Research

The World Health Organization lists air pollution, climate change, and antimicrobial resistance (AMR) among the greatest threats to global health. Guided by the One Health approach, which recognizes that human, animal, and environmental health are deeply interconnected, we use metagenomics to track the microorganisms and resistance genes circulating around us. Using cutting-edge ultra-low biomass sequencing, we characterize the urban microbiome of Rio de Janeiro from swabs collected on public surfaces, revealing which microbes circulate in densely populated areas and their potential role in future outbreaks. Our goal is to build a risk map of pathogen circulation and AMR dissemination across the city, while also identifying AMR hotspots in urban and animal production environments. In addition, we take part in an international effort to study air microbiomes sampled across the globe, integrating them with meteorological and physicochemical data to better understand the airborne ecosystem.

Interactions between hosts and microorganisms are everywhere in nature, shaping animal physiology, fitness, behavior, and protection against infections. Using shotgun metagenomics, we study the microbial communities associated with insects that transmit diseases, either biologically or mechanically. Many of these insects thrive in densely populated areas, where disease transmission is amplified. Flies carry pathogens resistant to antimicrobials, potentially spreading them between animals, people, and the environment. Yet because they visit so many different environments, flies can also serve as natural sentinels, acting as “bio-drones” that reveal which pathogens are circulating around us. In the mosquito Aedes aegypti, we showed that the gut microbiome shifts dramatically during blood digestion, revealing putative symbionts that may help it digest blood. By understanding how these microbial communities change and which naturally occurring microbes influence key metabolic pathways, we aim to aid future microbiome-based strategies to control disease vectors.

With the advent of new sequencing platforms, a growing number of genomes have become available in public databases, and they can now be analyzed with methods at the intersection of phylogenetics and genomics. Our research integrates molecular data, the fossil record, geological events, and bioinformatics to estimate time-calibrated phylogenies (timetrees) for different groups, such as flies and turtles, reconstructing when and how these lineages diversified.

Unlike vertebrates, insects do not produce antibodies. To defend themselves against pathogens, they rely on an innate immune system that produces defense molecules such as lysozymes and antimicrobial peptides (AMPs). The genes encoding these molecules form gene families that expand and contract over evolutionary time. In this research line, we investigate how these changes relate to the feeding and ecological habits of calyptrate flies. By analyzing more than 2,000 lysozyme genes across nearly 300 insect genomes, we described new subtypes found only in flies and a pattern of copy-number variation that depends on each species’ ecological habits. We are now extending this work to understand how AMP families have evolved across diverse groups of flies.