Name: Acanthopleuribacter pedis FYK2218
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24718

Type strain:

Species: Acanthopleuribacter pedis

Strain Designation: FYK2218

Culture col. no.: DSM 28897, KCTC 12899, NBRC 101209

Strain history: <- Y Uchino, NBRC <- Y Fukunaga, NBDC

NCBI tax ID(s): 442870 (species)

SI-ID 399724

DSM 28897

Special Collections

Section

When using BacDive for research please cite our paper

Acanthopleuribacter pedis FYK2218 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from chiton Acanthopleura japonica.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Acidobacteriota*
	Class	*Holophagae*
	Order	*Acanthopleuribacterales*
	Family	*Acanthopleuribacteraceae*
	Genus	*Acanthopleuribacter*
	Species	**Acanthopleuribacter pedis**
	Full Scientific Name (LPSN)	Acanthopleuribacter pedis Fukunaga et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32501]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %90

[Ref.: #32501]	Cell length	2.4-4.7 µm

[Ref.: #32501]	Cell width	0.7-1 µm

[Ref.: #32501]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #32501]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #67771]	Flagellum arrangement	peritrichous

[Ref.: #21191]

Incubation period

3-7 days

[Ref.: #32501]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21191]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #21191]

Culture medium growth

[Ref.: #21191]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21191]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21191]	growth	28 °C
[Ref.: #32501]	growth	15-30 °C
[Ref.: #32501]	optimum	30 °C
[Ref.: #67771]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #32501]			optimum	07-08
[Ref.: #32501]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32501]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32501]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %95.4

[Ref.: #32501]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: MK-6(57.8%), MK-7(42.2%)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32501]	alanine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32501]	glucose ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #32501]	serine ChEBI	+	carbon source
[Ref.: #32501]	threonine ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32501]	alkaline phosphatase	+	3.1.3.1
[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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[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.: #21191]	catalase	+	1.11.1.6
[Ref.: #32501]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32501]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #21191]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[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.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #21191]	26686	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+
[Ref.: #21191]	26685	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.
[Ref.: #21191]	28460	-	-	-	-	-	-	-	-	+/-	+/-	-	-	-	-	+/-	-	-	-	-	-	not determinedn.d.

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.: #21191]	14867	-	+	-	-	-	-	-	-	+/-	-	+	-	-	-	-	-	-	+	-	-

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

[Ref.: #21191]	Sample type/isolated from	chiton Acanthopleura japonica
[Ref.: #21191]	Host species	Acanthopleura japonica
[Ref.: #21191]	Geographic location (country and/or sea, region)	Chia, Katsuura
[Ref.: #21191]	Country	Japan
[Ref.: #21191]	Country ISO 3 Code	JPN
[Ref.: #21191]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From chitone, `Acanthopleura japonica`
[Ref.: #67771]	Geographic location (country and/or sea, region)	Katsuura, Chiba
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Mollusca

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB303221 (>99% sequence identity) for Acanthopleuribacter pedis subclade from Microbeatlas

Aquatic Samples	1219
Soil Samples	60
Animal Samples	112
Plant Samples	12
Total Samples	1403

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

[Ref.: #21191]

Biosafety level

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.: #21191]	Acanthopleuribacter pedis gene for 16S rRNA, partial sequence	AB303221	1453	GenBank ENA	442870 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Acanthopleuribacter pedis KCTC 12899	GCA_017377855	contig	GenBank ENA	442870 tax ID	*
[Ref.: #66792]	Acanthopleuribacter pedis strain KCTC 12899	442870.4	wgs	PATRIC	442870 tax ID	*

[Ref.: #32501]

GC-content

56.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acanthopleuribacter pedis strain KCTC 12899 PATRIC: 442870.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	90	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	90.353	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	81.633	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	73.789	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	88.882	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	69.781	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acanthopleuribacter pedis KCTC 12899 NCBI: GCA_017377855
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	95.4
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	55.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	86.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	63.2

Availability in culture collections External links

[Ref.: #21191]

Culture collection no.

DSM 28897, KCTC 12899, NBRC 101209

[Ref.: #88548]

SI-ID 399724

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov.	Wang G, Li Y, Liu J, Chen B, Su H, Liang J, Huang W, Yu K	Front Microbiol	10.3389/fmicb.2022.778535	2022	*
Phylogeny	Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum 'Acidobacteria'.	Fukunaga Y, Kurahashi M, Yanagi K, Yokota A, Harayama S	Int J Syst Evol Microbiol	10.1099/ijs.0.65589-0	2008	*

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 )

#21191

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28897

#32501

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 #28721 (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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#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 .

#88548

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-ID399724.1 )

#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 .

#28721

IJSEM 2597 2008 ( DOI 10.1099/ijs.0.65589-0 , PubMed 18984699 )

* These data were automatically processed and therefore are not curated

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Acanthopleuribacter pedis strain KCTC 12899

Acanthopleuribacter pedis KCTC 12899

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