Cite this strain

Persicitalea jodogahamensis (MBIC 07417, IAM 15412, KCTC 12866)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134231

Type strain

Strain Designation Shu-9-SY12-35C

Culture col. no. MBIC 07417 IAM 15412 KCTC 12866 Shu-9-SY12-35C NBRC 103568 2 more

NCBI tax ID(s) 402147

Special Collections JCM KCTC CIP Literature strains

Links

Name and taxonomic classification

Persicitalea jodogahamensis Shu-9-SY12-35C is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 308624

IAM 15412, KCTC 12866, JCM 23195, NBRC 103568, CIP 109672

Last LPSN update 2024-12-09 10:49:21

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Persicitalea

Species Persicitalea jodogahamensis

Full scientific name Persicitalea jodogahamensis Yoon et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
32004	negative	4.5 µm	0.4 µm	rod-shaped
125439	negative
125438	negative

Pigmentation

32004

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
32004	positive	optimum	27.5	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
32004	positive	optimum	7
32004	positive	growth	05-10

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32004	NaCl	positive	growth	0-7 %
32004	NaCl	positive	optimum	3.5 %

Observation

67770

Observationquinones: MK-7

Spore formation

@ref	Spore formation
32004
125439

Enzymes

@ref	Value	Activity	Ec
32004	catalase	+	1.11.1.6
32004	cytochrome oxidase	+	1.9.3.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32004	22599 ChEBI	arabinose	+	carbon source
32004	17057 ChEBI	cellobiose	+	carbon source
32004	28757 ChEBI	fructose	+	carbon source
32004	33984 ChEBI	fucose	+	carbon source
32004	28260 ChEBI	galactose	+	carbon source
32004	17234 ChEBI	glucose	+	carbon source
32004	17716 ChEBI	lactose	+	carbon source
32004	17306 ChEBI	maltose	+	carbon source
32004	37684 ChEBI	mannose	+	carbon source
32004	28053 ChEBI	melibiose	+	carbon source
32004	506227 ChEBI	N-acetylglucosamine	+	carbon source
32004	16634 ChEBI	raffinose	+	carbon source
32004	26546 ChEBI	rhamnose	+	carbon source
32004	17814 ChEBI	salicin	+	carbon source
32004	17992 ChEBI	sucrose	+	carbon source
32004	27082 ChEBI	trehalose	+	carbon source
32004	18222 ChEBI	xylose	+	carbon source

Oxygen tolerance

@ref	Oxygen tolerance
32004	aerobe
125438	aerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type
32004	seawater
67770	Seawater in Jodogahama

Taxonmaps

69479

Global distribution of 16S sequence AB272165 (>99% sequence identity) for Persicitalea jodogahamensis subclade from Microbeatlas

Aquatic Samples	1245
Soil Samples	354
Animal Samples	153
Plant Samples	17
Total Samples	1769

Safety information

Sequence information

GC content

@ref	GC-content (mol%)
32004	56.3
67770	56.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
32004	Persicitalea jodogahamensis gene for 16S rRNA, partial sequence	AB272165	1464		402147
124043	Persicitalea jodogahamensis gene for 16S rRNA, partial sequence, strain: NBRC 103568.	AB682132	1437		402147

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Persicitalea jodogahamensis KCTC 12866	GCA_014651615	scaffold		402147
66792	Persicitalea jodogahamensis strain KCTC 12866	402147.3	wgs	PATRIC	402147

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Persicitalea jodogahamensis KCTC 12866
NCBI: GCA_014651615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.10	no
125439	motility	BacteriaNetⓘ	no	66.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	82.30	no

Predictions from Diaspora project based on:
Persicitalea jodogahamensis KCTC 12866
NCBI: GCA_014651615.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.35	yes
125438	anaerobic	anaerobicⓘ	no	96.25	no
125438	aerobic	aerobicⓘ	yes	90.81	no
125438	spore-forming	spore-formingⓘ	no	83.94	yes
125438	thermophilic	thermophileⓘ	no	93.85	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Persicitalea jodogahamensis gen. nov., sp. nov., a marine bacterium of the family 'Flexibacteraceae', isolated from seawater in Japan.	Yoon J, Ishikawa S, Kasai H, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64792-0	2007

Straininfo Link

@ref	Straininfo	Culture collections
91825	308624	IAM 15412, KCTC 12866, JCM 23195, NBRC 103568, CIP 109672

Culture collection no.

Culture collection no.
MBIC 07417
IAM 15412
KCTC 12866
Shu-9-SY12-35C
NBRC 103568
CIP 109672
JCM 23195

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 )
#32004	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 #28258 (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) .
#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 .
#91825	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-ID308624.1 )
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .

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