Name: Cephaloticoccus capnophilus CV41
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140168

Type strain:

Species: Cephaloticoccus capnophilus

Strain Designation: CV41

Culture col. no.: DSM 100879, ATCC TSD-39, NCIMB 15005

Strain history: <- J. Lin, Calvin College, Biology, Grand Rapids, USA; CV41 <- J. Wertz

NCBI tax ID(s): 1548208 (species)

Section

Cephaloticoccus capnophilus CV41 is an obligate aerobe, Gram-negative, coccus-shaped bacterium that was isolated from gut of the arboreal ant Cephalotes varians.

coccus-shaped
Gram-negative
obligate aerobe
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	*Verrucomicrobiota*
	Class	*Opitutia*
	Order	*Opitutales*
	Family	*Opitutaceae*
	Genus	"Cephaloticoccus"
	Species	"Cephaloticoccus capnophilus"
	Full Scientific Name (LPSN)	Cephaloticoccus capnophilus Lin et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43581]	Gram stain	negative

[Ref.: #43581]	Cell length	0.5-0.6 µm

[Ref.: #43581]	Cell shape	coccus-shaped

[Ref.: #43581]	Motility	no

[Ref.: #43581]	Colony color	Cream
[Ref.: #43581]	Cultivation medium used	TSA agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43581]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #43581]

Culture medium growth

[Ref.: #42775]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #42775]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #42775]

Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #42775]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #42775]	growth	25 °C
[Ref.: #43581]	growth	23-37 °C
[Ref.: #43581]	optimum	37 °C

[Ref.: #42775]	Temperature range	mesophilic
[Ref.: #43581]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43581]			optimum	7
[Ref.: #43581]			growth	6.9-7.3

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43581]

Oxygen tolerance

obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43581]		NaCl		growth	0.5-1.5	%(w/v)
[Ref.: #43581]		NaCl		optimum	1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43581]	acetate ChEBI	-	respiration
[Ref.: #43581]	alpha-lactose ChEBI	+	respiration
[Ref.: #43581]	aspartate ChEBI	-	respiration
[Ref.: #43581]	cellobiose ChEBI	+	respiration
[Ref.: #43581]	citrate ChEBI	-	respiration
[Ref.: #43581]	D-alanine ChEBI	-	respiration
[Ref.: #43581]	D-arabitol ChEBI	+	respiration
[Ref.: #43581]	D-fructose ChEBI	+	respiration
[Ref.: #43581]	D-galactose ChEBI	+	respiration
[Ref.: #43581]	D-glucose ChEBI	+	respiration
[Ref.: #43581]	D-mannitol ChEBI	+	respiration
[Ref.: #43581]	D-mannose ChEBI	+	respiration
[Ref.: #43581]	D-psicose ChEBI	-	respiration
[Ref.: #43581]	D-serine ChEBI	-	respiration
[Ref.: #43581]	D-sorbitol ChEBI	-	respiration
[Ref.: #43581]	dextrin ChEBI	+	respiration
[Ref.: #43581]	DL-carnitine ChEBI	-	respiration
[Ref.: #43581]	formate ChEBI	-	respiration
[Ref.: #43581]	gentiobiose ChEBI	+	respiration
[Ref.: #43581]	L-arabinose ChEBI	-	respiration
[Ref.: #43581]	L-asparagine ChEBI	-	respiration
[Ref.: #43581]	L-fucose ChEBI	-	respiration
[Ref.: #43581]	L-glutamate ChEBI	-	respiration
[Ref.: #43581]	L-histidine ChEBI	-	respiration
[Ref.: #43581]	L-leucine ChEBI	-	respiration
[Ref.: #43581]	L-proline ChEBI	-	respiration
[Ref.: #43581]	lactate ChEBI	+	respiration
[Ref.: #43581]	lactulose ChEBI	-	respiration
[Ref.: #43581]	maltose ChEBI	+	respiration
[Ref.: #43581]	melibiose ChEBI	-	respiration
[Ref.: #43581]	methyl beta-D-glucopyranoside ChEBI	+	respiration
[Ref.: #43581]	monomethyl succinate ChEBI	+	respiration
[Ref.: #43581]	propionate ChEBI	-	respiration
[Ref.: #43581]	raffinose ChEBI	-	respiration
[Ref.: #43581]	succinate ChEBI	+	respiration
[Ref.: #43581]	sucrose ChEBI	+	respiration
[Ref.: #43581]	trehalose ChEBI	+	respiration
[Ref.: #43581]	turanose ChEBI	+	respiration
[Ref.: #43581]	xylitol ChEBI	-	respiration
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #43581]	acid phosphatase	+	3.1.3.2
[Ref.: #43581]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43581]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43581]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43581]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43581]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43581]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43581]	beta-galactosidase	+	3.2.1.23
[Ref.: #43581]	beta-galactosidase	-	3.2.1.23
[Ref.: #43581]	beta-glucosidase	-	3.2.1.21
[Ref.: #43581]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43581]	catalase	-	1.11.1.6
[Ref.: #43581]	cystine arylamidase	-	3.4.11.3
[Ref.: #43581]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43581]	esterase (C 4)	+
[Ref.: #43581]	esterase Lipase (C 8)	+
[Ref.: #43581]	leucine arylamidase	-	3.4.11.1
[Ref.: #43581]	lipase (C 14)	-
[Ref.: #43581]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43581]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43581]	trypsin	-	3.4.21.4
[Ref.: #43581]	urease	+	3.5.1.5
[Ref.: #43581]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine 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]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	purine metabolism	58.51	55 of 94
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ppGpp biosynthesis	50	2 of 4
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	flavin biosynthesis	40	6 of 15
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	lysine metabolism	35.71	15 of 42
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lipid metabolism	25.81	8 of 31
[Ref.: #66794]	butanoate fermentation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		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.: #42775]	Sample type/isolated from	gut of the arboreal ant Cephalotes varians
[Ref.: #42775]	Host species	Cephalotes varians
[Ref.: #42775]	Geographic location (country and/or sea, region)	Florida, Key Largo, Crocodile Lake National Wildlife Refuge (25.29° N 80.31° W)
[Ref.: #42775]	Country	USA
[Ref.: #42775]	Country ISO 3 Code	USA
[Ref.: #42775]	Continent	North America
[Ref.: #42775]	Geographic location	25.2900°/-80.3100°

