Name: Campylobacter pinnipediorum subsp. caledonicus CCUG 68650
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 157015

Type strain:

Species: Campylobacter pinnipediorum subsp. caledonicus

Culture col. no.: CCUG 68650, LMG 29473, DSM 112310, RM 18020

Strain history: <- CCUG; CCUG 68650 <- G. Foster, SAC, Scottish Agricultural College; RM18020

NCBI tax ID(s): 1874362 (subspecies)

SI-ID 405878

DSM 112310, CCUG 68650

Section

Campylobacter pinnipediorum subsp. caledonicus CCUG 68650 is a microaerophile, mesophilic bacterium that was isolated from Lung abscess,grey seal.

mesophilic
microaerophile
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	*Campylobacteraceae*
	Genus	*Campylobacter*
	Species	**Campylobacter pinnipediorum subsp. caledonicus**
	Full Scientific Name (LPSN)	Campylobacter pinnipediorum subsp. caledonicus Gilbert et al. 2017

Information on culture and growth conditions Culture and growth conditions

[Ref.: #67675]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #67675]

Culture medium growth

[Ref.: #67675]

Culture medium link

Medium recipe at MediaDive

[Ref.: #67675]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #63506]			growth	37 °C
[Ref.: #67675]			growth	37 °C

[Ref.: #63506]	Temperature range	mesophilic
[Ref.: #67675]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63506]

Oxygen tolerance

microaerophile

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	61.54	8 of 13
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	purine metabolism	54.26	51 of 94
[Ref.: #66794]	phenylalanine metabolism	53.85	7 of 13
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	pyrimidine metabolism	51.11	23 of 45
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	glycolysis	47.06	8 of 17
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	non-pathway related	44.74	17 of 38
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	methylglyoxal degradation	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	methionine metabolism	34.62	9 of 26
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	lipid metabolism	29.03	9 of 31
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	tryptophan metabolism	26.32	10 of 38
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	tyrosine metabolism	21.43	3 of 14
[Ref.: #66794]	arginine metabolism	20.83	5 of 24
[Ref.: #66794]	histidine metabolism	20.69	6 of 29
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #63506]	Sample type/isolated from	Lung abscess,grey seal
[Ref.: #63506]	Sampling date	2010-11-15
[Ref.: #63506]	Geographic location (country and/or sea, region)	Inverness
[Ref.: #63506]	Country	United Kingdom
[Ref.: #63506]	Country ISO 3 Code	GBR
[Ref.: #63506]	Continent	Europe

[Ref.: #67675]	Sample type/isolated from	lung abscess, grey seal
[Ref.: #67675]	Geographic location (country and/or sea, region)	Inverness, Scotland
[Ref.: #67675]	Country	United Kingdom
[Ref.: #67675]	Country ISO 3 Code	GBR
[Ref.: #67675]	Continent	Europe
[Ref.: #67675]	Geographic location	57.4833°/-4.2167°
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Aquatic mammal
#Host Body-Site	#Other	#Abscess
#Host Body-Site	#Oral cavity and airways	#Lung

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Campylobacter pinnipediorum subsp. caledonicus M302/10/6	GCA_002021985	complete	GenBank	1874362 tax ID	*
[Ref.: #66792]	Campylobacter sp. RM18020 strain RM18020	1660070.3	complete	PATRIC	1874362 tax ID	*
[Ref.: #66792]	Campylobacter pinnipediorum caledonicus RM18020	2791355310	complete	JGI IMG/M	1874362 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Campylobacter pinnipediorum subsp. caledonicus RM18020 NCBI: GCA_002021985.1
[Ref.: #69480]	flagellated	yes	69.12	no
[Ref.: #69480]	gram-positive	no	98.91	no
[Ref.: #69480]	anaerobic	no	76.678	no
[Ref.: #69480]	aerobic	no	97.813	yes
[Ref.: #69480]	halophile	no	74.584	no
[Ref.: #69480]	spore-forming	no	94.203	no
[Ref.: #69480]	glucose-util	no	88.415	no
[Ref.: #69480]	thermophile	no	90.298	yes
[Ref.: #69480]	motile	yes	89.893	no
[Ref.: #69480]	glucose-ferment	no	85.657	no

Availability in culture collections External links

[Ref.: #67675]

Culture collection no.

CCUG 68650, LMG 29473, DSM 112310, RM 18020

[Ref.: #110157]

SI-ID 405878

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov.	Gilbert MJ, Miller WG, Leger JS, Chapman MH, Timmerman AJ, Duim B, Foster G, Wagenaar JA	Int J Syst Evol Microbiol	10.1099/ijsem.0.001894	2017	*

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 )

#63506 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 68650

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67675

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 112310

#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) .

#110157

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-ID405878.1 )

* These data were automatically processed and therefore are not curated

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Campylobacter pinnipediorum subsp. caledonicus RM18020

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