Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Populations and Design
2.2. Processing Metagenomic Sequences
2.3. Identifying Eukaryotes in Gut Metagenomes
2.4. Statistical Analyses
2.4.1. Descriptive Taxonomic Analysis
2.4.2. Cohort Analysis
2.4.3. Regression Analysis
3. Results
3.1. Detection of Eukaryotes in Gut Metagenomes
3.2. Distribution and Prevalence of Eukaryotes
3.2.1. Proportional Abundances
3.2.2. Species-Level Eukaryotic Prevalence
3.2.3. Shared and Unique Species
3.3. Effect of Faecal Microbiota Transplantation on Eukaryotes
3.4. Influence of Cohort Demographics on Gut Eukaryote Composition
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Cohort Characteristics | IBD Group (n = 355) | Control Group (n = 471) | |
---|---|---|---|
Sex | Female | 214 (60.28%) | 265 (56.26%) |
Male | 141 (39.72%) | 200 (42.46%) | |
Unspecified | 0 (0.00%) | 6 (1.27%) | |
Age (years) | Median (IQR) | 45.00 (34.25, 59.00) | 23.00 (21.00, 27.00) |
18–40 | 145 (41.43%) | 408 (87.74%) | |
41–60 | 132 (37.71%) | 31 (6.67%) | |
61–80 | 69 (19.71%) | 26 (5.59%) | |
81+ | 4 (1.14%) | 0 (0.00%) | |
Missing | 5 | 6 | |
BMI | Median (IQR) | 24.80 (21.70, 28.10) | 22.30 (20.72, 24.39) |
Missing | 0 | 14 | |
Smoking Status | Current | 78 (22.35%) | 60 (14.12%) |
Past | 146 (41.83%) | 65 (15.29%) | |
Never | 125 (35.82%) | 300 (70.59%) | |
Missing | 6 | 46 | |
Diagnosis | CD | 206 (58.03%) | NA |
UC | 126 (35.49%) | ||
IBDU | 23 (6.48%) |
Model | Coefficient | Blastocystis spp. 1 | Saccharomyces cerevisiae | ||||
---|---|---|---|---|---|---|---|
Estimate | Std. Error | p-Value | Estimate | Std. Error | p-Value | ||
Count | IBD | −0.34 | 0.39 | 0.38 | 1.05 | 0.34 | <0.01 |
Sex—male | 0.23 | 0.22 | 0.29 | −1.15 | 0.41 | 0.01 | |
Age | 0.01 | 0.01 | 0.35 | −0.03 | 0.01 | <0.01 | |
BMI—underweight | −0.85 | 0.40 | 0.04 | −2.19 | 0.61 | <0.01 | |
BMI—overweight | −0.81 | 0.28 | <0.01 | −0.69 | 0.45 | 0.13 | |
BMI—obese | −1.03 | 0.43 | 0.02 | 0.27 | 0.48 | 0.58 | |
Smoking—past | −0.15 | 0.33 | 0.64 | 0.52 | 0.50 | 0.30 | |
Smoking—current | −0.44 | 0.38 | 0.25 | −0.68 | 0.38 | 0.08 | |
Zero | IBD | 1.84 | 0.37 | <0.01 | −1.40 | 0.44 | <0.01 |
Sex—male | 0.32 | 0.24 | 0.18 | −0.47 | 0.35 | 0.18 | |
Age | −0.02 | 0.01 | 0.02 | 0.01 | 0.01 | 0.37 | |
BMI—underweight | −0.03 | 0.68 | 0.97 | −0.06 | 1.27 | 0.96 | |
BMI—overweight | 0.46 | 0.34 | 0.17 | 0.01 | 0.43 | 0.98 | |
BMI—obese | 0.88 | 0.78 | 0.26 | −0.53 | 0.50 | 0.29 | |
Smoking—past | 0.19 | 0.31 | 0.55 | 0.48 | 0.45 | 0.29 | |
Smoking—current | 0.66 | 0.39 | 0.10 | −0.42 | 0.39 | 0.27 |
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Guzzo, G.L.; Mittinty, M.N.; Llamas, B.; Andrews, J.M.; Weyrich, L.S. Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa. Microorganisms 2022, 10, 1910. https://doi.org/10.3390/microorganisms10101910
Guzzo GL, Mittinty MN, Llamas B, Andrews JM, Weyrich LS. Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa. Microorganisms. 2022; 10(10):1910. https://doi.org/10.3390/microorganisms10101910
Chicago/Turabian StyleGuzzo, Gina L., Murthy N. Mittinty, Bastien Llamas, Jane M. Andrews, and Laura S. Weyrich. 2022. "Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa" Microorganisms 10, no. 10: 1910. https://doi.org/10.3390/microorganisms10101910