## 5 Conclusions  
In conclusion, the co-occurrence of _Blastocystis_ and commensal _Entamoeba_ spp., despite the presence of other enteric pathogens including _G. duodenalis_, seems to preserve a high diversity, favor different bacterial consortia, and does not compromise the intrinsic ability of intestinal microbiota to restore and/or maintain homeostasis [74; 81; 82; 83; 84; 85]. However, the beneficial or potential regulatory effect of _Blastocystis_ is reduced in subjects positive for bacterial and viral pathogens without _G. duodenalis_ and commensal _Entamoeba_ spp., probably reducing the entity of symptoms. Finally, the complex scenario observed in this cohort from Cote d'Ivoire helps to provide an integrated view of human gut microbiota composition. Simultaneous testing of common intestinal pathogens supplies new data from Africa, still underrepresented in the global picture of the gut microbiota, and helps to better understand the balances of intestinal homeostasis. Future investigations are needed to verify if the influence of rural diet on gut microbiota can play a role in seasonal predisposition to endemic enteritis. It will be very important to extend the understanding of eukaryotic microorganisms' interactions in the gut microbiota in health status and intestinal infections. **Supplementary Materials:** The following are available online at [[https://www.mdpi.com/article/10.3390/microorganisms9081763/s1](https://www.mdpi.com/article/10.3390/microorganisms9081763/s1)]([https://www.mdpi.com/article/10.3390/microorganisms9081763/s1](https://www.mdpi.com/article/10.3390/microorganisms9081763/s1)), **Figure S1A**. The plot of top 15 bacterial relative abundances at the Family level in each age group; **Table S1A**. The top 15 bacterial relative abundances; **Figure S2**. Beta diversity of Cluster 1 versus Cluster 2 (Denovo clustering); **Table S3A**. Alpha diversity indices of positive and negative subjects, grouped in <1 year and >1 year; **Figure S3**. Positive versus negative subjects comparisons: Beta diversity analysis; **Table S4A**. All microorganisms detected in the 5 symptomatic subjects; **Table S4B**. Comparison of _Blastocistys_ groups: Alpha diversity index; **Table S4C**. Comparison of _Entamoeba_ species groups: Alpha diversity index; **Table S4E**. Comparison of _G. duodenalis_ and other intestinal pathogens positives: Alpha diversity index; **Table S5A**. Beta diversity analysis for _Entamoeba_ spp. presence; **Table S5B**. Beta diversity analysis for _Entamoeba_ spp. presence; **Table S5C**. Comparison of _Entamoeba_ spp. detection; **Table S5E**. Beta diversity analysis for _Entamoeba_ spp. presence. **Author Contributions:** Conceptualization: R.D., F.B. ; data curation: R.D., V.D.C., F.B., M.S., F.F., M.D., A.T.; formal analysis: F.F., A.T., M.D. ; funding acquisition: K.A.E., V.D.C. ; investigation: R.D., F.B., F.F., V.D.C., M.S., D.D.C., M.W., C.G. ; resources: K.A.E., V.D.C., R.K., M.J.G.T.V. ; visualization: R.D., V.D.C., F.F., F.B., D.D.C., M.J.G.T.V. ; writing--original draft: R.D., V.D.C., F.B. ; writing--review and editing: all authors. All authors have read and agreed to the published version of the manuscript. **Funding:** The present study was supported by the Koeln Fortune Program of the Faculty of Medicine of the University of Cologne (Germany) to V.D.C. **Institutional Review Board Statement:** All procedures performed in this study involving human participants were approved by the Don Orione Center's Medical Committee (Bonoua, Cote d'Ivoire) and followed the 1975 Helsinki Declaration and its later amendments. **Informed Consent Statement:** Adults' participation was voluntary after providing a verbal agreement on the methods and purposes of sampling. For minors, informed consent was obtained from their parents and guardians. A local dialect interpreter was used to explain the study's aims, procedures, and significance when necessary.