Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

Abstract

Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.

Blastocystis in Health and Disease: Are We Moving from a Clinical to a Public Health Perspective?

“…Analyzing fecal DNAs from 23 individuals in agrarian communities in Malawi, 13 U.S. residents, and 22 other mammals using 454 sequencing of amplicons generated by broad-specificity eukaryotic primers, Parfrey et al (25) recently compared the diversities of microbial eukaryotic gut communities in different populations and showed what could be interpreted as a "defaunation" of individuals adapted to a Western life style. Interestingly, the level of intestinal eukaryotic diversity observed in Malawian individuals was comparable to that seen in the nonhuman hosts investigated; meanwhile, eukaryotic microbiota of the U.S. cohort appeared depauperate.…”

Gut microbiota related to Giardia duodenalis, Entamoeba spp. and Blastocystis hominis infections in humans from Côte d’Ivoire

“…Microbiota is also characterized by the eukaryotic component encompassing helminths and protists [2,3]. Parasites react with the microbial community and with the host, greatly impacting the host/gut microbiota balance and influencing microbiota protective and immunomodulatory functions [1,3,[5][6][7][8].…”

An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases

“…Similar to the bacterial component of the human fecal microbiota, the micro-eukaryote community is dependent on geography (Parfrey et al, 2014; Yatsunenko et al, 2012). The fecal microbiome of United States residents, as compared to Malawians, has reduced abundance of fungi and other micro-eukaryotes both in adult and child populations (Parfrey et al, 2014; Yatsunenko et al, 2012).…”