GenBank	1122951 tax ID	*
[Ref.: #66792]	Perlucidibaca piscinae DSM 21586	1122951.3	wgs	PATRIC	1122951 tax ID	*
[Ref.: #66792]	Perlucidibaca piscinae DSM 21586	2524614877	draft	JGI IMG/M	1122951 tax ID	*

GC-content

63.1 mol%

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: Perlucidibaca piscinae DSM 21586 PATRIC: 1122951.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Perlucidibaca piscinae DSM 21586 PATRIC: 1122951.3
[Ref.: #69480]	motile	yes	88.466	yes
[Ref.: #69480]	flagellated	yes	57.315	no
[Ref.: #69480]	gram-positive	no	98.877	yes
[Ref.: #69480]	anaerobic	no	99.129	yes
[Ref.: #69480]	aerobic	yes	85.639	yes
[Ref.: #69480]	halophile	no	94.316	yes
[Ref.: #69480]	spore-forming	no	96.151	no
[Ref.: #69480]	glucose-util	no	85.458	no
[Ref.: #69480]	thermophile	no	98.545	yes
[Ref.: #69480]	glucose-ferment	no	93.046	no

Availability in culture collections External links

Culture collection no.

DSM 21586, KCCM 42363, NBRC 102354, IMCC 1704

SI-ID 399154

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amnimonas aquatica gen. nov., sp. nov., Isolated from a Freshwater River.	Lee Y, Park HY, Jeon CO	Curr Microbiol	10.1007/s00284-019-01652-5	2019	*
Phylogeny	Perlucidibaca aquatica sp. nov., isolated from fresh water.	Baek K, Han JH, Lee MH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001940	2017	*
Phylogeny	Paraperlucidibaca wandonensis sp. nov., isolated from seawater, and emended description of the genus Paraperlucidibaca Oh et al. 2011.	Yoon JH, Park S, Jung YT, Lee JS, Lee KC	Int J Syst Evol Microbiol	10.1099/ijs.0.048645-0	2013	*
Phylogeny	Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater.	Oh KH, Lee SY, Lee MH, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.023994-0	2010	*
Phylogeny	Perlucidibaca piscinae gen. nov., sp. nov., a freshwater bacterium belonging to the family Moraxellaceae.	Song J, Choo YJ, Cho JC	Int J Syst Evol Microbiol	10.1099/ijs.0.65039-0	2008	*

References

#15825

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21586

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#32149

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 #28392 (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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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) .

#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 )

#77612

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-ID399154.1 )

#28392

IJSEM 97 2008 ( DOI 10.1099/ijs.0.65039-0 , PubMed 18175691 )

* These data were automatically processed and therefore are not curated

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