The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemical Products
2.2. Sample Collection and Donor Descripion
2.3. Experimental Design of Long-Term L and M-SHIME®
2.3.1. Eubiosis Study
2.3.2. Dysbiosis Study
2.4. Metabolic Analysis
2.5. Microbial Community Analysis by qPCR
2.6. Microbial Community Analysis by 16S rRNA and ITS1 rRNA Gene-Targeted Sequencing
2.7. Data Analysis
3. Results
3.1. Wash-Out of Microbes during Stabilization Period in Eubiosis Conditions
3.1.1. Microbial Concentration in Eubiosis
3.1.2. Quantitative Microbiome Profiling and Microbial Diversity Dynamics in Eubiosis
3.2. Fungal Overgrowth Following Bacterial Diversity Reduction during Dysbiosis Induced with Different Antibiotic Treatments
3.2.1. Microbial Concentration during Eubiosis and the Antibiotic Treatment Period
3.2.2. Short-Chain Fatty Acid Production during Eubiosis and the Antibiotic Treatment Period
3.2.3. Quantitative Microbiome Profiling and Microbial Diversity Dynamics during Eubiosis and the Antibiotic Treatment Period
3.3. Specific Bacterial Signatures Are Associated with Changes in Fungal Concentration
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Marsaux, B.; Moens, F.; Marzorati, M.; Van de Wiele, T. The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model. J. Fungi 2023, 9, 877. https://doi.org/10.3390/jof9090877
Marsaux B, Moens F, Marzorati M, Van de Wiele T. The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model. Journal of Fungi. 2023; 9(9):877. https://doi.org/10.3390/jof9090877
Chicago/Turabian StyleMarsaux, Benoît, Frédéric Moens, Massimo Marzorati, and Tom Van de Wiele. 2023. "The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model" Journal of Fungi 9, no. 9: 877. https://doi.org/10.3390/jof9090877
APA StyleMarsaux, B., Moens, F., Marzorati, M., & Van de Wiele, T. (2023). The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model. Journal of Fungi, 9(9), 877. https://doi.org/10.3390/jof9090877