Deciphering Microbial Composition in Patients with Inflammatory Bowel Disease: Implications for Therapeutic Response to Biologic Agents
Abstract
:1. Introduction
2. Materials and Methods
- (1)
- Patients with an established diagnosis of IBD (CD or UC) who had started biologic therapy between June 2018 and August 2020.
- (2)
- Patients with active disease as assessed by clinical indices (namely, a Harvey–Bradshaw Index (HBI) score ≥5 and a Mayo partial score >2) and at least one of the following objective markers of disease activity: a C-reactive protein (CRP) concentration >5 mg/L, a fecal calprotectin level >250 µg/g and endoscopic or radiological signs of activity.
2.1. Assessment of Disease Activity
2.2. Laboratory Procedures
2.3. Bioinformatics and Statistical Data Analysis
3. Results
3.1. Clinicopathologic Characteristics and Diversity Analysis
3.2. 16S rRNA V3-V4 Region Sequencing
3.3. Microbial Diversity and Community Analyses
3.4. Microbial Ecosystem Analysis
3.5. Cross-Correlation Analysis
3.6. Discriminant Taxa from Pairwise Group Comparisons
3.7. Microbial Composition at Baseline, 14 Weeks and 52 Weeks
3.8. Baseline Microbial Composition as a Predictor for Response to Biologic Therapy
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Characteristics | n [%] or Mean, and Range |
---|---|
No. of patients | 39 |
Female | 14 [35.9%] |
Crohn’s disease [CD] | 20 [51.3%] |
Ulcerative colitis [UC] | 19 [48.7%] |
Montreal classification, UC | 19 |
E1/E2/E3 | 2 [10.5%]/10 [52.6%]/7 [36.8%] |
Montreal classification, CD | 20 |
L1/L2/L3/L4 | 13 [65%]/1 [5%]/6 [30%]/0 [0%] |
B1/B2/B3 | 8 [40%]/4 [20%]/8 [40%] |
Perianal disease | 4 [20%] |
Mayo score at baseline [UC patients] | 9.0 |
Harvey–Bradshaw Index (HBI) score at baseline [CD patients] | 8.5 |
Age at diagnosis, years | 34.5 [9–65] |
Duration of disease, years | 12.3 [4–42] |
Age at baseline, years | 42.56 [15–72] |
Smoking | 9 [23.1%] |
Extraintestinal manifestations | |
Arthritis/sacro-ileitis | 12 [30.8%] |
Skin manifestations | 4 [10.3%] |
Iritis/uveitis | 1 [2.6%] |
Primary sclerosing cholangitis | 0 |
Previous surgery | 8 [20.5%] |
Previous biologic therapy | 14 [36.9%] |
HC vs. IBD | HC vs. CD | HC vs. UC | UC vs. CD | |
---|---|---|---|---|
Pielou’s evenness | 0.0019 | 0.00014 | 0.20 | 0.0030 |
Faith’s phylogenetic distance | 0.000017 | 0.000003 | 0.015 | 0.013 |
Number of observed features | 0.00000015 | 0.00000019 | 0.0007 | 0.0007 |
Shannon’s entropy | 0.000002 | 0.000002 | 0.003 | 0.00015 |
HC vs. IBD | HC vs. CD | HC vs. UC | UC vs. CD | |
---|---|---|---|---|
Bray–Curtis dissimilarity | 0.00015 | 0.00020 | 0.00020 | 0.00030 |
Jaccard similarity | 0.00015 | 0.00020 | 0.00020 | 0.00024 |
Unweighted UniFrac dissimilarity | 0.00015 | 0.00020 | 0.00020 | 0.0067 |
Weighted UniFrac dissimilarity | 0.0018 | 0.0012 | 0.049 | 0.26 |
Network | Features (Nodes) | Links/Density | p = 0.25 Links/Density | p = 0.50 Links/Density | p = 0.75 Links/Density | Max Links |
---|---|---|---|---|---|---|
IBD | 23 | 25/0.099 | 56/0.221 | 130/0.514 | 192/0.76 | 253 |
CD | 74 | 93/0.034 | 710/0.262 | 1351/0.5 | 1958/0.725 | 2701 |
UC | 78 | 138/0.046 | 773/0.257 | 1545/0.514 | 2245/0.748 | 3003 |
HC | 57 | 137/0.086 | 408/0.256 | 750/0.47 | 1214/0.76 | 1596 |
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Palmieri, O.; Bossa, F.; Castellana, S.; Latiano, T.; Carparelli, S.; Martino, G.; Mangoni, M.; Corritore, G.; Nardella, M.; Guerra, M.; et al. Deciphering Microbial Composition in Patients with Inflammatory Bowel Disease: Implications for Therapeutic Response to Biologic Agents. Microorganisms 2024, 12, 1260. https://doi.org/10.3390/microorganisms12071260
Palmieri O, Bossa F, Castellana S, Latiano T, Carparelli S, Martino G, Mangoni M, Corritore G, Nardella M, Guerra M, et al. Deciphering Microbial Composition in Patients with Inflammatory Bowel Disease: Implications for Therapeutic Response to Biologic Agents. Microorganisms. 2024; 12(7):1260. https://doi.org/10.3390/microorganisms12071260
Chicago/Turabian StylePalmieri, Orazio, Fabrizio Bossa, Stefano Castellana, Tiziana Latiano, Sonia Carparelli, Giuseppina Martino, Manuel Mangoni, Giuseppe Corritore, Marianna Nardella, Maria Guerra, and et al. 2024. "Deciphering Microbial Composition in Patients with Inflammatory Bowel Disease: Implications for Therapeutic Response to Biologic Agents" Microorganisms 12, no. 7: 1260. https://doi.org/10.3390/microorganisms12071260