Expanding Human Gut Microbiome Diversity Beyond Western Populations: Methanogens and Helminths

Abstract

The human gut harbors a constantly changing community of microbes that influences the immune system and affects many aspects of host health. Within this community are not only bacteria, but also eukaryotic parasites and methanogenic archaea, whose contributions are important, yet often overlooked. Soil-transmitted helminths (STHs) are common and endemic in most parts of sub-Saharan Africa, thriving in poor sanitation and causing chronic illnesses such as anaemia. These STH infections modulate the host immune system and can substantially alter the host gut microbiome composition. In parallel, methanogens such as Methanobrevibacter smithii play a central role in hydrogen metabolism and support microbial fermentation through close interactions with bacterial communities. However, the relationships between parasites and microbiota, and the diversity of methanogens outside Western populations, are not well described. This thesis clarifies two main findings from a study of an African population: (1) metagenomic sequencing reliably detects STH infections and reveals their associations with specific shifts in gut microbial diversity, and (2) comparative genomics uncovers new diversity and geographical structuring of Methanobrevibacter species, revealing distinct evolutionary patterns for human-associated archaea across continents. In the first part, I performed metagenomic and qPCR analyses of stool samples from 310 Gabonese individuals. I showed that k-mer counts from metagenomic sequencing strongly correlate with qPCR for some STH parasites, confirming the effectiveness of metagenomics in detecting both parasites and bacteria. I observed significant changes in microbial alpha and beta diversity associated with parasite burden, particularly across different locations and age groups. These findings show that geography plays a significant role in how STH parasites interact with the gut microbiome, and demonstrate that metagenomic sequence data provide an effective method for linking parasite detection to microbial ecology. In the second part, I performed targeted enrichment and isolation of Methanobrevibacter species from Gabon, Germany, and Vietnam, which enabled the first cultivation of M. intestini from Central Africa. I expanded this cultivation effort to obtain 200 strains, predominantly of M. smithii and M. intestini, from Gabon, Germany, and Vietnam. Using both Average Nucleotide Identity (ANI) and phylogenetic analyses based on single-copy marker genes, we found that M. smithii and M. intestini are distinct, confirming that they are separate species. Using whole-genome synteny analysis, we also identified hypervariable genomic regions enriched for adhesins, mobile-element–associated functions, and defense genes. Also, key to our findings is the observed evolutionary pattern of partial co-divergence between human hosts and M. smithii, supporting long-term host–archaea relationships shaped by environmental and host-biological factors. This work integrates metagenomic detection of parasites, cultivation, and comparative genomics to bridge ecological and evolutionary perspectives of the human archaeome. Among others, this work's contributions include the first cultivation-based identification of M. intestini in Central Africa, the demonstration of the geographical structuring of Methanobrevibacter diversity, and evidence that integrating parasite and archaeal data advances understanding of gut ecosystem complexity.