## 3 Results
### Commensal Entamoeba spp  
_Entamoeba_ spp. was isolated in 49% (33/67) subjects, mostly associated with _Blastocytis_ (94%, 31/33). Firstly, we compared _Entamoeba_ spp. negative versus _Entamoeba_ spp. positive subjects (Figure 6A and Table S5A and Table S5B). To better elucidate the association between _Entamoeba_ and _Blastocytis_, we then categorized _Entamoeba_ spp. negative (\(n=34\)) as follows: (i) a group carrying _Blastocytis_ (\(n=16\)), (ii) a group without _Blastocytis_ (\(n=18\)), and both groups were compared with patients harboring _Entamoeba_ spp. with/without _Blastocytis_ (\(n=33\)), regardless of other infecting microorganisms (data not shown). To better clarify the frequently detected association between _E. hartmanni_ and _Blastocytis_ we distinguished the following groups: (i) the control group (\(n=8\)), (ii) a group carrying _E. hartmanni_ and _Blastocytis_ (\(n=11\)), (iii) a group carrying _E. hartmanni_ and _Blastocytis_ and pathogens (\(n=9\)). The presence of _E. hartmanni_ produced a significant increase in alpha diversity indices (Table S4C). The UniFrac distances, using principal coordinate analysis (PCoA), showed the shifting of positive groups for _E. hartmanni_ (Figure 6B). At the genus level of the _Christensenelaceae_ R-7 group, _Ruminococcaceae_ UCG-002 increased in two groups carrying  
Figure 5: Beta diversity analysis in presence of _Blastocytis_. Group1: control group; Group 2: positive only for _Blastocytis_; Group 3: positive for _Blastocytis_ and _Entamoeba_ spp. ; Group 4a: positive for _Blastocytis_ and pathogenic virus and bacteria; Group 4b: positive for _Blastocytis_ and _Entamoeba_ spp. and _Entamoeba_ spp. and _Entamoeba_ spp. and pathogenic virus, and bacteria; (**A**) The UniFrac distances among groups, using principal coordinate analysis (PCoA). UniFrac showed low divergences along Axis 1 (8,6%) between people carrying _Blastocytis_ and _Entamoeba_ spp. (Groups 3, 4b, 5b) compared to the negative subjects (Group 1) and subjects carrying _Blastocytis_ but not _Entamoeba_ spp. (Groups 2 and 4a). (**B**) The plot of top 15 relative bacterial abundances at the genus level. The next step was to discriminate any differential relationship between the control group (Group 1E) and the subjects infected by pathogens, not including _Entamoeba_ spp. (Group 2E), or infected by different _Entamoeba_ species (Group 3E = positive for _En. coli_ and other pathogens; Group 4E = positive for _E. dispar_ and other pathogens; Group 5E = positive for _E. hartmanni_ and other pathogens). As for alpha diversity, a significant difference was found in Chao1 Index, Observed OTUs (_p_ < 0.05) and Faith's phylogenetic diversity (_p_ < 0.01), comparing Group 1E versus Group 5E; observed OTUs and Faith's phylogenetic diversity (_p_ < 0.05) comparing Group 2E versus Group 5E (Table S4D). Beta diversity analysis showed: (i) a lower abundance for _Bacteroides_ (_p_ < 0.05) and for _Lachnoclstidium_ (_p_ < 0.01) in Group 3E versus Groups 1E and 2E; (ii) a lower abundance for [_Ruminococcus_] torques group in Group 3E versus Group 2E; (iii) an increased abundance for _Ruminococcaceae_ UCG-002 and _Ruminococcaceae_ UCG-010 (_p_ < 0.05) in Group 5E versus  
Figure 6: Beta diversity analysis in presence of _Entamoeba_ spp. (**A**) The UniFrac distances between negative and positive subjects for _Entamoeba_ spp., using principal coordinate analysis (PCoA) (**B**) The UniFrac distances among negative group, subjects harboring _E. hartmanni_ and _Blastocystis_, and subjects harboring _E. hartmanni_, _Blastocystis_, and other pathogens, using principal coordinate analysis (PCoA). Group 1E: control group; Group: 2E: positive for pathogens not including _Entamoeba_ spp. ; Group 3E: subjects positive for _En. coli_ and other pathogens; Group 4E: subjects positive for _E. dispar_ and other pathogens; Group 5E: subjects positive for _E. hartmanni_ and other pathogens. (**C**) The UniFrac distances among Group 1E, 2E, 3E, 4E, and 5E using principal coordinate analysis (PCoA). The groups carrying _En.