Original art: HEXICO (El Gato y La Caja)
The ultimate goal of the Microbial Paleogenomics unit is to investigate how pathogens and human-associated microbes emerged, spread, and changed at the genomic level over the course of human history, and to use this information to better understand the complexity of modern infectious diseases and human commensal microbes. To do so, we bring together–and borrow–tools, concepts, and approaches from distinct fields, including ancient DNA, phylogenetics, microbial genomics, evolutionary biology, population genetics, bioinformatics, history, and archaeology. Most current knowledge about infectious diseases and human commensal microbiota derives from studies of modern microbial strains. Our projects aim to use genomic information from ancient pathogens and oral microbes to reconstruct where and when these species were in the past and to determine the relationships and genomic changes that took place over time, from past strains to those that thrive today. We also use these approaches to investigate the mobility and spread of microbial species in relation to their human host populations, and the roles played by different historical processes in shaping our microbial makeup.
Our main focus and study model are the human populations from the Southern Cone of the Americas, which we analyze over large temporal scales, from the earliest human groups on the continent to modern societies. This is motivated by the fact that we know very little about the pathogens and microbes associated with pre-Columbian populations, including those from this region, and to what extent this picture changed after the agricultural transition, the contact with populations from other continent after European arrival, the colonization process, and the post-industrial era. Moreover, it represents an independent and distinct model to study how infectious diseases and human microbes emerged, evolved, and spread, because these populations have been isolated from other worldwide populations for the past ~15–20 thousand years.
The unit’s research is organized into three complementary axes:
- Axis 1: Deep-time infectious diseases (One Health). We reconstruct the emergence, spread, reservoirs, and evolutionary change of human pathogens using ancient DNA from humans and relevant animals, integrating archaeological context, paleopathology, and historical evidence.
- Axis 2: Population history and social dynamics of the Southern Cone. We combine ancient human and microbial genomes with isotopes, archaeology, and other proxies to study demographic changes, mobility, interactions, kinship organization, subsistence transitions, crisis episodes, and their health implications, throughout the Late Holocene.
- Axis 3: Evolutionary ecology of the oral microbiome. Using dental calculus as a time-stable archive, we perform genome-resolved, strain-level analyses of oral communities across continents and up to deep time to model microbial population structure, dispersal with humans, recombination, selection, and niche stability.
Together, these axes provide a unified framework–grounded in ancient DNA and comparative genomics–to link past processes to present-day microbial diversity and disease.
The official song of the Microbial Paleogenomics Unit:
Microbial Time Travelers
A Song for the Microbial Paleogenomics Lab
