Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

Bushman, Frederic D.; Conrad, Máire A.; Ren, Yue; Zhao, Chunyu; Gu, Chong; Petucci, Christopher; Kim, Min‐Soo; Abbas, Arwa; Downes, Kevin J.; Devas, Nina; Mattei, Lisa M.; Breton, Jessica; Kelsen, Judith R.; Marakos, Sarah; Galgano, Alissa; Kachelries, Kelly; Erlichman, Jessi; Hart, Jessica L.; Moraskie, Michael; Kim, Dorothy; Zhang, Huanjia; Hofstaedter, Casey E.; Wu, Gary D.; Lewis, James D.; Zackular, Joseph P.; Li, Hongzhe; Bittinger, Kyle; Baldassano, Robert N.

doi:10.1016/j.chom.2020.07.020

Cited by 51 publications

(55 citation statements)

References 83 publications

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“…Of interest, it has been recently reported that succinate levels are increased in stool samples of paediatric CD patients infected with Clostridioides difficile compared with paediatric CD patients without infection. In this elegant study, the authors associate for the first time a metabolomic alteration with a specific bacterium [20]. In line with this, it has also been recently reported that succinate levels of intestinal aspirates from paediatric IBD patients positively correlates with the invasion of Escherichia Coli [21].…”

Section: Metabolite Alterationsupporting

confidence: 55%

Metabolomics as a Promising Resource Identifying Potential Biomarkers for Inflammatory Bowel Disease

Bauset

Gisbert-Ferrándiz

Cosín-Roger

2021

JCM

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Inflammatory bowel disease (IBD) is a relapsing chronic disorder of the gastrointestinal tract characterized by disruption of epithelial barrier function and excessive immune response to gut microbiota. The lack of biomarkers providing early diagnosis or defining the status of the pathology difficulties an accurate assessment of the disease. Given the different metabolomic profiles observed in IBD patients, metabolomics may reveal prime candidates to be studied, which may help in understanding the pathology and identifying novel therapeutic targets. In this review, we summarize the most current advances describing the promising metabolites such as lipids or amino acids found through untargeted metabolomics from serum, faecal, urine and biopsy samples.

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Section: Metabolite Alterationsupporting

confidence: 55%

Metabolomics as a Promising Resource Identifying Potential Biomarkers for Inflammatory Bowel Disease

Bauset

Gisbert-Ferrándiz

Cosín-Roger

2021

JCM

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“…Interestingly, one strain of an unnamed Clostridium bacterium capable of deconjugation shows increased growth when taurine was added to the growth medium, indicating that BSH activity might be nutritionally beneficial [48]. Taurine is also enriched in the feces of pediatric inflammatory bowel disease patients with CDI, indicating a potential association between C. difficile and taurine [49].…”

Section: Bile Salt Hydrolasesmentioning

confidence: 99%

Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium

Reed

Theriot

2021

Microorganisms

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Clostridioides difficile is an anaerobic pathogen that causes significant morbidity and mortality. Understanding the mechanisms of colonization resistance against C. difficile is important for elucidating the mechanisms by which C. difficile is able to colonize the gut after antibiotics. Commensal Clostridium play a key role in colonization resistance. They are able to modify bile acids which alter the C. difficile life cycle. Commensal Clostridium also produce other inhibitory metabolites including antimicrobials and short chain fatty acids. They also compete with C. difficile for vital nutrients such as proline. Understanding the mechanistic effects that these metabolites have on C. difficile and other gut pathogens is important for the development of new therapeutics against C. difficile infection (CDI), which are urgently needed.

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“…There are seven example workflows provided in iMAP. They were summarized from published metabolomic studies with different strategies for key metabolites selection, pathway analysis, and/or predictive model building (Sreekumar et al, 2009 ; Liu et al, 2019 ; Bushman et al, 2020 ). It's convenient to construct customized workflows by modifying these example workflows.…”

Section: Methodsmentioning

confidence: 99%

iMAP: A Web Server for Metabolomics Data Integrative Analysis

et al. 2021

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Metabolomics data analysis depends on the utilization of bioinformatics tools. To meet the evolving needs of metabolomics research, several integrated platforms have been developed. Our group has developed a desktop platform IP4M (integrated Platform for Metabolomics Data Analysis) which allows users to perform a nearly complete metabolomics data analysis in one-stop. With the extensive usage of IP4M, more and more demands were raised from users worldwide for a web version and a more customized workflow. Thus, iMAP (integrated Metabolomics Analysis Platform) was developed with extended functions, improved performances, and redesigned structures. Compared with existing platforms, iMAP has more methods and usage modes. A new module was developed with an automatic pipeline for train-test set separation, feature selection, and predictive model construction and validation. A new module was incorporated with sufficient editable parameters for network construction, visualization, and analysis. Moreover, plenty of plotting tools have been upgraded for highly customized publication-ready figures. Overall, iMAP is a good alternative tool with complementary functions to existing metabolomics data analysis platforms. iMAP is freely available for academic usage at https://imap.metaboprofile.cloud/ (License MPL 2.0).

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Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

Cited by 51 publications

References 83 publications

Metabolomics as a Promising Resource Identifying Potential Biomarkers for Inflammatory Bowel Disease

Metabolomics as a Promising Resource Identifying Potential Biomarkers for Inflammatory Bowel Disease

Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium

iMAP: A Web Server for Metabolomics Data Integrative Analysis

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