Trillions of microorganisms, including bacteria and viruses, inhabit the human intestinal tract. This community, known as the gut microbiome and virome, profoundly impacts essential biological functions such as metabolism, immunity and behavior, and provides biological adaptations that we did not evolve on our own. While our microbial partners and their viruses have co-speciated with humans over millions of years, most of our knowledge comes from microbiome studies conducted on urban industrialized populations, while viruses have so far been the forgotten siblings of the microbiome family. How much has this gastrointestinal community diverged from its ancestral state? What was the impact of population migrations, and other critical historical transitions into our gut microbiome and virome? Archaeological materials such as mummified tissues, coprolites and dental calculus have the potential to shed light on our shared evolutionary journey, but not at the scale and resolution of historical cesspits, the focus of CessOmics. Cesspits are common, well-preserved features in archaeological sites that preserve everything from microfossils to the eggs of gut parasites. However, they have historically been overlooked as rich sources of molecular information. By analyzing the faecal lipids, bacterial and viral DNA from these historical cesspits, CessOmics will dive deep into the complex microbiome and virome preserved in cesspit sediments to illuminate the migrations and interactions of communities, examining their evolving gut microbiome and virome. By combining multiple molecular records that encompass the bacterial and viral fractions, we stand on the edge of a potential breakthrough in our ability to explore the evolution of the human gut community.
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