Cuneatibacter caecimuris (DSM 29486, KCTC 15539, BARN-424-CC-10)

Name: Cuneatibacter caecimuris (DSM 29486, KCTC 15539, BARN-424-CC-10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131527

Type strain

Strain Designation BARN-424-CC-10

Culture col. no. DSM 29486 KCTC 15539 BARN-424-CC-10

NCBI tax ID(s) 1796618

Special Collections DSMZ KCTC Mouse DZIF

Links

Cuneatibacter caecimuris BARN-424-CC-10 is a microaerophile, mesophilic, rod-shaped prokaryote that was isolated from caecal content; TNF^deltaARE/+ C57BL/6 mouse.

rod-shaped microaerophile mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397974

KCTC 15539,DSM 29486

@ref 20215

Last LPSN update 2025-12-16 10:01:16

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Cuneatibacter

Species Cuneatibacter caecimuris

Full scientific name Cuneatibacter caecimuris Lagkouvardos et al. 2016

Morphology

Cell morphology

@ref	Cell shape
67771	rod-shaped
67771

Colony morphology

22754

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22754	WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)		Medium recipe at MediaDive	Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
22754	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22754	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
22754	microaerophile
67771	anaerobe
125439	anaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68380	beta-glucuronidase	+	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	L-lactaldehyde degradation	100	3 of 3
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	83.33	15 of 18
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	degradation of hexoses	77.78	14 of 18
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	pentose phosphate pathway	72.73	8 of 11
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	degradation of pentoses	67.86	19 of 28
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	purine metabolism	67.02	63 of 94
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	degradation of sugar acids	64	16 of 25
66794	d-xylose degradation	63.64	7 of 11
66794	methionine metabolism	61.54	16 of 26
66794	flavin biosynthesis	60	9 of 15
66794	methylglyoxal degradation	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	pyrimidine metabolism	60	27 of 45
66794	lipoate biosynthesis	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	polyamine pathway	56.52	13 of 23
66794	oxidative phosphorylation	56.04	51 of 91
66794	tryptophan metabolism	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	alanine metabolism	55.17	16 of 29
66794	leucine metabolism	53.85	7 of 13
66794	vitamin E metabolism	50	2 of 4
66794	acetate fermentation	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	adipate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	cysteine metabolism	50	9 of 18
66794	tetrahydrofolate metabolism	50	7 of 14
66794	lipid metabolism	48.39	15 of 31
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	vitamin B1 metabolism	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	molybdenum cofactor biosynthesis	44.44	4 of 9
66794	glutathione metabolism	42.86	6 of 14
66794	lysine metabolism	42.86	18 of 42
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	vitamin B6 metabolism	36.36	4 of 11
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	tyrosine metabolism	28.57	4 of 14
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	carotenoid biosynthesis	27.27	6 of 22
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
22754	-	-	+	+	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
22754	-	-	+	+	-	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-
22754	-	-	+	+	-	+	+	+	+	-	-	-	-	+/-	-	-	-	-	-	-	-	-	+/-	+/-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body-Site	#Gastrointestinal tract	#Large intestine
#Host Body Product	#Gastrointestinal tract	#Caecal content

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22754	caecal content; TNF^deltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe
67771	From mouse instine, caecal content; TNFdeltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364760 (>99% sequence identity) for Cuneatibacter caecimuris subclade from Microbeatlas

Aquatic Samples	214
Soil Samples	36
Animal Samples	22542
Plant Samples	44
Total Samples	22836

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22754	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM421677v1 assembly for Cuneatibacter caecimuris DSM 29486	scaffold	GCA_004216775	1796618.3	2802428826	1796618	74.04

Genome browser: GCA_004216775

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22754	Cuneatibacter caecimuris strain BARN-424-CC-10 16S ribosomal RNA gene, partial sequence	KR364760	1485		1796618

GC content

@ref	GC-content (mol%)	Method
22754	49.1	sequence analysis
67771	49.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cuneatibacter caecimuris DSM 29486
NCBI: GCA_004216775

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	83.40	no
125439	motility	BacteriaNetⓘ	yes	83.10	no
125439	gram_stain	BacteriaNetⓘ	positive	67.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cuneatibacter caecimuris DSM 29486
NCBI: GCA_004216775.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	78.17	yes
125438	anaerobic	anaerobicⓘ	yes	86.67	no
125438	aerobic	aerobicⓘ	no	97.16	no
125438	spore-forming	spore-formingⓘ	yes	54.74	no
125438	thermophilic	thermophileⓘ	no	93.95	yes
125438	flagellated	motile2+ⓘ	no	63.19	no

Literature

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 )
#22754	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29486
#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;
#68380	Automatically annotated from API rID32A .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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