Pectinatus haikarae (DSM 16980, VTT E-88329)

Name: Pectinatus haikarae (DSM 16980, VTT E-88329)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17146

Type strain

Culture col. no. DSM 16980 VTT E-88329

NCBI tax ID(s) 349096

Special Collections DSMZ Literature strains

History <- R. Juvonen <- VTT

Links

Pectinatus haikarae DSM 16980 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from air, bottling hall in a brewery.

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

Name and taxonomic classification

SI-ID 286033

DSM 16980,VTT E-88329

@ref 20215

Last LPSN update 2026-02-09 11:22:08

Domain Bacteria

Phylum Bacillota

Class Negativicutes

Order Selenomonadales

Family Selenomonadaceae

Genus Pectinatus

Species Pectinatus haikarae

Full scientific name Pectinatus haikarae Juvonen and Suihko 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
31505	negative	03-50 µm	0.6-0.8 µm	rod-shaped

Colony morphology

@ref	Type of hemolysis	Incubation period
6599	gamma	3-7 days

Pigmentation

31505

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6599	MRS pre-reduced (DSMZ Medium 11b)		Medium recipe at MediaDive	Name: MRS MEDIUM (pre-reduced) (DSMZ Medium 11b) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Resazurin 0.001 g/l Distilled water
6599	BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)		Medium recipe at MediaDive	Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6599	positive	growth	30	mesophilic
31505	positive	growth	15-30
31505	positive	optimum	20-30

Culture pH

@ref	Ability	Type	PH
31505	positive	optimum	7
31505	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6599	anaerobe
31505	anaerobe

Spore formation

31505

Spore formationno

Observation

31505

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	+	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	-	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
31505	24265 ChEBI	gluconate	+	carbon source
68367	17754 ChEBI	glycerol	+	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	+	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
31505	17716 ChEBI	lactose	+	carbon source
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
31505	29864 ChEBI	mannitol	+	carbon source
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
31505	28053 ChEBI	melibiose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
31505	17272 ChEBI	propionate	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	+	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite
31505	16136 ChEBI	hydrogen sulfide
68380	35581 ChEBI	indole	from API rID32A
68367	35581 ChEBI	indole	from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

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
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68367	gelatinase	-		from API 20A
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
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
6599	-	-	+	+	+	-	-	-	+	+	-	-	+	-	+	-	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
6599	-	-	+	+	+	-	-	-	+	+	-	-	+	-	+	-	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
6599	-	-	+	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
6599	-	-	+	+	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Fermented
#Environmental	#Air	#Indoor Air
#Engineered	#Food production	#Beverage

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6599	air, bottling hall in a brewery	Finland	FIN	Europe

Taxonmaps

69479

Global distribution of 16S sequence DQ223731 (>99% sequence identity) for Pectinatus haikarae subclade from Microbeatlas

Aquatic Samples	150
Soil Samples	13
Animal Samples	371
Plant Samples	3
Total Samples	537

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6599	1	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
124043	ASM3081350v1 assembly for Pectinatus haikarae DSM 16980	contig	GCA_030813505	349096.6	2926546190	349096	70.68

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6599	Pectinatus haikarae strain VTT E-88329 16S ribosomal RNA gene, partial sequence	DQ223731	1535		349096

GC content

6599

GC-content (mol%)38.8

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Carbohydrate Metabolism Differentiates Pectinatus and Megasphaera Species Growing in Beer.	Arnold MJ, Ritter SW, Ehrmann MA, Kurniawan YN, Suzuki K, Becker TM, Liebl W.	Microorganisms	10.3390/microorganisms12102045	2024
Biotechnology	Comparative genetic and physiological characterisation of Pectinatus species reveals shared tolerance to beer-associated stressors but halotolerance specific to pickle-associated strains.	Kramer T, Kelleher P, van der Meer J, O'Sullivan T, Geertman JA, Duncan SH, Flint HJ, Louis P.	Food Microbiol	10.1016/j.fm.2020.103462	2020
	Modified multiplex PCR methods for comprehensive detection of Pectinatus and beer-spoilage cocci.	Iijima K, Asano S, Suzuki K, Ogata T, Kitagawa Y.	Biosci Biotechnol Biochem	10.1271/bbb.80297	2008
Phylogeny	Pectinatus sottacetonis sp. nov., isolated from a commercial pickle spoilage tank.	Caldwell JM, Juvonen R, Brown J, Breidt F.	Int J Syst Evol Microbiol	10.1099/ijs.0.047886-0	2013
Phylogeny	Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus.	Juvonen R, Suihko ML	Int J Syst Evol Microbiol	10.1099/ijs.0.63699-0	2006

References

#6599	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16980
#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 )
#27803	IJSEM 695 2006 ( DOI 10.1099/ijs.0.63699-0 , PubMed 16585679 )
#31505	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 #27803
#68367	Automatically annotated from API 20A .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Pectinatus haikarae (DSM 16980, VTT E-88329)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030813505

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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