Name: Paraferrimonas sedimenticola Mok-106
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134209

Type strain:

Species: Paraferrimonas sedimenticola

Strain Designation: Mok-106

Culture col. no.: NBRC 101628, CIP 109284

Strain history: CIP <- 2006, NBRC <- S. Tabrez Khan, NBRC: strain MoK-106, "Ferrimonas sp."

NCBI tax ID(s): 375674 (species)

SI-ID 309482

CIP 109284, NBRC 101628

Section

Paraferrimonas sedimenticola Mok-106 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from Environment, Sea sediment.

Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Alteromonadales*
	Family	*Ferrimonadaceae*
	Genus	*Paraferrimonas*
	Species	**Paraferrimonas sedimenticola**
	Full Scientific Name (LPSN)	Paraferrimonas sedimenticola Khan and Harayama 2007

Information on morphological and physiological properties Morphology

[Ref.: #31852]	Gram stain	negative
[Ref.: #122533]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #31852]	Cell length	1.75 µm

[Ref.: #31852]	Cell width	0.85 µm

[Ref.: #31852]	Cell shape	rod-shaped
[Ref.: #122533]	Cell shape	rod-shaped

[Ref.: #31852]	Motility	yes
[Ref.: #122533]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %97.466

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37499]

Culture medium

Marine agar (MA)

[Ref.: #37499]

Culture medium growth

[Ref.: #37499]

Culture medium composition

expand / minimize

[Ref.: #122533]

Culture medium

CIP Medium 13

[Ref.: #122533]

Culture medium growth

[Ref.: #122533]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #31852]	growth	15-40 °C
[Ref.: #31852]	optimum	27.5 °C
[Ref.: #37499]	growth	25 °C

[Ref.: #31852]	Temperature range	mesophilic
[Ref.: #37499]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31852]			optimum	7.5
[Ref.: #31852]			growth	6.0-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31852]	Oxygen tolerance	facultative anaerobe
[Ref.: #122533]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31852]		NaCl		growth	0.5-4.0	%
[Ref.: #31852]		NaCl		optimum	2.25	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31852]	acetate ChEBI	+	carbon source
[Ref.: #31852]	alanine ChEBI	+	carbon source
[Ref.: #31852]	aspartate ChEBI	+	carbon source
[Ref.: #31852]	esculin ChEBI	+	hydrolysis
[Ref.: #31852]	glucose ChEBI	+	carbon source
[Ref.: #31852]	glutamate ChEBI	+	carbon source
[Ref.: #122533]	nitrate ChEBI	+	reduction
[Ref.: #122533]	nitrite ChEBI	+	reduction
[Ref.: #31852]	threonine ChEBI	+	carbon source
[Ref.: #31852]	tween 40 ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #122533]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31852]	catalase	+	1.11.1.6
[Ref.: #122533]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31852]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #31852]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122533]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #122533]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122533]	11767	-	+	+	+	-	+	-	-	+	+	-	+	-	-	-	-	-	+	-	-

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

[Ref.: #122533]	Sample type/isolated from	Environment, Sea sediment
[Ref.: #122533]	Geographic location (country and/or sea, region)	Okinawa
[Ref.: #122533]	Country	Japan
[Ref.: #122533]	Country ISO 3 Code	JPN
[Ref.: #122533]	Continent	Asia
[Ref.: #122533]	Isolation date	2005
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AB252732 (>99% sequence identity) for Paraferrimonas sedimenticola subclade from Microbeatlas

Aquatic Samples	12
Soil Samples	1
Animal Samples	1
Plant Samples
Total Samples	14

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

[Ref.: #122533]

Biosafety level

Risk group (French classification)

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.: #31852]	Paraferrimonas sedimenticola gene for 16S rRNA, partial sequence, strain: Mok-106	AB252732	1463	GenBank	375674 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paraferrimonas sedimenticola NBRC 101628	GCA_002282855	contig	GenBank	375674 tax ID	*
[Ref.: #66792]	Paraferrimonas sedimenticola strain NBRC 101628	375674.3	wgs	PATRIC	375674 tax ID	*
[Ref.: #66792]	Paraferrimonas sedimenticola NBRC 101628	2831818083	draft	JGI IMG/M	375674 tax ID	*

[Ref.: #31852]

GC-content

50.5 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: Paraferrimonas sedimenticola strain NBRC 101628 PATRIC: 375674.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paraferrimonas sedimenticola strain NBRC 101628 PATRIC: 375674.3
[Ref.: #69480]	gram-positive	no	99.19	yes
[Ref.: #69480]	anaerobic	no	95.617	no
[Ref.: #69480]	halophile	yes	60.073	no
[Ref.: #69480]	spore-forming	no	97.682	no
[Ref.: #69480]	glucose-util	yes	88.107	no
[Ref.: #69480]	aerobic	no	53.356	no
[Ref.: #69480]	motile	yes	90.065	yes
[Ref.: #69480]	flagellated	yes	75.199	no
[Ref.: #69480]	thermophile	no	98.329	yes
[Ref.: #69480]	glucose-ferment	no	58.91	no

Availability in culture collections External links

[Ref.: #31852]

Culture collection no.

NBRC 101628, CIP 109284

[Ref.: #91805]

SI-ID 309482

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Psychrobium conchae gen. nov., sp. nov., a psychrophilic marine bacterium isolated from the Iheya North hydrothermal field.	Nogi Y, Abe M, Kawagucci S, Hirayama H	Int J Syst Evol Microbiol	10.1099/ijs.0.066738-0	2014	*
Phylogeny	Paraferrimonas sedimenticola gen. nov., sp. nov., a marine bacterium of the family Ferrimonadaceae.	Khan ST, Harayama S	Int J Syst Evol Microbiol	10.1099/ijs.0.64529-0	2007	*
Phylogeny	Paraferrimonas haliotis sp. nov., isolated from the intestine of abalone, Haliotis discus hannai and emendation of description of the genus Paraferrimonas.	Huang J, Huang Z, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.002414	2017	*

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 )

#31852

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 #28116 (see below)

#37499 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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 )

#91805

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-ID309482.1 )

#122533 Collection of Institut Pasteur ; Curators of the CIP; CIP 109284

#28116

IJSEM 1493 2007 ( DOI 10.1099/ijs.0.64529-0 , PubMed 17625182 )

* These data were automatically processed and therefore are not curated

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Paraferrimonas sedimenticola strain NBRC 101628

Paraferrimonas sedimenticola strain NBRC 101628

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