Dielma fastidiosa (DSM 26099, CSUR P149, JC13)

Name: Dielma fastidiosa (DSM 26099, CSUR P149, JC13)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24006

Type strain

Strain Designation JC13

Culture col. no. DSM 26099 CSUR P149 JC13

NCBI tax ID(s) 1034346

Special Collections DSMZ Cadoret human gut

Links

Dielma fastidiosa JC13 is an anaerobe, mesophilic prokaryote that was isolated from human feces.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 399006

DSM 26099

@ref 20215

Last LPSN update 2025-12-16 09:52:46

Domain Bacillati

Phylum Bacillota

Class Erysipelotrichia

Order Erysipelotrichales

Family Erysipelotrichaceae

Genus Dielma

Species Dielma fastidiosa

Full scientific name Dielma fastidiosa Ramasamy et al. 2016

BacDive ID	Other strains from **Dielma fastidiosa** (1)	Type strain
156386	D. fastidiosa CCUG 61462

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21310	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21310	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

21310

Oxygen toleranceanaerobe

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	peptidoglycan biosynthesis	93.33	14 of 15
66794	threonine metabolism	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	vitamin B1 metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	pyrimidine metabolism	80	36 of 45
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	starch degradation	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	palmitate biosynthesis	77.27	17 of 22
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	purine metabolism	73.4	69 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	d-xylose degradation	63.64	7 of 11
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	NAD metabolism	61.11	11 of 18
66794	factor 420 biosynthesis	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	methylglyoxal degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	alanine metabolism	58.62	17 of 29
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	molybdenum cofactor biosynthesis	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	non-pathway related	52.63	20 of 38
66794	adipate degradation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	sphingosine metabolism	50	3 of 6
66794	citric acid cycle	50	7 of 14
66794	ethanol fermentation	50	1 of 2
66794	glutamate and glutamine metabolism	50	14 of 28
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	proline metabolism	45.45	5 of 11
66794	cysteine metabolism	44.44	8 of 18
66794	valine metabolism	44.44	4 of 9
66794	degradation of pentoses	42.86	12 of 28
66794	tyrosine metabolism	42.86	6 of 14
66794	glutathione metabolism	42.86	6 of 14
66794	methionine metabolism	42.31	11 of 26
66794	vitamin K metabolism	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	tryptophan metabolism	39.47	15 of 38
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	isoleucine metabolism	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	lysine metabolism	35.71	15 of 42
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	CO2 fixation in Crenarchaeota	33.33	3 of 9
66794	lipid metabolism	32.26	10 of 31
66794	degradation of sugar alcohols	31.25	5 of 16
66794	propionate fermentation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	glycine metabolism	30	3 of 10
66794	arginine metabolism	29.17	7 of 24
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	urea cycle	23.08	3 of 13
66794	allantoin degradation	22.22	2 of 9
66794	lipid A biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Human
#Host Body Product	#Gastrointestinal tract

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21310	human feces	Guinean-Sudanian Zone, Dielmo	Senegal	SEN	Africa

Taxonmaps

69479

Global distribution of 16S sequence JF824807 (>99% sequence identity) for Dielma fastidiosa subclade from Microbeatlas

Aquatic Samples	386
Soil Samples	122
Animal Samples	34455
Plant Samples	81
Total Samples	35044

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21310	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	ASM320210v1 assembly for Dielma fastidiosa JC118	scaffold	GCA_003202105	1034346.5	2770939561	1034346	65.72
66792	ASM31356v2 assembly for Dielma fastidiosa JC13	scaffold	GCA_000313565	1034346.3	2547132147	1034346	47.43

Genome browser: GCA_003202105

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21310	Dielma fastidiosa strain JC13 16S ribosomal RNA gene, partial sequence	JF824807	1499		1034346

GC content

@ref	GC-content (mol%)	Method
21310	40.0	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dielma fastidiosa JC13
NCBI: GCA_000313565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	51.60	no
125439	motility	BacteriaNetⓘ	no	70.80	no
125439	gram_stain	BacteriaNetⓘ	positive	78.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	88.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dielma fastidiosa JC13
NCBI: GCA_000313565.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	78.39	no
125438	anaerobic	anaerobicⓘ	yes	79.67	yes
125438	aerobic	aerobicⓘ	no	88.51	no
125438	spore-forming	spore-formingⓘ	no	56.50	no
125438	thermophilic	thermophileⓘ	no	94.98	yes
125438	flagellated	motile2+ⓘ	no	80.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome sequence and description of Traorella massiliensis gen. nov., sp. nov., a new bacterial genus isolated from human left colon.	Bonnet M, Mailhe M, Ricaboni D, Labas N, Richez M, Vitton V, Benezech A, Fournier PE, Million M, Raoult D, Khelaifia S.	New Microbes New Infect	10.1016/j.nmni.2019.100520	2019
Genetics	Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae.	Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.3567059	2013

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 )
#21310	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26099
#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 .
#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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Dielma fastidiosa (DSM 26099, CSUR P149, JC13)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003202105

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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