Exposure to Parasitic Protists and Helminths Changes the Intestinal Community Structure of Bacterial Communities in a Cohort of Mother-Child Binomials from a Semirural Setting in Mexico

Abstract

An estimated 3.5 billion people are colonized by intestinal parasites worldwide. Intestinal parasitic eukaryotes interact not only with the host but also with the intestinal microbiota. In this work, we studied the relationship between the presence of multiple enteric parasites and the community structures of gut bacteria and eukaryotes in an asymptomatic mother-child cohort from a semirural community in Mexico. Fecal samples were collected from 46 mothers and their respective children, with ages ranging from 2 to 20 months. Mothers and infants were found to be multiparasitized by Blastocystis hominis, Entamoeba dispar, Endolimax nana, Chilomastix mesnili, Iodamoeba butshlii, Entamoeba coli, Hymenolepis nana, and Ascaris lumbricoides. Sequencing of bacterial 16S rRNA and eukaryotic 18S rRNA genes showed a significant effect of parasite exposure on bacterial beta-diversity, which explained between 5.2% and 15.0% of the variation of the bacterial community structure in the cohort. Additionally, exposure to parasites was associated with significant changes in the relative abundances of multiple bacterial taxa, characterized by an increase in Clostridiales and decreases in Actinobacteria and Bacteroidales. Parasite exposure was not associated with changes in intestinal eukaryote relative abundances. However, we found several significant positive correlations between intestinal bacteria and eukaryotes, including Oscillospira with Entamoeba coli and Prevotella stercorea with Entamoeba hartmanni, as well as the co-occurrence of the fungus Candida with Bacteroides and Actinomyces, Bifidobacterium, and Prevotella copri and the fungus Pichia with Oscillospira. The parasitic exposure-associated changes in the bacterial community structure suggest effects on microbial metabolic routes, host nutrient uptake abilities, and intestinal immunity regulation in host-parasite interactions. IMPORTANCE The impact of intestinal eukaryotes on the prokaryotic microbiome composition of asymptomatic carriers has not been extensively explored, especially in infants and mothers with multiple parasitic infections. In this work, we studied the relationship between protist and helminth parasite colonization and the intestinal microbiota structure in an asymptomatic population of mother-child binomials from a semirural community in Mexico. We found that the presence of parasitic eukaryotes correlated with changes in the bacterial gut community structure in the intestinal microbiota in an age-dependent way. Parasitic infection was associated with an increase in the relative abundance of the class Clostridia and decreases of Actinobacteria and Bacteroidia. Parasitic infection was not associated with changes in the eukaryote community structure. However, we observed strong positive correlations between bacterial and other eukaryote taxa, identifying novel relationships between prokaryotes and fungi reflecting interkingdom interactions within the human intestine.

Keywords: 16S sequencing; 18S sequencing; Mexico; bacteria; children; eukaryotes; helminths; microbiota; parasites; protists.

FIG 1

Proportions of parasites found in fecal samples from mother (a and c)-weaned child (b and d) binomials. (a) The intestinal parasites found in the mothers comprised Blastocystis hominis (Bh) (15 [32.6%]), Entamoeba coli (Ec) (11 [23.9%]), Entamoeba dispar (Ed) (5 [10.8%]), Endolimax nana (En) (5 [10.8%]), Iodamoeba butshlii (Ib) (2 [4.3%]), Giardia duodenalis (Gd) (1 [2.2%]), Chilomastix mesnili (Chm) (0 [0.0%]), Hymenolepis nana (Hn) (3 [6.5%]), and Ascaris lumbricoides (Al) (1 [2.2%]). (b) In children, the parasite frequencies were determined for Blastocystis hominis (4 [8.7%]), Entamoeba coli (4 [8.7%]), Entamoeba dispar (0 [0.0%]), Endolimax nana (1 [2.2%]), Iodamoeba butshlii (1 [2.2%]), Giardia duodenalis (0 [0.0%]), Chilomastix mesnili (1 [2.2%]), Hymenolepis nana (1 [2.2%]), and Ascaris lumbricoides (4 [8.7%]). (c) Cocolonizations by two or more parasites found in the mothers included Blastocystis hominis-Entamoeba coli (5 [10.8%]), Blastocystis hominis-Giardia duodenalis (1 [2.2%]), Blastocystis hominis-Hymenolepis nana (1 [2.2%]), Blastocystis hominis-Entamoeba coli-Entamoeba dispar (2 [4.3%]), Blastocystis hominis-Entamoeba coli-Endolimax nana (1 [2.2%]), Blastocystis hominis-Entamoeba dispar-Endolimax nana (1 [2.2%]), Blastocystis hominis-Endolimax nana-Iodamoeba butshlii (1 [2.2%]), Blastocystis hominis-Entamoeba dispar-Endolimax nana-Iodamoeba butshlii (1 [2.2%]), and Entamoeba coli-Entamoeba dispar-Endolimax nana-Hymenolepis nana (1 [2.2%]). (d) Cocolonizations found in children were Blastocystis hominis-Entamoeba coli (1 [2.2%]), Blastocystis hominis-Endolimax nana (1 [2.2%]), and Blastocystis hominis-Entamoeba coli-Chilomastix mesnili-Iodamoeba butshlii (1 [2.2%]).

