Maria Lopopolo

The field of ancient metagenomics provides insights into past microbiomes, but with a growing dataset size, methods that rely on reference databases have limited scope. Here, we introduce DIANA, a multi-task neural network that predicts key metadata categories from unitig abundances. Trained on 2,597 run accessions (1.72 Tbp of assembled unitig sequences), DIANA accurately identifies sample host (94.6%), community type (90.0%), and material (88.9%) on held-out test data and demonstrates robust generalisation on an independent validation set. A key innovation is DIANA’s ability to perform semantic generalisation, correctly classifying samples with labels unseen during training — such as novel subspecies — to their appropriate parent categories. By leveraging both known and uncharacterized genomic sequences, DIANA provides a rapid, data-driven system for metadata validation and quality control, accelerating discovery in ancient metagenomics research.

Une perspective paléométagénomique sur les grandes transformations des modes de vie dans les populations humaines: Ma thèse vise à aborder des questions importantes concernant l'émergence des maladies infectieuses dans les populations humaines et les transformations survenues pendant la transition agricole chez les populations sud-américaines précoloniales. Les récents progrès des techniques d'ADN ancien (aDNA) offrent une opportunité unique d'explorer les génomes des agents pathogènes qui circulaient autrefois dans les populations humaines, fournissant des informations précieuses sur leurs histoires épidémiologiques, évolutives et de propagation. En utilisant l'aDNA, j'enquête sur les agents pathogènes qui prévalaient dans les Amériques avant le contact européen, une période pour laquelle nos connaissances sont limitées. Une contribution significative de ma recherche est la découverte d'un agent pathogène producteur de lèpre appelé M. lepromatosis qui infectait les Amérindiens avant le contact avec les Européens. Cette découverte fournit une preuve directe des maladies infectieuses dans les Amériques à l'époque précoloniale. Nos investigations révèlent que cet agent pathogène était largement répandu à travers le continent, puisque nous avons détecté sa présence en Amérique du Nord et en Amérique du Sud. Pour explorer davantage son histoire évolutive, je réalise des analyses d'horloge moléculaire sur des souches modernes et anciennes de M. lepromatosis, qui jusqu'à présent soutiennent l'existence d'un ancêtre commun à toutes les souches connues après l'arrivée des humains en Amérique. De plus, j'ai adopté une approche interdisciplinaire qui intègre l'aDNA, la métagénomique et de données isotopiques archéologiques pour analyser un ensemble substantiel de microbiomes oraux anciens (>200 échantillons). Ces échantillons proviennent de dents archéologiques et de tartre d'ancêtres précoloniaux en Amérique du Sud. À travers cette analyse complète, je vise à évaluer les changements dans la composition microbienne et la prévalence des agents pathogènes oraux opportunistes dans les populations agricoles. Les analyses ont révélé des variations dans les microbiomes oraux des peuples autochtones du Cône Sud qui peuvent être liées à des différences dans les économies de subsistance et également aux périodes historiques. Ces résultats éclairent les effets des pratiques culturelles et des événements historiques sur la composition microbienne et la santé humaine.

The transition to agriculture was a transformative process in human history with wide-ranging demographic and social consequences¹. Across South America, agriculture was adopted at different times and through diverse pathways, resulting in a mosaic of regionally distinct farming histories^2,3. The Uspallata Valley, at the southern frontier of Andean farming, offers a unique opportunity to examine a case of late adoption of agriculture. Here we show that agriculture in the Uspallata Valley was adopted by local hunter-gatherers, as evidenced by genetic continuity between pre-farming and farming populations inferred from 46 newly sequenced ancient human genomes. These groups carried a distinct genetic component in Indigenous American diversity, indicating a unique population history in the region. Palaeodietary isotopes (δ¹³C/δ¹⁵N) reveal fluctuating maize intake consistent with flexible farming. Strontium isotopes (⁸⁷Sr/⁸⁶Sr) indicate the arrival of migrants from nearby regions between around 810-700 cal years BP, shortly before the Inka expansion. Genomic and isotopic analyses show that these migrants belonged to the same regional metapopulation as local groups, relied heavily on maize, probably moved in matrilineally organized family groups, exhibited stress markers (including malnutrition and diseases, such as tuberculosis, as confirmed by pathogen genomics) and experienced a long-term demographic decline. Our results suggest that these groups used social organization and migration as resilience strategies in the face of a multidimensional crisis.

Leprosy, caused primarily by Mycobacterium leprae , is considered a disease introduced into the Americas during European colonization. However, the recent discovery of a second pathogen causing leprosy, M. lepromatosis , mainly found in the Americas, challenges this view. Here, we show that M. lepromatosis infected humans in the Americas before European contact. By screening 389 ancient and 408 contemporary samples, we have expanded the genetic data available for the species. Phylogenetic analyses revealed distinct human-infecting clades of M. lepromatosis , with one dominating North America since colonial times. The presence of millennia-old strains in North and South America indicates that M. lepromatosis may have been widespread during the Late Holocene, demonstrating that M. lepromatosis leprosy has a long-standing history in the Americas before European arrival.

Background Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir. Results AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community. Conclusions Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.

Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading. Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community. Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.