[Ref.: #43581]	Sample type/isolated from	the guts of Cephalotes varians collected from hollow mangrove twigs
[Ref.: #43581]	Geographic location (country and/or sea, region)	Crocodile Lake National Wildlife Refuge, Key Largo, FL
[Ref.: #43581]	Country	USA
[Ref.: #43581]	Country ISO 3 Code	USA
[Ref.: #43581]	Continent	North America
[Ref.: #43581]	Geographic location	25.2900°/-80.3100°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Mangrove
#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	#Stomach
#Host Body-Site	#Plant	#Stem (Branch)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KM066003 (>99% sequence identity) for Cephaloticoccus capnophilus subclade from Microbeatlas

Aquatic Samples	23
Soil Samples	14
Animal Samples	25
Plant Samples	4
Total Samples	66

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

[Ref.: #42775]

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.: #42775]	Cephaloticoccus capnophilus strain CV41 16S ribosomal RNA gene, partial sequence	KM066003	1552	ENA	1548208 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cephaloticoccus capnophilus CV41	GCA_001580045	contig	GenBank	1548208 tax ID	*

[Ref.: #43581]	GC-content	60.5 mol%
[Ref.: #42775]	GC-content	60.5 mol%	sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cephaloticoccus capnophilus CV41 NCBI: GCA_001580045.1
[Ref.: #69480]	flagellated	no	97.477	yes
[Ref.: #69480]	gram-positive	no	97.845	yes
[Ref.: #69480]	anaerobic	no	95.78	yes
[Ref.: #69480]	aerobic	yes	61.695	yes
[Ref.: #69480]	halophile	no	88.207	yes
[Ref.: #69480]	spore-forming	no	97.807	no
[Ref.: #69480]	thermophile	no	61.683	yes
[Ref.: #69480]	glucose-util	yes	89.757	yes
[Ref.: #69480]	motile	no	92.661	yes
[Ref.: #69480]	glucose-ferment	no	76.632	no

Availability in culture collections External links

[Ref.: #42775]

Culture collection no.

DSM 100879, ATCC TSD-39, NCIMB 15005

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cephaloticoccus gen. nov., a new genus of 'Verrucomicrobia' containing two novel species isolated from Cephalotes ant guts.	Lin JY, Russell JA, Sanders JG, Wertz JT	Int J Syst Evol Microbiol	10.1099/ijsem.0.001141	2016	*

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 )

#42775

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100879

#43581

Jonathan Y. Lin, Jacob A. Russell, Jon G. Sanders, John T. Wertz: Cephaloticoccus gen. nov., a new genus of 'Verrucomicrobia' containing two novel species isolated from Cephalotes ant guts. IJSEM 66: 3034 - 3040 2016 ( DOI 10.1099/ijsem.0.001141 , PubMed 27154284 )

#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) .

* These data were automatically processed and therefore are not curated

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