Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns

Abstract

Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation. To explore this, we evaluated the fecal bacterial and eukaryotic microbiota in 156 asymptomatic adult subjects from a rural population in Xoxocotla, Mexico. Colonization with Blastocystis was strongly associated with an increase in bacterial alpha diversity and broad changes in beta diversity and with more discrete changes to the microbial eukaryome. More than 230 operational taxonomic units (OTUs), including those of dominant species Prevotella copri and Ruminococcus bromii, were differentially abundant in Blastocystis-colonized individuals. Large functional changes accompanied these observations, with differential abundances of 202 (out of 266) predicted metabolic pathways (PICRUSt), as well as lower fecal concentrations of acetate, butyrate, and propionate in colonized individuals. Fecal calprotectin was markedly decreased in association with Blastocystis colonization, suggesting that this ecological shift induces subclinical immune consequences to the asymptomatic host. This work is the first to show a direct association between the presence of Blastocystis and shifts in the gut bacterial and eukaryotic microbiome in the absence of gastrointestinal disease or inflammation. These results prompt further investigation of the role Blastocystis and other eukaryotes play within the human microbiome. IMPORTANCE Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition.

Keywords: Blastocystis; eukaryome; gut microbiome; host-microbe interactions; microbial ecology.

FIG 1

Variations in beta and alpha diversity of gut microbiome bacterial communities in relation to presence of Blastocystis. (A) Principal-component analysis (PCoA) ordination of variation in beta diversity of human gut bacterial communities based on Bray-Curtis dissimilarities among fecal samples. Colors represent the presence of Blastocystis in gut microbial communities (red for negative and blue for positive), and arrows represent the significant (P < 0.001) correlations between PCoA axes versus the relative abundances of bacterial genera in communities. (B and C) Shannon diversity (B) and Chao1 estimated richness (C) display differences in alpha diversity. Significant differences are shown by P values of Mann-Whitney tests for comparison between 2 groups. (D) Relative abundances of the 10 most abundant bacterial OTUs relative to the presence of Blastocystis. Significant differences are shown, calculated by DESeq2 (Wald test plus FDR).

FIG 2

Variations in beta and alpha diversity of gut microbiome eukaryotic communities explained by presence of Blastocystis. (A) Principal-component analysis (PCoA) ordination of variation in beta diversity of human gut eukaryotic communities based on Bray-Curtis dissimilarities among samples. Colors represent the presence of Blastocystis in gut microbial communities (red for negative and blue for positive). (B and C) Shannon diversity (B) and Chao1 estimated richness (C) display differences in alpha diversity. Significant differences are shown by P values of Mann-Whitney tests for comparison between 2 groups. (D) Relative abundances of the 10 most abundant eukaryotic OTUs relative to the presence of Blastocystis. Significant differences, calculated by DESeq2 (Wald test plus FDR), are shown.

FIG 3

Heatmap of biweight correlations (bicor method) between top 100 bacterial (x axis) and top 100 taxon (y axis) OTUs in fecal samples from study participants. Colors denote positive (red) and negative (blue) correlation values. Significant correlations are denoted with a plus sign (P < 0.05; FDR).

FIG 4

Short-chain fatty acid production in relation to Blastocystis colonization. Concentrations of fecal acetate, propionate, butyrate, isobutyrate, isovalerate, valerate, and caproate were measured by gas chromatography (N_pos = 102, N_neg = 54; *, P < 0.05; ***, P < 0.001 [Mann-Whitney]).

FIG 5

Gut mucosal immune changes associated with Blastocystis colonization. Concentrations of calprotectin (A) and total IgA (B) were determined by ELISA in feces in a subset of samples from this study (N_neg = 17, N_pos = 26; *, P < 0.05; ***, P < 0.001 [Mann-Whitney]).