Details of Microbe Species (MIC)

General Information of MIC (ID: MIC00396)
MIC Name Clostridioides difficile (firmicutes)
MIC Synonyms Bacillus difficilis
Body Site Gut
Lineage Kingdom: Bacteria
Phylum: Firmicutes
Class: Clostridia
Order: Clostridiales
Family: Peptostreptococcaceae
Genus: Clostridioides
Species: Clostridioides difficile
Oxygen Sensitivity Obligate anaerobe
Microbial Metabolism Proteolytic; Few carbohydrates fermented
Gram Positive
Host Relationship Opportunistic pathogen
Genome Size (bp) 4167076
No. of Coding Genes 3815
No. of Non-Coding Genes 83
No. of Small Non-Coding Genes 83
No. of Gene Transcripts 3898
No. of Base Pairs 4268322
Description Clostridium difficile, also known as Clostridioides difficile and often referred to as C. difficile or C. diff, is a Gram-positive, obligately anaerobic bacterium that can cause symptoms ranging from diarrhea to life-threatening inflammation of the colon.
External Links Taxonomy ID
1496
Genome Assembly ID
ASM331356v1
GOLD Organism ID
Go0508393
Disease Relevance
          Clostridium difficile enterocolitis  [ICD-11: 1A04]
             Description Clostridium difficile was associated with clostridium difficile infection. [1]
          Inflammatory bowel disease  [ICD-11: DD72]
             Description Clostridium difficile infection frequently complicates the course of inflammatory bowel disease. [2]
          Irritable bowel syndrome  [ICD-11: DD91]
             Description Clostridium difficile was associated with diarrhea. [3]
Host Immune Factors (HIFs)
          B cells
             HIF ID HIFC0001 HIF Info       Class B cells (BCs)
             Description At the species level, relative abundances of Clostridium difficile which is associated with B cells response. [4]
          Adenosine receptor A2a
             HIF ID HIFM0002 HIF Info       Class Checkpoint molecule (CM)
             Description Toxin A (TxA) release from Clostridium difficile can contribute to antibiotic-induced diarrhea and pseudomembranous colitis through A2aRs. [5]
          Natural killer cell receptor BY55
             HIF ID HIFM0010 HIF Info       Class Checkpoint molecule (CM)
             Description CD160 is responsible for a significant fraction of the colonic STAT3 phosphorylation in Clostridium difficile infection. [6]
          C-C motif chemokine 20
             HIF ID HIFM0023 HIF Info       Class Cytokine (Cyt)
             Description The CCL20 secretion by IECs after infection by Clostridium difficile was shown to be negatively modulated by preincubation with commensal bacteria. [7]
          C-C motif chemokine 5
             HIF ID HIFM0033 HIF Info       Class Cytokine (Cyt)
             Description RANTES propagated the inflammatory response to Clostridium difficile toxin A. [8]
          Interferon-12 subunit alpha
             HIF ID HIFM0130 HIF Info       Class Cytokine (Cyt)
             Description The surface layer proteins(SLPs) among Clostridium difficile induced the production of the proinflammatory IL-12. [9]
          Interferon-18
             HIF ID HIFM0136 HIF Info       Class Cytokine (Cyt)
             Description Clostridium difficile toxin induced the production of IL-18. [10]
          Interleukin-1 beta
             HIF ID HIFM0138 HIF Info       Class Cytokine (Cyt)
             Description The surface layer proteins (SLPs) among Clostridium difficile induced the production of the proinflammatory IL-1beta. [11]
          C-X-C motif chemokine 8
             HIF ID HIFM0153 HIF Info       Class Cytokine (Cyt)
             Description Clostridium difficile toxin induced the production of IL-8. [12]
          Tumor necrosis factor
             HIF ID HIFM0226 HIF Info       Class Cytokine (Cyt)
             Description The surface layer proteins(SLPs) among Clostridium difficile could induce the production of the proinflammatory TNF-alpha. [13]
          Macrophage inflammatory protein 1
             HIF ID HIFM0242 HIF Info       Class Cytokine (Cyt)
             Description Clostridium difficile toxin could induce the production of MIP-2. [14]
          Interferon gamma
             HIF ID HIFM0260 HIF Info       Class Cytokine (Cyt)
