Colonic Mucosal Microbiota and Association of Bacterial Taxa with the Expression of Host Antimicrobial Peptides in Pediatric Ulcerative Colitis
Abstract
:1. Introduction
2. Results
2.1. Study Cohort and Effect of Sampling on the Microbiota
2.2. Mucosal Microbiota Associated with UC
2.3. Mucosal Gene exPression and Correlations with Microbial Taxa
3. Discussion
4. Materials and Methods
4.1. Patients
4.2. Isolation of Host RNA and Microbial DNA
4.3. 16.S rDNA Amplicon Sequencing
4.4. qRT-PCR of Mucosal Gene Expression
4.5. 16.S rDNA Amplicon Data Analysis
4.6. Statistical Analysis
4.7. Ethical Considerations
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
IBD | Inflammatory bowel diseases |
UC | Ulcerative colitis |
CD | Crohn’s disease |
16S rDNA | Small sub-unit ribosomal RNA gene |
qRT-PCR | Quantitative reverse-transcriptase polymerase chain reaction |
OTU | Operational taxonomic unit |
PCoA | Principal co-ordinate analysis |
FDR | False discovery rate |
References
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UC Active | UC Inactive | Control (HC) | |
---|---|---|---|
Number of patients | n = 18 | n = 8 | n = 27 |
Age (range) | 13 (5–17) | 14 (10–16) | 8 (3–15) |
Biopsy collected | |||
ascending | 8 | 3 | 2 |
cecum | 4 | 4 | 17 |
descending | 6 | 1 | 8 |
Mayo score | |||
0 | - | 8 | 27 |
1 | 11 | - | - |
2 | 5 | - | - |
3 | 2 | - | - |
Diagnosis or reason for diagnoctic colonoscopy | |||
Pancolitis | 16 | 7 | - |
Left-sided colitis | 2 | 1 | - |
Diabetes mellitus | - | - | 2 |
Diarrhea | - | - | 7 |
Asthma | - | - | 1 |
Abdominal pain | - | - | 8 |
Hematochezia | - | - | 9 |
Medication | |||
None | 7 | 0 | 24 |
5-ASA | 11 | 8 | - |
Prednisolone | 1 | 0 | - |
Azathioprine | 4 | 3 | - |
Metotrexate | - | 1 | - |
Insulin | - | - | 2 |
Budesonide | - | - | 1 |
Taxon | Fold Change in UC as Compared to HC | p-Value | q-Value |
---|---|---|---|
Uncultured Bacteroidetes | 0.58 | 0.003 | 0.06 |
Uncultured Erysipelotrichia | 7.27 | 0.021 | 0.17 |
Uncultured Negativicutes | 0.61 | 0.005 | 0.06 |
Veillonellaceae | 2.93 | 0.013 | 0.13 |
Sutterellaceae | 4.35 | 2.96E-07 | 1.15E-05 |
Fold Change in Gene Expression | Associations between Gene-Expression and Microbiota | |||
---|---|---|---|---|
Gene Expression | UC/HC | UC Active/ UC Inactive | Negative | Positive |
CXCL16 | 1.31 * | 1.56 * | Lactobacillaceae | Veillonellaceae |
CXCR6 | ns. | ns. | - | Sutterellaceae, Veillonellaceae |
DEFB1 | 0.76 * | 0.34 *** | Enterobacteriaceae | - |
DEFB103B | ns. | ns. | - | - |
DEFB4A | ns. | ns. | Uncultured Betaproteobacteria | - |
IL8 | 68.19 *** | 38.36 *** | - | Sutterellaceae, Veillonellaceae |
LCN2 | 6.32 ** | 7.59 ** | - | Enterobacteriaceae |
MUC2 | ns. | ns. | - | Desulfovibrionaceae |
REGIIIg | ns. | ns. | Peptostreptococcaceae | - |
RETNLB | ns. | ns. | - | - |
S100A8 | 18.78 ** | 29.30 * | Lactobacillaceae | Actinomycetaceae |
S100A9 | 8.58 * | 17.12 ** | Lactobacillaceae | Actinomycetaceae |
TFF3 | ns. | ns. | - | - |
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Jalanka, J.; Cheng, J.; Hiippala, K.; Ritari, J.; Salojärvi, J.; Ruuska, T.; Kalliomäki, M.; Satokari, R. Colonic Mucosal Microbiota and Association of Bacterial Taxa with the Expression of Host Antimicrobial Peptides in Pediatric Ulcerative Colitis. Int. J. Mol. Sci. 2020, 21, 6044. https://doi.org/10.3390/ijms21176044
Jalanka J, Cheng J, Hiippala K, Ritari J, Salojärvi J, Ruuska T, Kalliomäki M, Satokari R. Colonic Mucosal Microbiota and Association of Bacterial Taxa with the Expression of Host Antimicrobial Peptides in Pediatric Ulcerative Colitis. International Journal of Molecular Sciences. 2020; 21(17):6044. https://doi.org/10.3390/ijms21176044
Chicago/Turabian StyleJalanka, Jonna, Jing Cheng, Kaisa Hiippala, Jarmo Ritari, Jarkko Salojärvi, Tarja Ruuska, Marko Kalliomäki, and Reetta Satokari. 2020. "Colonic Mucosal Microbiota and Association of Bacterial Taxa with the Expression of Host Antimicrobial Peptides in Pediatric Ulcerative Colitis" International Journal of Molecular Sciences 21, no. 17: 6044. https://doi.org/10.3390/ijms21176044