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.

BackgroundThe intestinal parasite Blastocystis is found in humans and animals around the world. It is spread through the consumption of contaminated food and water and has been associated with a variety of intestinal symptoms. Blastocystis is one of the most common intestinal parasites in humans, yet its prevalence and distribution in humans in North America is not well characterized.MethodsNext-generation amplicon sequencing of a region of the Blastocystis SSU rRNA gene was applied to DNA extracted from fecal specimens obtained from 182 inhabitants of a rural population in Mexico to characterize Blastocystis prevalence, subtype distribution, and intra-host subtype diversity in humans.ResultsOf the 182 samples tested in this study, 68.1% (124) contained one or more Blastocystis subtypes. Subtype 3 was the most common subtype observed and was found in 81.5% of the positive samples. Subtype 1, 16.9% of the positive samples, and subtype 2, 17.7% of the positive samples, were also found in this population. Mixed infections were observed in 13.7% of the positive samples. In this population, the odds of having Blastocystis increased in adulthood (> 15 years; OR: 1.72, P < 0.0001), and the odds of having subtype 1 increased in the presence of farm animals (OR: 1.51, P = 0.03). The odds of having subtype 1, subtype 2, or a mixed infection decreased in the presence of cement flooring (OR: − 1.61, P = 0.005; OR: − 1.14, P = 0.03; OR: − 1.48, P = 0.02) possibly indicating socioeconomic factors are involved in the risk of acquiring one of these subtypes.ConclusionsThese data contribute to our understanding of the epidemiology of Blastocystis infection in humans and can be used to shape future studies which aim to better characterize the transmission pathways and health outcomes of Blastocystis infections.

Blastocystis subtype 3 (ST3) is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of Blastocystis ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of Blastocystis ST3 from other regions of the planet. Our analyses reveled that diversity of Blastocystis ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity of Blastocystis ST3 worldwide.

In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant’s immune system or on the health of the infants later in life, remains to be investigated.

Plant viruses have been reported to be common in the gut of human adults, presumably as result of food ingestion. In this work, we report that plant viruses can also be found frequently in the gut and oropharynx of children during their first year of life, even when they are exclusively breast-fed. Fecal and oropharynx samples were collected monthly, from birth to 1 year of age, from three apparently healthy children in a semi-rural community and analyzed by next generation sequencing. In 100% of the fecal samples and 65% of the oropharynx samples at least one plant virus was identified. Tobamoviruses in the Virgaviridae family were by far the most frequently detected, with tropical soda apple mosaic virus, pepper mild mottle virus, and opuntia tobamovirus 2 being the most common species. Seventeen complete virus genomes could be assembled, and phylogenetic analyses showed a large diversity of virus strains circulating in the population. These results suggest that children are continuously exposed to an extensive and highly diverse collection of tobamoviruses. Whether the common presence of plant viruses at an early age influences the infant’s immune system, either directly or through interaction with other members of the microbiota, remains to be investigated.