ARCHAIC · Diversity of bacteriophages in the ancient human microbiome

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.