Name: Capsulimonas corticalis Ax-7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158453

Type strain:

Species: Capsulimonas corticalis

Strain Designation: Ax-7

Culture col. no.: DSM 105890, NBRC 113044

Strain history: <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki Univ., Japan <- J. Li; Ax-7

NCBI tax ID(s): 2219043 (species)

SI-ID 399782

DSM 105890

Section

Capsulimonas corticalis Ax-7 is a mesophilic, Gram-negative bacterium that was isolated from bark surface, beech tree Fagus crenata.

Gram-negative
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	*Armatimonadota*
	Class	*Armatimonadia*
	Order	*Capsulimonadales*
	Family	*Capsulimonadaceae*
	Genus	*Capsulimonas*
	Species	**Capsulimonas corticalis**
	Full Scientific Name (LPSN)	Capsulimonas corticalis Li et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.809

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65129]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #65129]

Culture medium growth

[Ref.: #65129]

Culture medium link

Medium recipe at MediaDive

[Ref.: #65129]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #65129]			growth	28 °C

[Ref.: #65129]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %98.806

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	isoprenoid biosynthesis	69.23	18 of 26
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cardiolipin biosynthesis	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
		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.: #65129]	Sample type/isolated from	bark surface, beech tree Fagus crenata
[Ref.: #65129]	Geographic location (country and/or sea, region)	Shirakami Mountains
[Ref.: #65129]	Country	Japan
[Ref.: #65129]	Country ISO 3 Code	JPN
[Ref.: #65129]	Continent	Asia
[Ref.: #65129]	Geographic location	40.5169°/140.2140°
* marker position based on {}

Isolation sources categories

#Host Body-Site	#Plant	#Bark
#Host	#Plants	#Tree

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC318429 (>99% sequence identity) for Capsulimonas corticalis subclade from Microbeatlas

Aquatic Samples	674
Soil Samples	5308
Animal Samples	629
Plant Samples	1121
Total Samples	7732

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.: #65129]	Capsulimonas corticalis gene for 16S ribosomal RNA, partial sequence, strain: AX-7	LC318429	1431	ENA	2219043 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Capsulimonas corticalis AX-7	GCA_003574315	complete	GenBank	2219043 tax ID	*
[Ref.: #66792]	Armatimonadia bacterium AX-7	2219043.3	wgs	PATRIC	2219043 tax ID	*
[Ref.: #66792]	Capsulimonas corticalis AX-7	2831870349	draft	JGI IMG/M	2219043 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: Armatimonadia bacterium AX-7 PATRIC: 2219043.3
[Ref.: #69481]	spore-forming	no	57	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Armatimonadia bacterium AX-7 PATRIC: 2219043.3
[Ref.: #69480]	motile	yes	72.191	no
[Ref.: #69480]	gram-positive	no	81.212	no
[Ref.: #69480]	anaerobic	no	98.177	no
[Ref.: #69480]	aerobic	yes	89.97	no
[Ref.: #69480]	halophile	no	94.975	no
[Ref.: #69480]	spore-forming	no	79.952	no
[Ref.: #69480]	glucose-util	yes	82.354	no
[Ref.: #69480]	flagellated	no	81.91	no
[Ref.: #69480]	thermophile	no	94.004	no
[Ref.: #69480]	glucose-ferment	no	86.639	no

Availability in culture collections External links

[Ref.: #65129]

Culture collection no.

DSM 105890, NBRC 113044

[Ref.: #111254]

SI-ID 399782

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Capsulimonas corticalis gen. nov., sp. nov., an aerobic capsulated bacterium, of a novel bacterial order, Capsulimonadales ord. nov., of the class Armatimonadia of the phylum Armatimonadetes.	Li J, Kudo C, Tonouchi A	Int J Syst Evol Microbiol	10.1099/ijsem.0.003135	2018	*

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 )

#65129

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105890

#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 )

#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 )

#111254

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-ID399782.1 )

* These data were automatically processed and therefore are not curated

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Armatimonadia bacterium AX-7

Armatimonadia bacterium AX-7

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