Helicobacter pametensis (DSM 29139, ATCC 51478, CCUG 29255)

Name: Helicobacter pametensis (DSM 29139, ATCC 51478, CCUG 29255)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24100

Type strain

Strain Designation B9, B9A

Culture col. no. DSM 29139 ATCC 51478 CCUG 29255 CIP 104249 B9 2 more

NCBI tax ID(s) 1408442 95149

Special Collections DSMZ CCUG CIP

History DSMZ <- CIP <- ATCC <- F. E. Dewhirst, Forsyth Dental Center, Boston, USA <- C. Seymor; B9 CIP <- 1996, ATCC <- 1991, F.E. Dewhirst, FDC, Boston, USA <- C. Seymour, Boston, USA: strain B9A

Links

Helicobacter pametensis B9 is a microaerophile, Gram-negative, motile bacterium that was isolated from Tern faeces.

Gram-negative motile rod-shaped microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 13918

LMG 12678,CCUG 29255,ATCC 51478,CIP 104249,NCTC 12887,CCUG 34905,DSM 29139

@ref 20215

Last LPSN update 2026-05-29 08:30:33

Domain Bacteria

Phylum Pseudomonadota

Class Epsilonproteobacteria

Order Campylobacterales

Family Helicobacteraceae

Genus Helicobacter

Species Helicobacter pametensis

Full scientific name Helicobacter pametensis Dewhirst et al. 1994

BacDive ID	Other strains from **Helicobacter pametensis** (4)	Type strain
137264	H. pametensis B12A, CIP 104250, ATCC 51479, CCUG 29257, ...
145685	H. pametensis CCUG 29253
145687	H. pametensis CCUG 29259
145688	H. pametensis CCUG 29260, LMG 12682

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
125438	negative			96.483
121522	negative	rod-shaped

Colony morphology

@ref	Incubation period	Hemolysis ability
20607	2-3 days
121522		1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
20607	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
37167	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121522	Brucella broth
121522	CIP Medium 6	Medium recipe at CIP
121522	CIP Medium 45	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
20607	positive	growth	37
37167	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
20607	microaerophile
125439	facultative anaerobe	92.634

Spore formation

@ref	Spore formation	Confidence
125439		99.744
125438		97.02

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121522	NaCl		growth	3.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121522	17632 ChEBI	nitrate	+	reduction
121522	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121522	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121522	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121522	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121522	gamma-glutamyltransferase	+	2.3.2.2
121522	gelatinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121522	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
121522	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Fatty acid profile

Metadata FA analysis

@ref

65611

Fatty acid	Percentage	ECL
C16:0	30.2	16
C14:0	26.8	14
C18:1 ω7c /12t/9t	23.9	17.824
C16:0 3OH	4.1	17.52
C18:2 ω6,9c/C18:0 ANTE	4.1	17.724
C14:0 3OH/C16:1 ISO I	3.4	15.485
C12:0	2.7	12
C16:1 ω7c	1.2	15.819
C18:1 ω9c	0.9	17.769
C18:0	0.8	18
C15:0	0.5	15
Unidentified	0.3	15.943
Unidentified	0.3	13.936
C13:0	0.2	13
C13:0 ISO 2OH	0.2	13.814
C17:0	0.2	17
unknown 14.503	0.2	14.503
C20:2 ω6,9c	0.1	19.735

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121522	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Birds	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
20607	Tern faeces	USA	USA	North America
121522	Tern, feces

Taxonmaps

69479

Global distribution of 16S sequence NR_114586 (>99% sequence identity) for Helicobacter pametensis subclade from Microbeatlas

Aquatic Samples	68
Soil Samples	44
Animal Samples	790
Plant Samples	4
Total Samples	906

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20607	1	Risk group (German classification)
121522	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM51822v1 assembly for Helicobacter pametensis ATCC 51478	scaffold	GCA_000518225	1408442.3	2546825547	1408442	74.26

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20607	Helicobacter pametensis strain B9A Seymour 16S small subunit ribosomal RNA gene, partial sequence	M88147	1481	95149
20607	Helicobacter pametensis strain ATCC 51478 16S ribosomal RNA, partial sequence	NR_114586	1439	95149
124043	Helicobacter pametensis 16S ribosomal RNA gene, partial sequence.	AF302105	1439	95149

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM51822v1 assembly for Helicobacter pametensis ATCC 51478
NCBI: GCA_000518225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.63	no
125439	gram_stain	BacteriaNetⓘ	negative	86.10	no
125439	motility	BacteriaNetⓘ	no	77.39	no
125439	spore_formation	BacteriaNetⓘ	no	99.74	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Helicobacter pametensis ATCC 51478 ATCC 51478
NCBI: GCA_000518225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.48	no
125438	anaerobic	anaerobicⓘ	no	74.86	yes
125438	aerobic	aerobicⓘ	no	90.20	no
125438	spore-forming	spore-formingⓘ	no	97.02	no
125438	thermophilic	thermophileⓘ	no	92.03	yes
125438	flagellated	motile2+ⓘ	yes	50.96	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host.	Gilbert MJ, Duim B, Timmerman AJ, Zomer AL, Wagenaar JA.	Sci Rep	10.1038/s41598-017-09091-7	2017
Phylogeny	Diagnosis of Genus Helicobacter through a hemi-nested PCR assay of 16S rRNA.	Qin H, Tang G, Yi P, Pan X, Huang H, Chang R, Shi Z, Ashraf MA.	Saudi Pharm J	10.1016/j.jsps.2016.04.015	2016
Metabolism	Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization.	Vinella D, Fischer F, Vorontsov E, Gallaud J, Malosse C, Michel V, Cavazza C, Robbe-Saule M, Richaud P, Chamot-Rooke J, Brochier-Armanet C, De Reuse H.	PLoS Pathog	10.1371/journal.ppat.1005312	2015
Enzymology	Detection and prevalence of Helicobacter infection in pet cats.	Neiger R, Dieterich C, Burnens A, Waldvogel A, Corthesy-Theulaz I, Halter F, Lauterburg B, Schmassmann A.	J Clin Microbiol	10.1128/jcm.36.3.634-637.1998	1998
Pathogenicity	Rapid detection, by PCR and reverse hybridization, of mutations in the Helicobacter pylori 23S rRNA gene, associated with macrolide resistance.	van Doorn LJ, Debets-Ossenkopp YJ, Marais A, Sanna R, Megraud F, Kusters JG, Quint WG.	Antimicrob Agents Chemother	10.1128/aac.43.7.1779	1999
Phylogeny	Helicobacter mesocricetorum sp. nov., A novel Helicobacter isolated from the feces of Syrian hamsters.	Simmons JH, Riley LK, Besch-Williford CL, Franklin CL.	J Clin Microbiol	10.1128/jcm.38.5.1811-1817.2000	2000

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 )
#20607	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29139
#37167	; Curators of the CIP;
#65611	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 29255
#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 .
#121522	Collection of Institut Pasteur ; Curators of the CIP; CIP 104249
#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 .
#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 )

Rate our new design

Content

About us

Helicobacter pametensis (DSM 29139, ATCC 51478, CCUG 29255)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Fatty acid profile

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000518225

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media