The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling
Abstract
:1. Introduction
2. Methods of Analysis
2.1. Metagenomics
2.1.1. Sample Collection and Storage
2.1.2. Lysis of Cells
2.1.3. Isolation and Extraction of DNA Sequences
2.1.4. Amplification and Sequencing
2.1.5. Bacterial Identification
2.2. Transcriptomics
2.2.1. Sample Storage and Cell Lysis
2.2.2. Purification and Enrichment of mRNA Product
2.2.3. MicroRNA: A New Method for Shaping the Gut Microbiota
2.3. Proteomics
2.3.1. Sample Storage
2.3.2. Protein Extraction
2.3.3. Digestion and Peptide Isolation
2.3.4. Detection
2.4. Metabonomics
2.4.1. GC–MS Analysis
2.4.2. LC–MS Analysis for Metabolites
3. CeD Disease Gut Profiling
3.1. CeD Microbial Profiling
3.2. CeD mRNA and microRNA Profiling
3.3. CeD Protein Biomarkers Profiling
3.4. CeD Metabolic Profiling
3.5. Chemometrics and Machine Learning (ML)
4. Conclusions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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Enzymes | Mode of Action |
---|---|
Lysozyme | Cleaves the bacterial cell wall [79] by catalyzing the hydrolysis of glycoside-linkages in the peptidoglycan layer [73]. |
Mutanolysin | Rapidly solubilizes cell walls and removes reducing sugars and free amino groups. Greatly effective against some streptococci strains [80] and Gram-positive cell wall [73]. |
Guanidine thiocyanate | A chaotropic agent, which disrupts the hydrogen bonding of a molecule and is used to inactivate DNase and RNase, enzymes that digest DNA and RNA, respectively [73,81]. |
RNAse A | Degrades single-stranded RNA [82] |
Proteinase K | Digests proteins by hydrolyzing peptide bonds [83] |
Lysostaphin | Specifically breaks some Staphylococcus spp. [84] by cleaving the pentaglycine cross bridges of its cell wall [73,85] |
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Gangadoo, S.; Rajapaksha Pathirannahalage, P.; Cheeseman, S.; Dang, Y.T.H.; Elbourne, A.; Cozzolino, D.; Latham, K.; Truong, V.K.; Chapman, J. The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling. Int. J. Mol. Sci. 2021, 22, 1965. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041965
Gangadoo S, Rajapaksha Pathirannahalage P, Cheeseman S, Dang YTH, Elbourne A, Cozzolino D, Latham K, Truong VK, Chapman J. The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling. International Journal of Molecular Sciences. 2021; 22(4):1965. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041965
Chicago/Turabian StyleGangadoo, Sheeana, Piumie Rajapaksha Pathirannahalage, Samuel Cheeseman, Yen Thi Hoang Dang, Aaron Elbourne, Daniel Cozzolino, Kay Latham, Vi Khanh Truong, and James Chapman. 2021. "The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling" International Journal of Molecular Sciences 22, no. 4: 1965. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041965