Name: Arcobacter anaerophilus JC84
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 23819

Type strain:

Species: Arcobacter anaerophilus

Strain Designation: JC84

Culture col. no.: DSM 24636, KCTC 15071, MTCC 10956, CECT 9783

Strain history: <- Ch Sasikala, Centre for Environment, IST, JNTU

NCBI tax ID(s): 877500 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Arcobacter anaerophilus JC84 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from estuarine sediment.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Epsilonproteobacteria*
	Order	*Campylobacterales*
	Family	*Arcobacteraceae*
	Genus	*Arcobacter*
	Species	**Arcobacter anaerophilus**
	Full Scientific Name (LPSN)	Arcobacter anaerophilus Sasi Jyothsna et al. 2013

	Synonym	Halarcobacter anaerophilus
	Synonym	"Haloarcobacter* anaerophilus"*

Information on morphological and physiological properties Morphology

[Ref.: #31159]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.6
[Ref.: #125438]	Gram stain	negative Confidence in %97.26

[Ref.: #31159]	Cell length	1.5 µm

[Ref.: #31159]	Cell width	0.2 µm

[Ref.: #31159]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31159]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #20311]

Incubation period

1-2 days

[Ref.: #31159]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #31159]	growth	25-37 °C
[Ref.: #31159]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31159]			optimum	7.5
[Ref.: #31159]			growth	07-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20311]	Oxygen tolerance	anaerobe
[Ref.: #31159]	Oxygen tolerance	anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #31159]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %96.6
[Ref.: #125438]	Ability of spore formation	no Confidence in %94.17

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31159]		NaCl		growth	0-6	%
[Ref.: #31159]		NaCl		optimum	2	%

[Ref.: #31159]	Observation	aggregates in clumps
[Ref.: #67771]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31159]	acetate ChEBI	+	carbon source
[Ref.: #31159]	arabinose ChEBI	+	carbon source
[Ref.: #31159]	cellobiose ChEBI	+	carbon source
[Ref.: #31159]	inosine ChEBI	+	carbon source
[Ref.: #31159]	L-arabitol ChEBI	+	carbon source
[Ref.: #31159]	lactose ChEBI	+	carbon source
[Ref.: #31159]	mannose ChEBI	+	carbon source
[Ref.: #31159]	melibiose ChEBI	+	carbon source
[Ref.: #31159]	nitrate ChEBI	+	reduction
[Ref.: #31159]	phenylethylamine ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #31159]		hydrogen sulfide ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31159]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	phenol degradation	70	14 of 20
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	denitrification	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	daunorubicin biosynthesis	22.22	2 of 9
		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.: #20311]	Sample type/isolated from	estuarine sediment
[Ref.: #20311]	Geographic location (country and/or sea, region)	West Bengal, Gangasagar
[Ref.: #20311]	Country	India
[Ref.: #20311]	Country ISO 3 Code	IND
[Ref.: #20311]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sediment sample from Gangasagar
[Ref.: #67771]	Geographic location (country and/or sea, region)	West Bengal
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Estuary
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Brackish

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence MG195889 (>99% sequence identity) for Arcobacter anaerophilus subclade from Microbeatlas

Aquatic Samples	1570
Soil Samples	77
Animal Samples	144
Plant Samples	30
Total Samples	1821

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

[Ref.: #20311]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #20311]	Arcobacter anaerophilus partial 16S rRNA gene, strain JC84, isolate D09-53	FR686494	1389	GenBank ENA	877500 tax ID
[Ref.: #67771]	Halarcobacter anaerophilus strain DSM 24636T 16S ribosomal RNA gene, partial sequence	MG195889	1505	GenBank ENA	877500 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halarcobacter anaerophilus DSM 24636	GCA_006459125	complete	GenBank ENA	877500 tax ID	*
[Ref.: #66792]	Halarcobacter anaerophilus DSM 24636	GCA_004116345	contig	GenBank ENA	877500 tax ID	*
[Ref.: #66792]	Arcobacter anaerophilus strain DSM 24636	877500.16	wgs	PATRIC	877500 tax ID	*
[Ref.: #66792]	Arcobacter anaerophilus strain DSM 24636	877500.17	complete	PATRIC	877500 tax ID	*
[Ref.: #66792]	Arcobacter anaerophilus DSM 24636	2871084118	draft	JGI IMG/M	877500 tax ID	*

[Ref.: #20311]	GC-content	24.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31159]	GC-content	24.6 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arcobacter anaerophilus DSM 24636 NCBI: GCA_006459125.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.26	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	55.494	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	60.081	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	94.17	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	85.98	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	81.981	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Arcobacter anaerophilus strain DSM 24636 PATRIC: 877500.17
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	52.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	85.1

Availability in culture collections External links

[Ref.: #20311]

Culture collection no.

DSM 24636, KCTC 15071, MTCC 10956, CECT 9783

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter.	Sasi Jyothsna TS, Rahul K, Ramaprasad EVV, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.054155-0	2013	*

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 )

#20311

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24636

#31159

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 #27487 (see below)

#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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#27487

IJSEM 4619 2013 ( DOI 10.1099/ijs.0.054155-0 , PubMed 23918794 )

* These data were automatically processed and therefore are not curated

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Arcobacter anaerophilus DSM 24636

Arcobacter anaerophilus strain DSM 24636

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