             Description Clostridium difficile toxin could induce the production of IFN-Gamma. [15]
          Dendritic cells
             HIF ID HIFC0003 HIF Info       Class Dendritic cells (DCs)
             Description Purified non-toxin Clostridium difficile molecules(SLPs) induced the production of both proinflammatory in dendritic cells. [4]
          Mast cells
             HIF ID HIFC0022 HIF Info       Class Granulocytes (Gra)
             Description Mast cells increase activation by Clostridium difficile toxins. [4]
          Neutrophils
             HIF ID HIFC0029 HIF Info       Class Granulocytes (Gra)
             Description Neutrophils increased the immune response to Clostridium difficile toxin A. [4]
          Immunoglobulin M
             HIF ID HIFM0266 HIF Info       Class Immunoglobulin (Ig)
             Description Serum IgG and IgM antibodies to SLPs have been observed in both Clostridium difficile patients and asymptomatic carriers. [4]
          Immunoglobulin G
             HIF ID HIFM0270 HIF Info       Class Immunoglobulin (Ig)
             Description Serum IgG and IgM antibodies to SLPs have been observed in both Clostridium difficile patients and asymptomatic carriers. [4]
          Immunoglobulin A
             HIF ID HIFM0272 HIF Info       Class Immunoglobulin (Ig)
             Description Clostridium difficile is a Gram-positive, anaerobic, spore-forming, toxin-producing bacterium.The role of Clostridium difficile as a pathogen and as a causative agent for antibiotic-associated diarrhea and pseudomembranous colitis was first defined in 1978. [4]
          Macrophages
             HIF ID HIFC0020 HIF Info       Class Macrophages (Mac)
             Description Clostridium difficile Toxins A and B induced inflammasome activation and signaling in macrophages. [4]
          Monocytes
             HIF ID HIFC0024 HIF Info       Class Monocytes (Mono)
             Description Clostridium difficile can stimulate the release of proinflammatory cytokines and chemokines from monocytes. [4]
          THP-1 monocyte cells
             HIF ID HIFC0027 HIF Info       Class Monocytes (Mono)
             Description Clostridium difficile Toxins A and B induced inflammasome activation and signaling in THP-1 cells. [4]
          THP-1 monocytes
             HIF ID HIFC0214 HIF Info       Class Monocytes (Mono)
             Description THP-1 monocytes response were associated with pathogenic inflammation caused by Clostridium difficile infection. [16]
          Nucleotide-binding oligomerization domain-containing protein 1
             HIF ID HIFM0184 HIF Info       Class Nod-like receptor (NLR)
             Description Clostridium difficile toxins can activate both surface and intracellular innate immune sensors, such as the NOD1 signaling pathways. [4]
          Nuclear factor kappa B signaling pathway
             HIF ID HIFP0028 HIF Info       Class Signaling pathway (SP)
             Description Toxins are a major Clostridium difficile virulence factor, they could disrupt the actin cytoskeleton and activate the inflammasome and NFkappaB-mediated pathways that lead to proinflammatory cytokine and chemokine production. [4]
          T cells
             HIF ID HIFC0002 HIF Info       Class T cells (TCs)
             Description Exposure of lamina propria cells to Clostridium difficile toxin A in vitro induced apoptosis in T cells. [17]
          Toll-like receptor 4
             HIF ID HIFM0219 HIF Info       Class Toll-like receptor (TLR)
             Description TLR4 / mice had significantly (p<0.05) higher numbers of Clostridium difficile spores in the cecum after Clostridium difficile infection day 3. [4]
          Toll-like receptor 5
             HIF ID HIFM0220 HIF Info       Class Toll-like receptor (TLR)
             Description TLR5 stimulation could decrease Clostridium difficile-induced injury. [4]
Environmental Factor(s)
             Disbiome ID
      194
             gutMDisorder ID
      gm0200
References
1 Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria. PLoS Pathog. 2018 Sep 12;14(9):e1007191. doi: 10.1371/journal.ppat.1007191. eCollection 2018 Sep.
