Name: Pontibacter akesuensis AKesu 4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23884

Type strain:

Species: Pontibacter akesuensis

Strain Designation: AKesu 4, ASK 1

Culture col. no.: DSM 18820, CCTCC AB 206086, KCTC 12758, AKS 1

Strain history: <- R Lai, Nanjing Agricultural Univ., China

NCBI tax ID(s): 388950 (species)

SI-ID 405247

DSM 18820

Section

Pontibacter akesuensis AKesu 4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from desert soil.

Gram-negative
rod-shaped
aerobe
mesophilic
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Hymenobacteraceae*
	Genus	*Pontibacter*
	Species	**Pontibacter akesuensis**
	Full Scientific Name (LPSN)	Pontibacter akesuensis Zhou et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31959]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #31959]	Cell length	1.5-1.6 µm

[Ref.: #31959]	Cell width	0.7-0.75 µm

[Ref.: #31959]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31959]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #31959]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21095]

Culture medium

LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)

[Ref.: #21095]

Culture medium growth

[Ref.: #21095]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21095]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21095]	growth	28 °C
[Ref.: #31959]	growth	04-36 °C
[Ref.: #31959]	optimum	29 °C
[Ref.: #67771]	growth	28-30 °C

[Ref.: #21095]	Temperature range	mesophilic
[Ref.: #31959]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31959]			optimum	7.8
[Ref.: #31959]			growth	7-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31959]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31959]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31959]		NaCl		growth	0-4	%
[Ref.: #31959]		NaCl		optimum	2	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31959]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #31959]	4-hydroxy-L-proline ChEBI	+	carbon source
[Ref.: #31959]	acetate ChEBI	+	carbon source
[Ref.: #31959]	alanine ChEBI	+	carbon source
[Ref.: #31959]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #31959]	arabinose ChEBI	+	carbon source
[Ref.: #31959]	asparagine ChEBI	+	carbon source
[Ref.: #31959]	aspartate ChEBI	+	carbon source
[Ref.: #31959]	cellobiose ChEBI	+	carbon source
[Ref.: #31959]	dextrin ChEBI	+	carbon source
[Ref.: #31959]	DL-carnitine ChEBI	+	carbon source
[Ref.: #31959]	esculin ChEBI	+	hydrolysis
[Ref.: #31959]	fructose ChEBI	+	carbon source
[Ref.: #31959]	fucose ChEBI	+	carbon source
[Ref.: #31959]	galactose ChEBI	+	carbon source
[Ref.: #31959]	galacturonate ChEBI	+	carbon source
[Ref.: #31959]	gluconate ChEBI	+	carbon source
[Ref.: #31959]	glucose ChEBI	+	carbon source
[Ref.: #31959]	glutamate ChEBI	+	carbon source
[Ref.: #31959]	glycogen ChEBI	+	carbon source
[Ref.: #31959]	histidine ChEBI	+	carbon source
[Ref.: #31959]	inosine ChEBI	+	carbon source
[Ref.: #31959]	itaconate ChEBI	+	carbon source
[Ref.: #31959]	L-alaninamide ChEBI	+	carbon source
[Ref.: #31959]	L-arabitol ChEBI	+	carbon source
[Ref.: #31959]	leucine ChEBI	+	carbon source
[Ref.: #31959]	maltose ChEBI	+	carbon source
[Ref.: #31959]	melibiose ChEBI	+	carbon source
[Ref.: #31959]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #31959]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #31959]	myo-inositol ChEBI	+	carbon source
[Ref.: #31959]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31959]	ornithine ChEBI	+	carbon source
[Ref.: #31959]	phenylalanine ChEBI	+	carbon source
[Ref.: #31959]	proline ChEBI	+	carbon source
[Ref.: #31959]	propionate ChEBI	+	carbon source
[Ref.: #31959]	putrescine ChEBI	+	carbon source
[Ref.: #31959]	quinate ChEBI	+	carbon source
[Ref.: #31959]	raffinose ChEBI	+	carbon source
[Ref.: #31959]	rhamnose ChEBI	+	carbon source
[Ref.: #31959]	serine ChEBI	+	carbon source
[Ref.: #31959]	sorbitol ChEBI	+	carbon source
[Ref.: #31959]	succinate ChEBI	+	carbon source
[Ref.: #31959]	sucrose ChEBI	+	carbon source
[Ref.: #31959]	threonine ChEBI	+	carbon source
[Ref.: #31959]	thymidine ChEBI	+	carbon source
[Ref.: #31959]	trehalose ChEBI	+	carbon source
[Ref.: #31959]	xylitol ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31959]		alpha-galactosidase	+	3.2.1.22
[Ref.: #31959]		gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	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]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	lipid metabolism	83.87	26 of 31
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	isoprenoid biosynthesis	73.08	19 of 26
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of pentoses	57.14	16 of 28
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	valine metabolism	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #21095]	Sample type/isolated from	desert soil
[Ref.: #21095]	Geographic location (country and/or sea, region)	Akesu, XinJiang Province
[Ref.: #21095]	Country	China
[Ref.: #21095]	Country ISO 3 Code	CHN
[Ref.: #21095]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From desert soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Xinjiang Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil
#Condition	#Xerophilic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ672723 (>99% sequence identity) for Pontibacter akesuensis from Microbeatlas

