Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d'Ivoire

Abstract

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d'Ivoire.

Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays.

Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected.

Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis.

Keywords: Blastocystis; Entamoeba coli; Entamoeba dispar; Entamoeba hartmanni; G. duodenalis; bacteria; biotype; intestinal co-infection; virus.

Figure 1

Differences between age groups. (A): UniFrac distances among infants and other age groups. The samples were visualized using principal coordinate analysis (PCoA). Differences with other age groups are statistically significant. (B): The plot of top 15 relative bacterial abundances at genus level. The statistical significances are shown in Table S1A.

Figure 2

The plot of top 15 relative bacterial abundances at genus level. The subjects were distinguished by sex and age.

Figure 3

The plot of top 15 relative bacterial abundances. (A): the family level. (B): the genus level. The groups were based on the season of collection: the heavy dry season (HDS), heavy rainy season (HRS), and the low rainy season (LRS).

Figure 4

The UniFrac distances between enteric pathogen positive versus enteric pathogen negative subjects is displayed by age groups, using principal coordinate analysis (PCoA). The infant group tends to separate out according to Axis 1 (7.6%) and Axis 2 component (7%). The differences of the infant group from other age groups as shown in Figure 1, are also confirmed for comparisons of enteric pathogen negative versus enteric pathogen positive subjects.

Figure 5

Beta diversity analysis in presence of Blastocystis. Group1: control group; Group 2: positive only for Blastocystis; Group 3: positive for Blastocystis and Entamoeba spp.; Group 4a: positive for Blastocystis and pathogenic virus and bacteria; Group 4b: positive for Blastocystis and Entamoeba spp. and pathogenic virus and bacteria; Group 5b: positive for Blastocystis and Entamoeba spp. and G. duodenalis 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 Blastocystis and Entamoeba spp. (Groups 3, 4b, 5b) compared to the negative subjects (Group 1) and subjects carrying Blastocystis but not Entamoeba spp. (Groups 2 and 4a). (B) The plot of top 15 relative bacterial abundances at the genus level.

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. coli, E. dispar, and E. hartmanni (Groups 3E, 4E, and 5E), clearly were separated from groups not harboring Entamoeba species (Groups 1E and 2E). (D) The plot of top 15 relative bacterial abundances at the genus level. All the significances relating to (A–D) are summarized in Table S5D.

Figure 7

Beta diversity analysis for the subjects positive for G. duodenalis and other intestinal pathogens. Groups A: control group; Groups C: positive for Blastocystis only; Groups D: positive for Blastocystis and E. hartmanni without other pathogens; Groups E1: positive for E. hartmanni, Blastocystis and G. duodenalis, and pathogenic bacteria and viruses; Groups E2: positive for En. coli, Blastocystis and G. duodenalis, and pathogenic bacteria and viruses; Groups E3: positive for Blastocystis, G. duodenalis, and pathogenic bacteria and viruses; Groups M: positive for Blastocystis and mixed infection of pathogenic bacteria and viruses, without G. duodenalis and Entamoeba spp. (A) PCoA UniFrac showing low divergences along Axis 1 (9,3%) between positives with Blastocystis and E. hartmanni without pathogens (Group D) and Groups E1 and E2 including positives for G. duodenalis and other intestinal microorganisms. (B) Histogram of the linear discriminant analysis (LDA scores indicate the higher difference between clades of A, C, E1, and E2 groups. (C) The plot of top 15 relative bacterial abundances at the family level. (D) The plot of top 15 relative bacterial abundances at the genus level.