Pyramidobacter piscolens (DSM 21147, CCUG 55836, KCTC 15164)

Name: Pyramidobacter piscolens (DSM 21147, CCUG 55836, KCTC 15164)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17785

Type strain

Strain Designation W5455

Culture col. no. DSM 21147 CCUG 55836 KCTC 15164 W5455 JCM 16336

NCBI tax ID(s) 638849

Special Collections DSMZ CCUG JCM KCTC Literature strains

History <- J. Downes; W5455 <- L. Fernandes-Naglik {2000} CCUG 55836 <-- J. Downes W5455. <- DSM <- J Downes, W5455 <- L Fernandes-Naglik

Links

Pyramidobacter piscolens W5455 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from aspirate from oral abscess.

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

Name and taxonomic classification

SI-ID 408315

KCTC 15164,JCM 16336,DSM 21147,CCUG 55836

@ref 20215

Last LPSN update 2026-02-09 11:22:18

Domain Bacteria

Phylum Synergistota

Class Synergistia

Order Synergistales

Family Dethiosulfovibrionaceae

Genus Pyramidobacter

Species Pyramidobacter piscolens

Full scientific name Pyramidobacter piscolens Downes et al. 2009

BacDive ID	Other strains from **Pyramidobacter piscolens** (1)	Type strain
154949	P. piscolens CCUG 55837

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
28882	negative	1.5 µm	0.75 µm	rod-shaped
67771
67771	negative
125439	negative				95.1

Colony morphology

60748

Incubation period2 days

Pigmentation

28882

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15564	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15564	positive	growth	37	mesophilic
28882	positive	optimum	30	mesophilic
60748	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
15564	anaerobe
28882	anaerobe
60748	anaerobe
67771	anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98

Observation

28882

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28882	30089 ChEBI	acetate	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
28882	18401 ChEBI	phenylacetate	+	carbon source
28882	17272 ChEBI	propionate	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
28882	30031 ChEBI	succinate	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
28882	16136 ChEBI	hydrogen sulfide
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	+		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
15564	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Oral cavity and airways	#Mouth
#Host Body-Site	#Other	#Abscess

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
15564	aspirate from oral abscess		London	United Kingdom	GBR	Europe
60748	Human abscess aspirate,oral odontogenic	2000-12-19	London	United Kingdom	GBR	Europe
67770	Human oral cavity
67771	From human odontogenic abscess		London	United Kingdom	GBR	Europe

Taxonmaps

69479

Global distribution of 16S sequence EU309492 (>99% sequence identity) for Pyramidobacter piscolens subclade from Microbeatlas

Aquatic Samples	264
Soil Samples	174
Animal Samples	10378
Plant Samples	58
Total Samples	10874

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15564	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM17733v1 assembly for Pyramidobacter piscolens W5455	contig	GCA_000177335	352165.18	647000302	352165	49.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15564	Pyramidobacter piscolens W5455 16S ribosomal RNA gene, partial sequence	EU309492	1445		352165
67770	Pyramidobacter piscolens gene for 16S ribosomal RNA, partial sequence	AB565480	1484		352165

GC content

@ref	GC-content (mol%)	Method
15564	59	high performance liquid chromatography (HPLC)
28882	59
67771	59.0	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pyramidobacter piscolens W5455
NCBI: GCA_000177335

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	74.10	no
125439	gram_stain	BacteriaNetⓘ	negative	95.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	69.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pyramidobacter piscolens W5455
PATRIC: 352165.18

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	79.06	no
125438	anaerobic	anaerobicⓘ	yes	89.99	no
125438	spore-forming	spore-formingⓘ	no	78.39	no
125438	aerobic	aerobicⓘ	no	95.62	yes
125438	thermophilic	thermophileⓘ	no	85.21	yes
125438	flagellated	motile2+ⓘ	no	87.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Characterization and survey in cattle of a rumen Pyrimadobacter sp. which degrades the plant toxin fluoroacetate.	Kang S, Khan S, Webb R, Denman S, McSweeney C	FEMS Microbiol Ecol	10.1093/femsec/fiaa077	2020
Phylogeny	Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity.	Downes J, Vartoukian SR, Dewhirst FE, Izard J, Chen T, Yu WH, Sutcliffe IC, Wade WG	Int J Syst Evol Microbiol	10.1099/ijs.0.000364-0	2009

References

#15564	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21147
#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 )
#25322	IJSEM 972 2009 ( DOI 10.1099/ijs.0.000364-0 , PubMed 19406777 )
#28882	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 #25322
#60748	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55836
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68380	Automatically annotated from API rID32A .
#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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Pyramidobacter piscolens (DSM 21147, CCUG 55836, KCTC 15164)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000177335

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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