Aquatic Samples	168
Soil Samples	225
Animal Samples	60
Plant Samples	19
Total Samples	472

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

[Ref.: #21095]

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.: #21095]	Pontibacter akesuensis strain AKS 1 16S ribosomal RNA gene, partial sequence	DQ672723	1408	ENA	388950 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pontibacter akesuensis DSM 18820	GCA_900116885	contig	GenBank	388950 tax ID	*
[Ref.: #66792]	Pontibacter akesuensis KCTC 12758	GCA_014651555	scaffold	GenBank	388950 tax ID	*
[Ref.: #66792]	Pontibacter akesuensis strain DSM 18820	388950.6	wgs	PATRIC	388950 tax ID	*
[Ref.: #66792]	Pontibacter akesuensis strain KCTC 12758	388950.7	wgs	PATRIC	388950 tax ID	*
[Ref.: #66792]	Pontibacter akesuensis DSM 18820	2622736541	draft	JGI IMG/M	388950 tax ID	*

[Ref.: #31959]

GC-content

51.4 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pontibacter akesuensis KCTC 12758 NCBI: GCA_014651555.1
[Ref.: #69480]	motile	no	90.223	yes
[Ref.: #69480]	flagellated	no	96.351	yes
[Ref.: #69480]	gram-positive	no	98.494	no
[Ref.: #69480]	anaerobic	no	99.105	yes
[Ref.: #69480]	aerobic	yes	90.333	yes
[Ref.: #69480]	halophile	no	77.946	no
[Ref.: #69480]	spore-forming	no	95.423	yes
[Ref.: #69480]	thermophile	no	97.632	no
[Ref.: #69480]	glucose-util	yes	89.412	yes
[Ref.: #69480]	glucose-ferment	no	87.227	no

Availability in culture collections External links

[Ref.: #21095]

Culture collection no.

DSM 18820, CCTCC AB 206086, KCTC 12758, AKS 1

[Ref.: #87894]

SI-ID 405247

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pontibacter silvestris sp. nov., isolated from the soil of a Populus euphratica forest and emended description of the genus Pontibacter.	Osman G, Wang Z, Wang N, Shayimu G, Hou M, Guo W, Yang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.002972	2018	*
Genetics	Complete Genome Sequence of Pontibacter akesuensis Strain AKS 1T, Which Exhibits Robust Nutrient Metabolism in Harsh Environments.	Wang Y, He K, Jiang Y, Shen J, Yu B	Genome Announc	10.1128/genomeA.00997-16	2016	*
Phylogeny	Pontibacter akesuensis sp. nov., isolated from a desert soil in China.	Zhou Y, Wang X, Liu H, Zhang KY, Zhang YQ, Lai R, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64716-0	2007	*

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 )

#21095

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18820

#31959

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 #28215 (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 .

#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) .

#87894

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-ID405247.1 )

#28215

IJSEM 321 2007 ( DOI 10.1099/ijs.0.64716-0 , PubMed 17267972 )

* These data were automatically processed and therefore are not curated

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Pontibacter akesuensis KCTC 12758

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