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Parasites Influence Makeup of Human Gut Microbiome, BoG Speaker Reports

Double helix sculpture at CSHL

COLD SPRING HARBOR, NY (GenomeWeb) – The eukaryotic residents of the human gut influence its microbial makeup and diversity, according to Laure Ségurel from the Musée de l'Homme in Paris.

Ségurel and her colleagues studied the gut microbiomes of 64 people living in rural Cameroon. As Ségurel told the audience at the Biology of Genomes meeting here Thursday evening, they found that the gut parasite Entamoeba appeared to affect microbiome composition and diversity. At the same time, they found that whether the person was a hunter-gatherer or a fisher also affected their microbial gut community.

The gut microbiome is highly variable, Ségurel noted, with a high degree of variability between individuals, and that variability is influenced by age and diet, as well as other factors. 

Previous studies, she added, have shown differences in the gut microbiomes of industrialized and non-industrialized individuals. In particular, industrialized individuals exhibit a loss of diversity, possibly due to differences in diet, antibiotic use, and hygiene practices. Meanwhile, non-industrialized populations are enriched for the presence of Prevotella and Treponema in their gut microbiomes, and the increased presence of those microbes has been tentatively linked to higher fiber diets.

However, Ségurel said that many of these previous microbiome studies examined very different populations: they compared rural and non-industrialized populations to urban industrialized populations. That introduces a number of confounding factors like diet, antibiotic use, genetics, and climate, she said.

For her study, Ségurel then focused on Pygmy hunter-gatherers and Bantu farmers and fishers living in southwest Cameroon. While the Pygmy hunter-gatherers and Bantu farmers and fishers have differing subsistence approaches and do vary genetically — the population diverged some 60,000 years ago — they share a similar environment and limited access to medical resources like antibiotics, thus limiting the effect of some of those confounding factors.

She and her colleagues reported some of this work in PLOS Genetics late last year.

The researchers collected fecal samples as well as diet and medical questionnaire data from more than 60 individuals. They performed 16S rRNA sequence analysis on the fecal samples to generate some 176,000 reads per individual and, through shotgun sequencing, generated 76 million reads per individual. They also collected saliva samples to examine host genetics.

Through a microscope-based examination of the fecal samples collected, they identified three worms and one amoeba and uncovered additional ones by aligning sequencing data to reference genomes. Nearly half the population Ségurel studied harbored a parasite.

Within these gut microbiomes, Ségurel and her colleagues teased out the presence of 93 operational taxonomic units (OTUs). Using PERMOVA, Ségurel then tested for associations between the abundance of these OTUs and a number of covariates. While village location, subsistence style, and ancestry were linked with variation in microbiome composition, other covariates like age, sex, and BMI were not.

Entamoeba infection, though, had the greatest influence on gut microbiome composition, Ségurel said. Typically, she noted, the people in her study were infected with E. dispar, which is not pathogenic.

Still, Entamoeba infection leaves its mark on the gut microbiome. For instance, she noted that it was linked with an increase in intra-host diversity. This suggests that the decreased gut microbiome diversity observed in individuals from industrialized populations could be in part due to decreased parasite infection and changed hygiene practices, she added.

Entamoeba infectionwas also linked with decreased Prevotella abundance.

Diet and subsistence approach also had a subtle effect on the gut microbiome, Ségurel reported. When they controlled for amoeba infection, she and her colleagues found some microbial species like those in the genus Bifidobacterium were more common among fishers while Sarcina was only found among hunter-gatherers.

She noted, though, that Bifidobacterium is strongly linked to the consumption of dairy, something that typically isn't part of these populations' diet. However, she added that the fishers have access to neighboring villages and occasionally consumed yogurt, which could account for its presence.

That the Entamoeba influences the gut microbiome also suggested to Ségurel that researchers "need to better take into account eukaryote commensalates in studies of human microbiome."

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