MiMeDB: Clostridioides difficile (MMDBm0000108)

Microbe Identification

Microbe name

Clostridioides difficile

NCBI Taxonomy ID

1496

Microbe Taxonomy

Superkingdom

Bacteria

Kingdom

Eubacteria

Phylum

Firmicutes

Class

Clostridia

Order

Clostridiales

Family

Peptostreptococcaceae

Genus

Clostridioides

Species

difficile

Strain

Not Available

Microbe Properties

Gram staining properties

Positive

Shape

Bacilli

Mobility

Yes

Flagellar presence

Yes?

Number of membranes

Oxygen preference

Anaerobe

Optimal temperature

Temperature range

Mesophilic

Habitat

Multiple

Biotic relationship

Free living

Cell arrangement

Chains-Pairs-Singles

Sporulation

Sporulating

Metabolism

Proteolytic, few carbohydrates fermented

Energy source

Chemoorganotroph

Host and Biospecimens

Host	Body site	Biospecimen	Details	Data Source	Reference
Human	Gut	Feces	Not Available	GutFeeling KnowledgeBase	31509535
Goat	Gut	Feces	Not Available		https://doi.org/10.1080/16583655.2020.1864930
Sheep	Gut	Feces	Not Available		https://doi.org/10.1080/16583655.2020.1864930
Human	Large intestine		Not Available	BacDive	34718743
Human	Large intestine		Not Available	BacDive	34718743
Human	Large intestine		Not Available	BacDive	34718743
Human	Large intestine		Not Available	BacDive	34718743
Human	Large intestine	Feces	Not Available	Disbiome	12173102
Human	Large intestine	Feces	Not Available	Disbiome	26691472
Human	Large intestine	Feces	Not Available	Disbiome	20848492
Human	Large intestine	Feces	Not Available	Disbiome	26940651
Human	Large intestine	Feces	Not Available	Disbiome	21820992
Human	Large intestine	Feces	Not Available	Disbiome	25986361
Human	Large intestine	Feces	Not Available	Disbiome	32296918

Health Effects

Host	Related Health Condition	Microbal response/effect	Data Source	Reference
Human	Colitis		BacDive
Human	Colitis		BacDive
Human	Diarrhea		BacDive
Human	Diarrhea		BacDive
Human	Diarrhea		BacDive
Human	Autism	Elevated	Disbiome	12173102
Human	Colorectal cancer	Elevated	Disbiome	26691472
Human	Crohn's disease	Elevated	Disbiome	20848492
Human	Crohn's disease	Elevated	Disbiome	20848492
Human	Crohn's disease	Elevated	Disbiome	26313691
Human	Cystic fibrosis	Elevated	Disbiome	26940651
Human	Irritable bowel syndrome	Elevated	Disbiome	21820992
Human	Ulcerative colitis	Elevated	Disbiome	25986361
Human	Ulcerative colitis	Reduced	Disbiome	29533950
Human	Clostridium Difficile Infection	Elevated	Disbiome	32296918

Related Metabolites

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0012860	(2R)-2-phosphoglyceric acid	Phosphoenolpyruvic acid	Enolase	Enolization	RHEA	34755880
MMDBr0012876	Deoxyuridine triphosphate	dUMP	Probable deoxyuridine 5'-triphosphate nucleotidohydrolase	Dephosphorylation; Hydrolysis of bond	RHEA	34755880
MMDBr0013391	L-Glutamic acid	alpha-Ketoglutarate	NAD-specific glutamate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0013505	(S)-3-Hydroxybutanoyl-CoA	Acetoacetyl-CoA	3-hydroxybutyryl-CoA dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0013766	Chloramphenicol	chloramphenicol 3-acetic acid	Chloramphenicol acetyltransferase	N-Acetylation	RHEA	34755880
MMDBr0014240	p-Hydroxyphenylacetic acid	p-Cresol	4-hydroxyphenylacetate decarboxylase glycyl radical subunit	Decarboxylation	RHEA	34755880
MMDBr0014241	p-Hydroxyphenylacetic acid	p-Cresol	4-hydroxyphenylacetate decarboxylase glycyl radical subunit	Decarboxylation	RHEA	34755880
MMDBr0016264	(R)-2-hydroxy-4-methylpentanoyl-CoA	4-methylpent-2-enoyl-CoA	(R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0016751	4-Hydroxyproline	1-Pyrroline-5-carboxylic acid	Trans-4-hydroxy-L-proline dehydratase	Hydration/dehydration of C-O bond	RHEA	34755880
MMDBr0017243	3,4-Dihydroxybenzeneacetic acid	4-Methylcatechol	4-hydroxyphenylacetate decarboxylase glycyl radical subunit	Decarboxylation	RHEA	34755880
MMDBr0017244	3,4-Dihydroxybenzeneacetic acid	4-Methylcatechol	4-hydroxyphenylacetate decarboxylase glycyl radical subunit	Decarboxylation	RHEA	34755880
MMDBr0017251	2-hydroxy-2-(4-hydroxyphenyl)acetic acid	4-Hydroxybenzyl alcohol	4-hydroxyphenylacetate decarboxylase glycyl radical subunit	Decarboxylation	RHEA	34755880
MMDBr0017252	2-hydroxy-2-(4-hydroxyphenyl)acetic acid	4-Hydroxybenzyl alcohol	4-hydroxyphenylacetate decarboxylase glycyl radical subunit	Decarboxylation	RHEA	34755880
MMDBr0017835	L-Proline	D-Proline	Proline racemase	Racemization	RHEA	34755880
MMDBr0025766	Glycine	5'-Deoxyadenosine	Putative glycyl-radical enzyme activating enzyme MJ1227	Reduction; Synthesis	RHEA	34755880
MMDBr0025875	L-Threonine	Uridine 5'-diphosphate	Cytotoxin-L	Not Available	RHEA	34755880
MMDBr0025876	L-Threonine	Uridine 5'-diphosphate	Cytotoxin-L	Not Available	RHEA	34755880

Genome Data

Genome Link

MMDBm0000108

Genome Length

4147551 bp

# Predicted Proteins

7658

GenBank Sequence Modification Date

17-FEB-2022

MiMeDB Deposition Date

2022-08-25 17:24:17 UTC

Reference

PMID: 17704766

Source Links

GenBank

NZ_CP076401