Frisingicoccus caecimuris (DSM 28559, KCTC 15538, PG-426-CC-1)

Name: Frisingicoccus caecimuris (DSM 28559, KCTC 15538, PG-426-CC-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131519

Type strain

Strain Designation PG-426-CC-1

Culture col. no. DSM 28559 KCTC 15538 PG-426-CC-1

NCBI tax ID(s) 1796636

Special Collections DSMZ KCTC Mouse DZIF

Links

Frisingicoccus caecimuris PG-426-CC-1 is an anaerobe, mesophilic, rod-shaped prokaryote that was isolated from caecal content; TNF^deltaARE/+ C57BL/6 mouse.

rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 398654

KCTC 15538,DSM 28559

@ref 20215

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

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Frisingicoccus

Species Frisingicoccus caecimuris

Full scientific name Frisingicoccus caecimuris Lagkouvardos et al. 2016

Morphology

Cell morphology

@ref	Cell shape
68367	rod-shaped	from API 20A
68367		from API 20A
67771	rod-shaped
67771

Colony morphology

22746

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22746	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
22746	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22746	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
22746	anaerobe
67771	anaerobe
125438	anaerobe
125439	anaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	-	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68367	16024 ChEBI	D-mannose	-	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	-	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68367	35581 ChEBI	indole	-	from API 20A

Enzymes

@ref	Value	Activity	Ec
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68367	catalase	-	1.11.1.6	from API 20A
68367	gelatinase	-		from API 20A
68367	urease	-	3.5.1.5	from API 20A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ribulose monophosphate pathway	100	2 of 2
66794	vitamin B1 metabolism	100	13 of 13
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	L-lactaldehyde degradation	100	3 of 3
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	starch degradation	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	vitamin B12 metabolism	82.35	28 of 34
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	phenylalanine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	glutamate and glutamine metabolism	75	21 of 28
66794	butanoate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	pyrimidine metabolism	64.44	29 of 45
66794	heme metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	methionine metabolism	57.69	15 of 26
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	citric acid cycle	57.14	8 of 14
66794	oxidative phosphorylation	56.04	51 of 91
66794	histidine metabolism	55.17	16 of 29
66794	leucine metabolism	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	suberin monomers biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	urea cycle	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	lysine metabolism	42.86	18 of 42
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	non-pathway related	42.11	16 of 38
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arginine metabolism	41.67	10 of 24
66794	arachidonate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	metabolism of disaccharids	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	lipid A biosynthesis	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	degradation of sugar alcohols	31.25	5 of 16
66794	sulfate reduction	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	glycine metabolism	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	vitamin B6 metabolism	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17
66794	polyamine pathway	21.74	5 of 23

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
22746	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	+	-

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
22746	caecal content; TNF^deltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe
67771	From caecal content, TNFdeltaARE/+ C57BL/6 mouse	Freising	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364774 (>99% sequence identity) for Frisingicoccus caecimuris subclade from Microbeatlas

Aquatic Samples	108
Soil Samples	15
Animal Samples	4840
Plant Samples	10
Total Samples	4973

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22746	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	ASM434097v1 assembly for Frisingicoccus caecimuris DSM 28559	scaffold	GCA_004340975	1796636.8	2795385452	1796636	71.45
66792	ASM2462258v1 assembly for Frisingicoccus caecimuris DSM 28559	contig	GCA_024622585	1796636.21	8062480370	1796636	70.58

Genome browser: GCA_004340975

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22746	Frisingicoccus caecimuris strain PG-426-CC-1 16S ribosomal RNA gene, partial sequence	KR364774	1448		1796636

GC content

@ref	GC-content (mol%)	Method
22746	43.7	sequence analysis
67771	43.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Frisingicoccus caecimuris DSM 28559
NCBI: GCA_004340975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	78.20	no
125439	motility	BacteriaNetⓘ	yes	78.20	no
125439	gram_stain	BacteriaNetⓘ	positive	68.00	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: Frisingicoccus caecimuris DSM 28559
NCBI: GCA_004340975.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.67	no
125438	anaerobic	anaerobicⓘ	yes	90.94	yes
125438	aerobic	aerobicⓘ	no	95.95	no
125438	spore-forming	spore-formingⓘ	no	54.75	no
125438	thermophilic	thermophileⓘ	no	92.93	yes
125438	flagellated	motile2+ⓘ	no	84.09	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 )
#22746	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28559
#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;
#68367	Automatically annotated from API 20A .
#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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