The CessOmics project focuses on understanding how major historical transitions, such as urbanization, globalization, and industrialization, have influenced human-associated microbiomes and viromes over time. By analyzing cesspit sediments—an underutilized molecular archive—this project reconstructs the evolution of microbial communities and their relationship to human behavior, health, and environmental changes. It also investigates human bacteriophage diversity as a novel tool for assessing population interactions and mobility.
This research is highly relevant to modern society, as it sheds light on declining microbiome diversity caused by industrialized diets and provides insights into the historical interplay between microbial communities, adaptation, and disease. Beyond health implications, the project contributes to fields like microbiome restoration, phage therapeutics, and environmental sustainability, offering solutions to societal and industrial challenges while aligning with European policy objectives on health and innovation.
CessOmics pursued three primary scientific objectives:
Co-evolution of human gut communities over time on a population level – To analyze lipidomic and genomic data from cesspits and fecal samples across time and geography, revealing the evolutionary trajectory of human-associated microbial communities.
Impact of cultural transitions on the gut microbiome and virome – To evaluate how historical transitions affected microbial diversity and composition, with a focus on urbanization, globalization, and industrialization.
Enhancing population interaction resolution through viruses – To use human bacteriophage diversity to investigate population mobility and interactions, providing a novel perspective on historical human behavior.
The project also included five complementary training objectives, focusing on developing technical and professional skills in DNA extraction, bioinformatics, virome analysis, and dissemination.
CessOmics successfully achieved many of its research, training, and dissemination goals, overcoming challenges such as COVID-19 restrictions and maternity leave. Highlights include:
Lipidomic and genomic analysis of over 160 samples, offering groundbreaking insights into the evolution of ancient microbiomes and viromes.
Detection of viruses in samples up to 50,000 years old, representing a significant advancement in virome research.
The establishment of foundational knowledge for future studies, such as multiomic approaches to prehistoric fecal material, which support ongoing grant applications and manuscript preparations.
The project has demonstrated the value of cesspit sediments in uncovering historical human behavior, environmental impacts, and microbial evolution. Its interdisciplinary approach and innovative findings pave the way for future research in areas such as phage therapeutics, microbiome restoration, and ancient metabolomics, with implications for societal health, environmental sustainability, and European innovation strategies.
