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.

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25Around 3.5 billion people are colonized by intestinal parasites worldwide. Intestinal parasitic 26 eukaryotes interact not only with the host, but also with the intestinal microbiota. In this work, we studied 27 the relationship between the presence of multiple enteric parasites and the community structure of the 28 bacterial and eukaryote intestinal microbiota in an asymptomatic cohort of mother-child binomials from a 29 semi-rural community in Mexico. The intestinal parasites identified were Blastocystis hominis, Entamoeba 30 histolytica/dispar, Endolimax nana, Chilomastix mesnili, Iodamoeba butshlii, Entamoeba coli, 31 Hymenolepis nana and Ascaris lumbricoides. We sequenced bacterial 16S rDNA and eukaryotic 18S 32 rDNA in fecal samples of 46 mothers and their respective children, with ages ranging from two to twenty 33 months. Although we did not find significant alpha-diversity changes, we found a significant effect of 34 parasite exposure on bacterial beta-diversity, which explained between 5.2% and 15.0% of the variation of 35 the bacterial community structure. Additionally, exposure to parasites was associated with significant 36 changes in relative abundances of bacterial taxa, characterized by increases in the Clostridia and decreased 37 Actinobacteria and Bacteroidia abundances. There were no significant changes of intestinal 38 microeukaryote abundances associated with parasite exposure. However, we found several significant 39 positive correlations between intestinal bacteria and eukaryotes, including co-occurrence of the fungi 40Candida tropicalis with Bacteroides and Actinomyces, and Saccharomycetales with Bifidobacterium and 41 Prevotella copri. These bacterial community structure changes associated with parasite exposure imply 42 effects on microbial metabolic routes, host nutrient uptake abilities and intestinal immunity regulation in 43 host-parasite interactions. 44 45 46 IMPORTANCE 47The impact of intestinal eukaryotes on the prokaryotic microbiome composition of asymptomatic 48 carriers has not been extensively explored, especially in children and in hosts with multiple parasites. In 49 this work, we studied the relationship between protist and helminth parasite colonization and intestinal 50 microbiota structure in an asymptomatic population of mother-child binomials from the semi-rural 51 community of Morelos in Mexico. We found that the presence of parasitic eukaryotes correlated with 52 changes in the bacterial community structure in the intestinal microbiota in an age-dependent way. This 53 was characterized by an increase of the relative abundance of the class Clostridia and the decrease of 54 Actinobacteria and Bacteroidia. While there were no significant associations between the presence of 55 parasites and microeukaryote community structure, we observed strong positive correlations between 56 bacterial and eukaryote taxa, identifying novel relationships between prokaryotes and fungi, and reflecting 57 the diet of the human population studied. 58 59 60 KEY WORDS 61 Parasites/Euk...

Cervical cancer is an important health concern worldwide and is one of the leading causes of deaths in Mexican women. Previous studies have shown changes in the female genital tract microbe community related to Human Papillomavirus (HPV) infection and cervical cancer, yet this link remains unexplored in many human populations. This study evaluated the vaginal bacterial community among Mexican women with pre-cancerous Squamous Intraepithelial Lesions (SIL). We sequenced the V3 region of the 16S rRNA gene (Illumina Miseq) in cervical samples from 300 Mexican women, including 157 patients with SIL, most of which were HPV positive, and 143 healthy women without HPV infection or SIL. Beta-diversity analysis showed that 14.6% of the variance in vaginal bacterial community structure is related to the presence of SIL.  Presence of SIL was also associated with a higher species richness (Chao 1). MaAsLiN analysis yielded independent associations between SIL/HPV status and an increase in the relative abundance Brachybacterium conglomeratum, as well as a decrease in Sphingobium yanoikuyae and Lactobacillus spp. We also identified independent associations between HPV-16, the most common HPV subtype linked to SIL, and Brachybacterium conglomeratum. Our work indicates that the presence of SIL and HPV infection is associated with important changes in the vaginal microbiome, some of which may be specific to this human population.