Response of the human gut and saliva microbiome to urbanization in Cameroon

Abstract

Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. to unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. to do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.Humans living in urban areas from highly industrialized countries host less diverse gut microbiomes than those in rural areas from the less industrialized ones. This effect of industrialization (as we refer to it hereafter) has been reported by numerous studies comparing urban areas in Europe or North America with rural ones in Africa, Asia or South America 1-8 . Loss in alpha diversity is further accompanied by systematic shifts in bacterial composition (see e.g. 9,10 ). Despite crucial implications for human health 11,12 , the factors responsible for these ecological changes are still unclear. Two main (non-exclusive) hypotheses have been proposed: (i) decreased consumption of dietary fibers 13,14 and (ii) improved sanitation and access to medical care (including antibiotics 15 ). In addition, geographical latitude could be a confounding factor, given that it is a proxy for the diversity of environmental bacteria 16 . Indeed, the only two studies that did not find a loss of diversity with industrialization were studies considering rural populations not living in a warm tropical environment 17,18 .To disentangle various factors potentially leading to this observed diversity loss, some authors focused on smaller geographical scales, contrasting urban and rural individuals from the same countries (referred to hereafter as the effect of urbanization). Such studies reported inconsistent results: no significant differences in Russia 19 and Nigeria 20 , some differences in China 21 , and season and altitude dependent shifts in Mongolia 22 and India 23 , respectively. These discrepancies can be partially explained by different definitions of rural areas used in these studies (from iso...

Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations

“…These genetic differences complement differential abundance and highlight an alternative route for functional effects to take place. The rural microbiome traits can also be seen with eukaryotes, which are rarely detected but have large potential to affect microbial ecosystems 22 . Twenty-two samples contained at least one of three detected fungal taxa: Saccharomyces cerevisiae, Naumovozyma, and Eremothecium, the latter two only classified at the genus level (Fig.…”

“…Identifying precise immunomodulatory pathways has been challenging due to limited computational tools and reference genomes 21 , requiring cohorts harboring large microbial diversity. African populations encompass a diversity of lifestyles and opportunities to detect ecological niches 5,22,23 , as well as a pervasiveness of autoimmune diseases 24 and epidemics 25,26 . Leveraging the diversity of these populations to dissect the dynamics of competitive microbial interactions that have led to the evolution of complex molecules that allow bacteria to interact with host immunity and utilize it to their own advantage [27][28][29] might unveil promising therapeutic strategies or dietary interventions.…”

Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon

“…Children living in Cameroon and in SSA broadly have been underrepresented in studies of the gut microbiome, with studies conducted in SSA often focusing on populations with specific lifestyles such as agrarian, pastoralist, or hunter-gathers 4 , 19 – 26 . However, one study conducted in individuals in three populations along an urbanization gradient in Cameroon indicated that urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas 27 . Our results are consistent with this work, with the ethnically diverse Cameroonian children surveyed here harboring a microbiota characteristic of agrarian-associated enterotypes with communities characterized by high Prevotella and low Bacteroides and various lineages of Clostridia , regardless of HIV-infection status.…”

Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

“…We obtained the informed consent of each participant for contributing to this research. These samples are part of the dataset previously published ( Lokmer et al., 2020 ). The average age was 38 years with a range between 18 and 64 years.…”

“…To achieve this, given that Entamoeba colonization is rare (if not absent) in industrialized countries, our study focused on the intestinal microbiota of healthy adults from rural, semi-urban and urban areas in Cameroon. In this study, we used the 16S rRNA gene amplicon sequencing data from 134 Cameroonians generated in a previous survey ( Lokmer et al., 2020 ) to profile the bacterial composition and diversity of their gut microbiota. The detection and identification of Blastocystis STs and Entamoeba species was performed by analyzing shotgun metagenomic data from the same individuals generated for this study.…”