Periodic Reporting for period 1 - CessOmics (CessOmics, using cesspits to assess past population interactions and the evolution of microbiomes and viromes)
Reporting period: 2021-05-01 to 2023-04-30
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.
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.
From the beginning of the CessOmics project to the end of the reporting period, the project achieved notable progress in advancing knowledge of ancient microbiomes and viromes. Over 160 cesspit and fecal samples, spanning diverse locations and historical periods, were collected and analyzed using lipidomics. This work provided critical insights into human-associated microbial communities, environmental changes, and pollution, as well as biomarkers for selecting the most promising samples for metagenomic sequencing. Despite delays caused by COVID-19 restrictions and late sample availability, 43 samples were successfully sequenced, with an additional 23 currently being processed. Key findings include the detection of viruses in 50,000-year-old samples from Picareiro, Portugal, representing the oldest known Homo gastrointestinal microbiome, and medieval microbiome data from Viking Age coprolites in Ribe, Denmark.
The project developed innovative tools and methodologies that improved the resolution of microbial analyses, revealing the impacts of urbanization, industrialization, and cultural transitions on the human gut microbiome. These findings have significant implications for understanding microbiome evolution and its modern applications, including phage therapeutics and microbiome restoration.
Dissemination efforts were adapted to challenges posed by the pandemic and maternity leave, with virtual seminars, public engagement events, and media outreach ensuring the research reached diverse audiences. Manuscripts summarizing key findings are being prepared for publication, ensuring lasting scientific impact.
Overall, the outcomes of CessOmics have established the Lipid Laboratory as a core facility at the Globe Institute and strengthened interdisciplinary collaborations. The project has created new opportunities for innovation and exploration, positioning its findings to contribute to future research and societal benefits.
The project developed innovative tools and methodologies that improved the resolution of microbial analyses, revealing the impacts of urbanization, industrialization, and cultural transitions on the human gut microbiome. These findings have significant implications for understanding microbiome evolution and its modern applications, including phage therapeutics and microbiome restoration.
Dissemination efforts were adapted to challenges posed by the pandemic and maternity leave, with virtual seminars, public engagement events, and media outreach ensuring the research reached diverse audiences. Manuscripts summarizing key findings are being prepared for publication, ensuring lasting scientific impact.
Overall, the outcomes of CessOmics have established the Lipid Laboratory as a core facility at the Globe Institute and strengthened interdisciplinary collaborations. The project has created new opportunities for innovation and exploration, positioning its findings to contribute to future research and societal benefits.
CessOmics advanced scientific understanding by integrating lipidomics, sedimentary DNA (sedDNA), and metagenomics to analyze human-associated microbiomes and viromes preserved in cesspit sediments. It achieved groundbreaking results, including the detection of viruses in 50,000-year-old samples from Picareiro, Portugal—the oldest evidence of a Homo gastrointestinal microbiome. These findings support the hypothesis of a core microbiome originating in early human evolution.
The project also developed tools for analyzing ancient viromes, improving microbial community resolution, and reconstructing historical changes in diet, pollution, and urbanization. This interdisciplinary approach bridged archaeology, molecular biology, and environmental science.
Results Achieved
Analysis of over 160 samples, including metagenomic and lipidomic studies, revealing the evolution of human microbiomes and viromes.
Identification of ancient viruses, with significant findings on microbial evolution and adaptation.
Submission of manuscripts to high-impact journals and establishment of methodologies that position the Lipid Laboratory as a core research hub at the Globe Institute.
Development of collaborations and tools that support future studies on phage therapeutics, microbiome restoration, and environmental sustainability.
Potential Impacts
Scientific Impact:
CessOmics has pioneered methodologies for studying ancient microbiomes and viromes, advancing fields like archaeology and microbiology. Its findings enhance understanding of microbial evolution and health applications.
Socio-Economic and Societal Impacts:
The project’s insights into ancient microbial stability provide potential applications in addressing antibiotic resistance and microbiome restoration. It highlights the long-term effects of urbanization and industrialization on microbial diversity, contributing to sustainable policy development.
Public engagement through outreach, seminars, and media appearances increased awareness of the importance of microbiome research, aligning with European objectives in health, innovation, and sustainability.
The project also developed tools for analyzing ancient viromes, improving microbial community resolution, and reconstructing historical changes in diet, pollution, and urbanization. This interdisciplinary approach bridged archaeology, molecular biology, and environmental science.
Results Achieved
Analysis of over 160 samples, including metagenomic and lipidomic studies, revealing the evolution of human microbiomes and viromes.
Identification of ancient viruses, with significant findings on microbial evolution and adaptation.
Submission of manuscripts to high-impact journals and establishment of methodologies that position the Lipid Laboratory as a core research hub at the Globe Institute.
Development of collaborations and tools that support future studies on phage therapeutics, microbiome restoration, and environmental sustainability.
Potential Impacts
Scientific Impact:
CessOmics has pioneered methodologies for studying ancient microbiomes and viromes, advancing fields like archaeology and microbiology. Its findings enhance understanding of microbial evolution and health applications.
Socio-Economic and Societal Impacts:
The project’s insights into ancient microbial stability provide potential applications in addressing antibiotic resistance and microbiome restoration. It highlights the long-term effects of urbanization and industrialization on microbial diversity, contributing to sustainable policy development.
Public engagement through outreach, seminars, and media appearances increased awareness of the importance of microbiome research, aligning with European objectives in health, innovation, and sustainability.