2 Epidemiology, Diagnosis, and Management of Clostridium difficile Infection in Patients with Inflammatory Bowel Disease. Inflamm Bowel Dis. 2016 Jul;22(7):1744-54. doi: 10.1097/MIB.0000000000000793.
3 Gut Bifidobacteria Populations in Human Health and Aging. Front Microbiol. 2016 Aug 19;7:1204. doi: 10.3389/fmicb.2016.01204. eCollection 2016.
4 Immune responses to Clostridium difficile infection.Trends Mol Med. 2012 Nov;18(11):658-66. doi: 10.1016/j.molmed.2012.09.005. Epub 2012 Oct 16.
5 New bioinformatics approach to analyze gene expressions and signaling pathways reveals unique purine gene dysregulation profiles that distinguish between CD and UC.Inflamm Bowel Dis. 2009 Jul;15(7):971-84. doi: 10.1002/ibd.20893.
6 Interleukin-22 and CD160 play additive roles in the host mucosal response to Clostridium difficile infection in mice.Immunology. 2015 Apr;144(4):587-97. doi: 10.1111/imm.12414.
7 CCL20 Displays Antimicrobial Activity Against Cryptosporidium parvum, but Its Expression Is Reduced During Infection in the Intestine of Neonatal Mice.J Infect Dis. 2015 Oct 15;212(8):1332-40. doi: 10.1093/infdis/jiv206. Epub 2015 Apr 2.
8 TLR signaling in B-cell development and activation.Cell Mol Immunol. 2013 Mar;10(2):103-6. doi: 10.1038/cmi.2012.61. Epub 2012 Dec 17.
9 Interruption of CXCL13-CXCR5 axis increases upper genital tract pathology and activation of NKT cells following chlamydial genital infection.PLoS One. 2012;7(11):e47487. doi: 10.1371/journal.pone.0047487. Epub 2012 Nov 26.
10 Performance of LBSap vaccine after intradermal challenge with L. infantum and saliva of Lu. longipalpis: immunogenicity and parasitological evaluation.PLoS One. 2012;7(11):e49780. doi: 10.1371/journal.pone.0049780. Epub 2012 Nov 26.
11 IL12B SNPs and copy number variation in IL23R gene associated with susceptibility to leprosy.J Med Genet. 2013 Jan;50(1):34-42. doi: 10.1136/jmedgenet-2012-101214.
12 Role of proinflammatory CD68(+) mannose receptor(-) macrophages in peroxiredoxin-1 expression and in abdominal aortic aneurysms in humans.Arterioscler Thromb Vasc Biol. 2013 Feb;33(2):431-8. doi: 10.1161/ATVBAHA.112.300663. Epub 2012 Dec 13.
13 A critical review of the role of Fc gamma receptor polymorphisms in the response to monoclonal antibodies in cancer.J Hematol Oncol. 2013 Jan 4;6:1. doi: 10.1186/1756-8722-6-1.
14 Intestinal antimicrobial peptides during homeostasis, infection, and disease.Front Immunol. 2012 Oct 9;3:310. doi: 10.3389/fimmu.2012.00310. eCollection 2012.
15 Hibernation is associated with depression of T-cell independent humoral immune responses in the 13-lined ground squirrel.Dev Comp Immunol. 2013 Mar;39(3):154-60. doi: 10.1016/j.dci.2012.11.004. Epub 2012 Nov 24.
16 Bile acid analogues are activators of pyrin inflammasome.J Biol Chem. 2019 Mar 8;294(10):3359-3366. doi: 10.1074/jbc.RA118.005103. Epub 2019 Jan 15.
17 Contributions of dendritic cells and macrophages to intestinal homeostasis and immune defense.Immunol Cell Biol. 2013 Mar;91(3):232-9. doi: 10.1038/icb.2012.79. Epub 2013 Feb 12.

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