ARCHAIC · Diversity of bacteriophages in the ancient human microbiome
Horizon Europe — Marie Skłodowska-Curie Actions
- Duration
- 2023-05-01 → 2025-04-30
- EU contribution
- €199,694
- Participants
- 2
- Scheme
- HORIZON-TMA-MSCA-PF-EF
Lines connect the coordinator with its partners.
Results in brief
Diversity of bacteriophages in the ancient human microbiome
The ARCHAIC project addressed a critical gap in microbiome research: the lack of evolutionary insight into the human virome, specifically bacteriophages (phages), through deep-time metagenomic analyses. Previous paleogenomic efforts primarily focused on bacterial components, leaving viral fractions, especially phages, largely unexplored. Given the central role of phages in shaping microbial communities and influencing host-microbe interactions, ARCHAIC set out to reconstruct phage diversity, persistence, and evolution using ancient gut metagenomes. Using state-of-the-art bioinformatic and molecular methods, the project focused on high-quality ancient DNA extracted from paleofeces across multiple archaeological sites and historical periods. The primary objective was to trace the diversity and dynamics of viral communities over time, with an emphasis on highly abundant and conserved phage groups such as crAssphages. A key innovation of the project was the benchmarking and optimization of taxonomic classifiers tailored for ancient viral metagenomes, ensuring robust detection even in highly degraded samples. By integrating ecological, evolutionary, and computational approaches, ARCHAIC contributes to broader discussions on microbial co-evolution, ancestral microbiota baselines, and the long-term dynamics of phage-bacterial relationships in human-associated ecosystems.
Data: CORDIS, © European Union
Project objective
While recent work has begun to shed light on the microbiota, which includes the trillions of bacteria and phages that inhabit our body, our understanding of its evolution over the course of human history is limited. To answer research questions regarding the development of the human microbiota over time, researchers have begun to sequence ancient DNA from well-preserved fecal and dental samples to understand their bacterial community composition. However, an important group of the microbiota, bacterial viruses (or bacteriophages), which play a large role in influencing bacterial community structure and can affect human health and disease, are often understudied in these ancient samples. Here, we propose ARCHAIC (bActeRiophage in the anCient HumAn mICrobiome), a project which aims to answer key questions regarding these important viral populations in these ancient samples. Using an integrative and collaborative approach, we will use sequencing data of ancient paleofeces and dental calculus to study the oral and gut microbiome from a variety of time periods. This novel work will allow us to develop a pipeline to identify viruses in ancient samples and answer the question - do ancient bacteriophage populations resemble modern ones? In addition, by identifying phages in these ancient samples, we will be able to probe the sequencing data for insights on phage evolution, the development of bacterial defense systems against phages, as well as reconstruct ancient phage genomes to identify novel phage/host pairs. ARCHAIC will move the field of phage biology forward by identifying phages in these relatively understudied ancient samples and will have results that will be applicable to the fields of bacterial evolution, anthropology, and bioinformatics.
Original text from CORDIS.
Participants
Links
- View on CORDIS
- DOI: 10.3030/101111040
- https://ec.europa.eu/research/participants/documents/downloadPublic?documentIds=080166e502e85b2a&appId=PPGMS
- https://ec.europa.eu/research/participants/documents/downloadPublic?documentIds=080166e51cd3fcb5&appId=PPGMS
Data: CORDIS, © European Union