FIG 2

Microbial diversity in unweaned infants (younger than 5 months of age). (a and b) Principal-component analysis (PCoA) ordination of variation in beta-diversities of human gut bacterial (a) and eukaryote (b) communities based on Bray-Curtis dissimilarities. Color and shape represent maternal exposure to parasites (blue circles represent negative exposure, and purple squares represent positive exposure). PERMANOVAs indicate that maternal exposure to parasites explains 15% (P = 0.003) of the variation in the infant bacterial community structure but is not a significant (P = 0.774) driver of the eukaryote community structure. (c and d) Shannon diversity of gut bacterial (c) and eukaryote (d) community structures. (e and f) Estimated richness of gut bacterial (e) and eukaryote (f) community structures. No significant differences were detected by Mann-Whitney tests for alpha-diversity comparisons between the parasite-positive and -negative groups.

FIG 3

Microbial diversity in individuals older than 1 year of age. (a and b) Principal-component analysis (PCoA) ordination of the variation in the beta-diversity of human gut bacterial (a) and eukaryote (b) communities based on Bray-Curtis dissimilarities. Color and shape represent maternal exposure to parasites (turquoise circles for negative and dark-red squares for positive exposure). PERMANOVAs indicate that maternal exposure to parasites and age explain 5.2% and 6.7% (P < 0.001) of the variation in the bacterial community structure, respectively, while age explains 4.3% (P < 0.001) of the variation in the eukaryote community structure. Ellipses represent the confidence intervals at 95%. (c and d) Shannon diversity of gut bacterial (c) and eukaryote (d) community structures. No significant differences were detected by Mann-Whitney tests for Shannon diversity between the parasite-positive and -negative groups. (e and f) Estimated richness of gut bacterial (e) and eukaryote (f) community structures. A significant difference was detected for bacterial community richness by Mann-Whitney tests for comparisons between two groups.

FIG 4

Microbial diversity in weaned infants between 1 year and 2 years of age. (a and b) Principal-component analysis (PCoA) ordination of the variation in the beta-diversity of human gut bacterial (a) and eukaryote (b) communities based on Bray-Curtis dissimilarities. Color and shape represent maternal exposure to parasites (turquoise circles for negative and dark-red squares for positive exposure). PERMANOVAs indicate that exposure to parasites and age explain 8.7% (P < 0.01) and 7.7% (P = 0.026) of the variation in the infant gut bacterial community structure, respectively. Ellipses represent the confidence intervals at 95%. No significant effects of age or exposure to parasites were detected for the eukaryote community structure. (c and d) Shannon diversity of gut bacterial (c) and eukaryote (d) community structures. A significant difference was detected only for eukaryote community alpha-diversity by Mann-Whitney tests for comparisons between the two groups. (e and f) Estimated richness of gut bacterial (e) and eukaryote (f) community structures. No significant differences were detected by Mann-Whitney tests for Chao1 estimated richness between the parasite-positive and -negative groups.

FIG 5

Microbial diversity in mothers. (a and b) Principal-component analysis (PCoA) ordination of the variation in beta-diversity of human gut bacterial (a) and eukaryote (b) communities based on Bray-Curtis dissimilarities. Color and shape represent maternal exposure to parasites (turquoise circles for negative and dark-red squares for positive exposure). PERMANOVAs indicate that exposure to parasites explains 5.6% (P < 0.01) of the variation in mother gut bacterial community structure. Ellipses represent the confidence intervals at 95%. No significant effects of age or exposure to parasites were detected for the eukaryote community structure. (c and d) Shannon diversity of gut bacterial (c) and eukaryote (d) community structures. (e and f) Estimated richness of gut bacterial (e) and eukaryote (f) community structures. No significant differences were detected by Mann-Whitney tests for richness and alpha-diversity between the parasite-positive and -negative groups.

FIG 6

Relative abundances of gut bacterial (a to d) and eukaryote (e to h) compositions of parasite-exposed individuals. (a and e) Bacterial and eukaryote compositions in unweaned infants younger than 5 months of age. (b to d and f to h) Relative abundances depending on parasite colonization in individuals over 1 year of age (b and f), only in weaned infants between 1 and 2 years of age (c and g), and only in mothers (d and h).

FIG 7

Heat map of biweight correlations (Pearson) between the top 50 bacterial (x axis) and the top 50 eukaryote (y axis) taxon OTUs in fecal samples of unweaned infants (∼3 to 4 months old). Colors denote positive (red) and negative (blue) correlation values. Significant correlations are denoted with a plus sign (P < 0.05 [false discovery rate {FDR}]).

FIG 8

Heat map of biweight correlations (Pearson) between the top 50 bacterial (x axis) and the top 50 eukaryote (y axis) taxon OTUs in fecal samples of weaned children (>1 year old) and mothers. Colors denote positive (red) and negative (blue) correlation values. Significant correlations are denoted with a plus sign (P < 0.05 [FDR]).