Adaptation of the human gut microbiome to ancient and recent changes in dietary regimes and lifestyle – MICROREGAL

This project proposes to collect fecal and saliva samples in about 250 individuals, in populations with contrasted lifestyles (rural, semi-urban and urban area in Cameroon, as well as urban area in France), in order to obtain genetic data not only on the human host but also on its gut microbes. A targeted-sequencing approach (16S) will allow to know the gut microbiome diversity and composition, and parasitological analyses will allow to identify the eukaryotes that are present in the feces. In parallel, dietary, medical and environmental data will be collected to be able to jointly analyze the genetic data with anthropological data of interest. Statistical and bioinformatics tools will allow to identify the determinants of the gut microbiome variability in the various cultural areas and to explore the factors responsible for the loss of microbial diversity in industrialized countries. Finally, the genetic basis of the gut microbiome variability will be studied thanks to genome-wide association approaches. This database will then be compared with other samples obtained with a similar protocol (collaboration with the MIT, Boston, USA).

A first field mission has been carried out in Cameroon in May 2017 to collect biological samples and anthropological information in 145 individuals from rural, semi-urban and urban areas. Parasitological analyses showed an important prevalence of amoebas (Entamoeba hartmanni, E. coli and E. dispar/histolytica) in rural, semi-urban and urban areas (51%, 42% and 38%, respectively), with a higher prevalence in rural areas. Furthermore, molecular biology analyzes and metagenomic approaches allowed us to show that no individual is infected by Entamoeba histolytica, but individuals are rather carrying the non-pathogenic E. dispar (these two species being undistinguishable by microscopy). For intestinal worms, the prevalence is milder but also more important in rural areas (18%, 6% and 3%, respectively). Bacteriological analyzes further showed a poor quality of water in rural areas, confirming the expected differences in sanitary state between populations. DNA from the fecal and saliva samples have been extracted and we obtained satisfying quantities of DNA for downstream genomic analyzes for most individuals.
In parallel, we have reanalyzed data collected in Cameroon in 2013 and showed that individuals from Cameroon carrying Blastocystis present a higher microbial diversity as compared to non-carriers, a result replicating the findings of Audebert et al (2016) in French individuals carrying Blastocystis, and also mirroring our own results in individuals from Cameroon carrying Entamoeba (Morton et al, 2015).

The data collected in 2017 along a gradient of urbanization will be analyzed, and then compared to data sampled in individuals migrating from Cameroon to France (Paris) collected in the beginning of 2018. These analyses will allow to identify the principal factors associated with the gut microbiome diversity and composition in a non-industrialized environment, and to better understand the mechanisms that led to the observed loss of microbial diversity in Europe and the United States.
We further plan to collect additional data in another region of the world, in populations with contrasted cultural characteristics, in order to validate our results in Cameroon and to bring out general trends about the gut microbiome.
As a next step, we are interested in obtaining metagenomic data (whole genomes) in a subset of individuals, in order to better understand the selective pressures acting on the bacterial species and genomes, thanks to population genetics approaches.

Publications:
- Chabé M, Lokmer A, Ségurel L. 2017. Gut Protozoa: Friends or Foes of the Human Gut Microbiota? Trends Parasitol. pii: S1471-4922(17)30210-6. doi: 10.1016/j.pt.2017.08.005. PMID: 28870496
- Dikongué E, Ségurel L. 2017. Latitude as a co-driver of human gut microbial diversity? Bioessays. 39(3). doi: 10.1002/bies.201600145. Epub 2017 Jan 13. PMID: 28083908

Oral presentations:
- September 2017: Invited talk at EMBO: « Anaeorobic protists : Integrating parasitology with mucosal microbiota and immunology » (Newcastle, UK)
- August 2017: Invited talk at the XVIst ESEB meeting (European Society for Evolutionary Biology), Groningen, the Netherlands
- Mai 2017: International conference on Holobionts, Paris, France - Mai 2016 : 29th annual meeting of The Biology of Genomes, Cold Spring Harbor Laboratory, USA
- Mars 2017: Symposium « Symbiosis in evolution, biology and human health », IBPS, Paris, France
- Juin 2016: Journée scientifique Bilille - Metagenomics, Institut Pasteur de Lille, Lille, France
- Mars 2016: Belgium-French meeting on Bioinformatics and Evolutionary Genomics (ALPHY), Lille, France

Human populations are evolving in close interaction with their environment, that they in turn shape. However, this intimate adequacy has been challenged many times during human evolutionary history, for example at the Neolithic revolution 10,000 years ago during the transition from a nomadic hunter-gatherer to a sedentary farming mode of subsistence, or more recently with the industrialization of human societies. While the influence of human activities on various ecosystems is largely recognized, little is know about the effect of ancient and recent changes in lifestyle, notably dietary regimes and access to medicine, on the symbiotic relationship we maintain with the microorganisms living in our guts, the gut microbiome. Our own gut microbial ecosystem is however currently considered to be essential for human health, and seems notably implicated in multiple metabolic and immune diseases. It also appears to be highly variable among individuals and populations, and at least partially heritable, making it a potential target for natural selection. The human gut microbiome therefore represents a phenotype of evolutionary, ecological and medical relevance.
Although it appears that the gut microbiome interacts with its host (through e.g., diet, antibiotics use and the immune response) and with other intestinal communities (parasites, viruses), the respective influence of various environmental (whether ecological or cultural) and genetic factors on its composition is not clear. Notably, the loss of microbial biodiversity observed in urban industrialized populations (as compared to rural developing countries) could be due to their dietary specialization, hygiene practices, and/or other variables. This project aims at disentangling the interactions that exist between these different factors to understand (i) how the microbial ecosystem has coevolved in the long-term with humans dietary regimes and parasitism since the Neolithic revolution 10,000 years ago, (ii) how rapid changes in lifestyle, notably industrialisation, has impacted the gut microbial diversity and (iii) what is the influence of genetic determinants on the microbiome composition. To tackle these issues, we propose to sample and compare the gut microbiome of individuals from contrasted subsistence modes (hunter-gatherers versus farmers) and along a gradient of urbanisation (from African rural villages to African cities to a European city) in Cameroon and France. We will collect both anthropological data (nutritional, medical and ethnological questionnaires, and anthropometric measures) and biological data (intestinal parasitism, microbial and human genetic data), and jointly analyze the influence of variables of interest on the gut microbiome, using various statistical and bioinformatics tools.
Bringing together classical biological anthropology approaches and next-generation sequencing technologies, this innovative project aims at dissecting how various ecological, cultural and genetic factors have impacted the gut microbial communities in the past, and likely continue to do so in the future, in the context of a rapid homogenization of food and hygiene practices across the World. This project will likely have an important impact in the fields of anthropology, ecology and evolution, as well as substantial implications in public health.