Name: Helicobacter pametensis B9
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24100

Type strain:

Species: Helicobacter pametensis

Strain Designation: B9, B9A

Culture col. no.: DSM 29139, ATCC 51478, CCUG 29255, CIP 104249, LMG 12678

Strain history: CIP <- 1996, ATCC <- 1991, F.E. Dewhirst, FDC, Boston, USA <- C. Seymour, Boston, USA: strain B9A

NCBI tax ID(s): 1408442 (strain), 95149 (species)

SI-ID 13918

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

Other strains from Helicobacter pametensis

H. pametensis B12A, CIP 104250, ATCC 51479, CCUG ...
H. pametensis CCUG 29253
H. pametensis CCUG 29259
H. pametensis CCUG 29260, LMG 12682

Section

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

motile
mesophilic
microaerophile
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	*Epsilonproteobacteria*
	Order	*Campylobacterales*
	Family	*Helicobacteraceae*
	Genus	*Helicobacter*
	Species	**Helicobacter pametensis**
	Full Scientific Name (LPSN)	Helicobacter pametensis Dewhirst et al. 1994

Information on morphological and physiological properties Morphology

[Ref.: #121522]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #121522]	Cell shape	rod-shaped

[Ref.: #121522]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.816

[Ref.: #121522]	Hemolysis ability	1

[Ref.: #20607]	Incubation period	2-3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20607]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #20607]

Culture medium growth

[Ref.: #20607]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20607]

Culture medium composition

expand / minimize

[Ref.: #37167]

Culture medium

MEDIUM 6 - Columbia agar with 10 % horse blood

[Ref.: #37167]

Culture medium growth

[Ref.: #37167]

Culture medium composition

expand / minimize

[Ref.: #121522]

Culture medium

Brucella broth

[Ref.: #121522]

Culture medium growth

[Ref.: #121522]

Culture medium

CIP Medium 6

[Ref.: #121522]

Culture medium growth

[Ref.: #121522]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121522]

Culture medium

CIP Medium 45

[Ref.: #121522]

Culture medium growth

[Ref.: #121522]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #20607]			growth	37 °C
[Ref.: #37167]			growth	37 °C

[Ref.: #20607]	Temperature range	mesophilic
[Ref.: #37167]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20607]

Oxygen tolerance

microaerophile

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #121522]		NaCl	no	growth	3.5	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #121522]		nitrate ChEBI	+	reduction
[Ref.: #121522]		nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #121522]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #121522]		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.: #121522]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #121522]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #121522]	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.: #121522]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121522]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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:

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.: #121522]	7859	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #20607]	Sample type/isolated from	Tern faeces
[Ref.: #20607]	Country	USA
[Ref.: #20607]	Country ISO 3 Code	USA
[Ref.: #20607]	Continent	North America

[Ref.: #121522]	Sample type/isolated from	Tern, feces
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #20607]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121522]	Biosafety level	2	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.: #20607]	Helicobacter pametensis strain ATCC 51478 16S ribosomal RNA, partial sequence	NR_114586	1439	GenBank	95149 tax ID
[Ref.: #20607]	Helicobacter pametensis strain B9A Seymour 16S small subunit ribosomal RNA gene, partial sequence	M88147	1481	ENA	95149 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Helicobacter pametensis ATCC 51478	GCA_000518225	scaffold	GenBank	1408442 tax ID	*
[Ref.: #66792]	Helicobacter pametensis ATCC 51478	1408442.3	wgs	PATRIC	1408442 tax ID	*
[Ref.: #66792]	Helicobacter pametensis ATCC 51478	2546825547	draft	JGI IMG/M	1408442 tax ID	*

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: Helicobacter pametensis ATCC 51478 PATRIC: 1408442.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Helicobacter pametensis ATCC 51478 ATCC 51478 NCBI: GCA_000518225.1
[Ref.: #69480]	motile	yes	88.632	no
[Ref.: #69480]	flagellated	no	50	no
[Ref.: #69480]	gram-positive	no	99.247	no
[Ref.: #69480]	anaerobic	no	76.638	yes
[Ref.: #69480]	halophile	no	79.653	no
[Ref.: #69480]	spore-forming	no	96.528	no
[Ref.: #69480]	thermophile	no	65.608	yes
[Ref.: #69480]	glucose-util	no	76.776	no
[Ref.: #69480]	aerobic	no	97.795	yes
[Ref.: #69480]	glucose-ferment	no	80.579	no

Availability in culture collections External links

[Ref.: #20607]

Culture collection no.

DSM 29139, ATCC 51478, CCUG 29255, CIP 104249, LMG 12678

[Ref.: #88062]

SI-ID 13918

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 .

#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 )

#88062

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-ID13918.1 )

#121522 Collection of Institut Pasteur ; Curators of the CIP; CIP 104249
* These data were automatically processed and therefore are not curated

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Helicobacter pametensis ATCC 51478

Helicobacter pametensis ATCC 51478 ATCC 51478

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