Periodic Reporting for period 2 - PaleoMetAmerica (A microbial perspective of major historical events in the Southern Cone of the Americas)
Période du rapport: 2022-05-01 au 2023-10-31
The project "PaleoMetAmerica" aims to unravel the intricate relationship between ancient human populations and their associated microbes, both commensal and pathogenic, throughout the history of the Southern Cone of the Americas. The investigation seeks to address the significant knowledge gap regarding the pathogens and microbes that were prevalent among pre-Columbian populations in this region, as well as how these microbial communities transformed following contact with the wider world. By focusing on key historical events, such as the agricultural transition and European colonization, the project endeavors to explore the impact of these events on the transmission of infectious diseases and alterations in oral microbial compositions.
The Southern Cone of the Americas provides a unique and distinct model for studying the emergence, evolution, and dissemination of infectious diseases and human microbes. These populations have remained geographically isolated from other global populations for an extensive period spanning approximately 15,000 to 20,000 years. Analyzing the dynamics within this region not only enhances our understanding of the health status of past populations but also offers valuable insights into the history of human migrations and the coevolutionary relationship between humans and microbes.
Through comprehensive research and analysis, the "PaleoMetAmerica" project aims to shed light on the intricate interplay between ancient human populations and their microbial companions. By uncovering the microbial landscapes of pre-Columbian societies, examining the consequences of major historical transitions in the microbial makeup, and investigating the impact of European colonization on infectious diseases and intercontinental microbial exchange, this project contributes to the broader understanding of human history and the complex interactions between humans and microbes over long time scales.
The Southern Cone of the Americas provides a unique and distinct model for studying the emergence, evolution, and dissemination of infectious diseases and human microbes. These populations have remained geographically isolated from other global populations for an extensive period spanning approximately 15,000 to 20,000 years. Analyzing the dynamics within this region not only enhances our understanding of the health status of past populations but also offers valuable insights into the history of human migrations and the coevolutionary relationship between humans and microbes.
Through comprehensive research and analysis, the "PaleoMetAmerica" project aims to shed light on the intricate interplay between ancient human populations and their microbial companions. By uncovering the microbial landscapes of pre-Columbian societies, examining the consequences of major historical transitions in the microbial makeup, and investigating the impact of European colonization on infectious diseases and intercontinental microbial exchange, this project contributes to the broader understanding of human history and the complex interactions between humans and microbes over long time scales.
Significant progress has been achieved in various aspects since the inception of the project. A highly competent and dedicated team has been successfully established, comprising PhD students, postdocs, lab technicians, research engineers, and master students. Despite the unprecedented challenges imposed by the COVID-19 pandemic, the team has effectively fostered a collaborative, friendly and hard-working environment. The collection and processing of archaeological samples encountered logistical obstacles, exacerbated by the pandemic's impact. However, the team's efforts and determination have surpassed initial expectations, resulting in the acquisition of an extensive sample collection and the execution of comprehensive DNA sequencing efforts. Consequently, a large ancient DNA dataset of ancient microbes from the Southern Cone of the Americas has been generated. This invaluable resource encompasses oral microbiome profiles and the identification of systemic pathogens.
Noteworthy advancements have been made within each work package of the project. The exploration of the microbial landscape of pre-Columbian populations has unveiled the phylogenetic diversity of oral microbial species prevalent in the Americas. Additionally, an extensive dataset of oral microbiome profiles has been generated, encompassing both hunter-gatherer and agriculturalist communities from the late Holocene period. This dataset serves as a valuable resource for investigating the influence of the agricultural transition on microbial composition and population health, which is currently being analyzed by different members of the team.
Furthermore, the project has initiated various community engagement initiatives aimed at fostering dialogue and involving local and indigenous populations residing in the regions under study. We have also established a collaborative network comprising numerous archaeologists from Argentina and Chile. Through these collaborations, valuable insights and perspectives are being shared, facilitating a comprehensive understanding of the region's history and archaeological contexts.
In summary, the project has made substantial progress on multiple fronts, including team formation, sample collection, data generation, and scientific advancements within each work package. These achievements have significantly enriched our understanding of the microbial landscape in pre-Columbian populations and the impact of the agricultural transition in their microbial makeup.
Noteworthy advancements have been made within each work package of the project. The exploration of the microbial landscape of pre-Columbian populations has unveiled the phylogenetic diversity of oral microbial species prevalent in the Americas. Additionally, an extensive dataset of oral microbiome profiles has been generated, encompassing both hunter-gatherer and agriculturalist communities from the late Holocene period. This dataset serves as a valuable resource for investigating the influence of the agricultural transition on microbial composition and population health, which is currently being analyzed by different members of the team.
Furthermore, the project has initiated various community engagement initiatives aimed at fostering dialogue and involving local and indigenous populations residing in the regions under study. We have also established a collaborative network comprising numerous archaeologists from Argentina and Chile. Through these collaborations, valuable insights and perspectives are being shared, facilitating a comprehensive understanding of the region's history and archaeological contexts.
In summary, the project has made substantial progress on multiple fronts, including team formation, sample collection, data generation, and scientific advancements within each work package. These achievements have significantly enriched our understanding of the microbial landscape in pre-Columbian populations and the impact of the agricultural transition in their microbial makeup.
The achievements of the project thus far are pushing the boundaries of knowledge in several fields. The generation of a comprehensive ancient DNA dataset from the Southern Cone of the Americas provides a valuable resource for studying the history and genetic diversity of Native American populations and their associated microbes. Novel methodologies and bioinformatic pipelines have been developed, which will greatly facilitate the analysis of ancient microbial genomes and oral microbiomes. We are also exploring methodological approaches to combine and integrate microbial phylogenomics with human population genetics. Our results so far suggest that we will be able to contribute unprecedented insights into the pathogens and microbial communities that existed in the Americas before contact with the outside world, some of which were not suspected in the Americas in pre-Columbian times.
The project's expected results until the end of the project include further analysis of the collected samples, publication of scientific papers for each of the work packages, and continue developing the engagement with local communities. By combining genetic, archaeological, and historical data, the project aims to reconstruct migration histories of humans and their microbes (pathogenic or commensal), investigate the intercontinental exchange of human microbes in colonial and post-colonial times, and gain a deeper understanding of the health of past populations from the Southern Cone of the Americas. Moreover, the project's emphasis on community engagement and ethical considerations could also results in new modes of inclusion of indigenous and local voices in the scientific process, fitted to the realities and particularities of this region.
In summary, the PaleoMetAmerica project has achieved significant milestones in unraveling the intricate relationship between ancient human populations and their microbial companions in the Americas. The project's contributions to scientific knowledge, methodology development, equitable international collaboration and community engagement are poised to have a lasting impact on our understanding of human history, health, and cultural heritage.
The project's expected results until the end of the project include further analysis of the collected samples, publication of scientific papers for each of the work packages, and continue developing the engagement with local communities. By combining genetic, archaeological, and historical data, the project aims to reconstruct migration histories of humans and their microbes (pathogenic or commensal), investigate the intercontinental exchange of human microbes in colonial and post-colonial times, and gain a deeper understanding of the health of past populations from the Southern Cone of the Americas. Moreover, the project's emphasis on community engagement and ethical considerations could also results in new modes of inclusion of indigenous and local voices in the scientific process, fitted to the realities and particularities of this region.
In summary, the PaleoMetAmerica project has achieved significant milestones in unraveling the intricate relationship between ancient human populations and their microbial companions in the Americas. The project's contributions to scientific knowledge, methodology development, equitable international collaboration and community engagement are poised to have a lasting impact on our understanding of human history, health, and cultural heritage.