Microbial Genomics and Bioinformatics
Research
Genomic dynamics of microbiomes, local adaptation and epidemiology
We are carrying out studies that allow us to have an understanding of how pathogenic microorganisms flow between terrestrial, aquatic and anthropogenic environments, and to this end, we carry out the functional analysis of the metagenome and metapangenome.
We also study the evolutionary dynamics of antibiotic resistance and bacterial virulence in both bacterial genomes and microbiomes belonging to different environments (e.g. human and animal gut, and natural environments). We aim to understand how these genetic traits are spread between different microbiomes, linking animal, human and environmental health, in line with the OneHealth concept.
So far, our studies have allowed us to model the effect of human contact on the transmission of antibiotic resistance genes, as well as to compare the correlation between the abundance and diversity of resistance genes and those of bacterial virulence, in human, animal and environmental microbiomes with different types of antibiotic exposure and anthropogenic contact.
Recent projects:
Representative publications:
Daniel G. Silva; Célia P. F. Domingues; João F. Figueiredo; Francisco Dionisio; Ana Botelho; Teresa Nogueira. "Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the Resistome". Biology (2022): https://doi.org/10.3390/biology11111681.
João Rebelo; Celia P. F. Domingues; Francisco Dionisio; Manuel Carmo Gomes; Ana Botelho; Nogueira, Teresa. "COVID-19 lockdowns may reduce resistance genes diversity in the human microbiome and the need for antibiotics". International Journal of Molecular Sciences 22 13 (2021): 6891. https://doi.org/10.3390/ijms22136891.
Célia P. F. Domingues; João S. Rebelo; Francisco Dionisio; Ana Botelho; Teresa Nogueira. "The Social Distancing Imposed To Contain COVID-19 Can Affect Our Microbiome: a Double-Edged Sword in Human Health". mSphere (2020): https://doi.org/10.1128/mSphere.00716-20.
Pedro Escudeiro; Joël Pothier; Francisco Dionisio; Teresa Nogueira. "Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes". mSphere (2019): https://doi.org/10.1128/mSphere.00135-19.
Role of bacterial mobile genetic elements on genome evolution
We aim to understanding how genome plasticity, mediated by mobile genetic elements such as plasmids, transposons, integrons, phages, ICEs, etc., contributes to microbial communities that respond to stress conditions, such as antibiotic exposure or anthropogenic contact, and adapt to the environment.
We have studied the correlation between the diversity and abundance of different types of bacterial mobile genetic elements, and antibiotic resistance genes, both in microbiomes and in a collection of over 16,000 bacterial reference genomes. Our results suggest that genes encoding for antibiotic resistance that are most commonly used in human medicine, veterinary medicine and agriculture are those with the greatest potential to be epidemic-prone.
We want to better understand the spread of plasmids in bacterial communities.
Recent projects:
PhD fellowship FCT UI/BD/153078/2022 - Celia Domingues (Biodiv doctoral program cE3c-FCUL) - ongoing
Representative publications:
Celia P. F. Domingues; Joao S. Rebelo; Francisco Dionisio; Nogueira, Teresa. "Multi-Drug Resistance in Bacterial Genomes—A Comprehensive Bioinformatic Analysis". International Journal of Molecular Sciences 24 14 (2023): 11438. https://doi.org/10.3390/ijms241411438
Dionisio, Francisco; Domingues, Célia P. F.; Rebelo, João S.; Monteiro, Francisca; Nogueira, Teresa. "The Impact of Non-Pathogenic Bacteria on the Spread of Virulence and Resistance Genes". International Journal of Molecular Sciences 24 3 (2023): 1967. http://dx.doi.org/10.3390/ijms24031967.
Helena Darmancier; Celia P. F. Domingues; Joao S. Rebelo; Ana Amaro; Dionisio, Francisco; Joël Pothier; Serra, Octávio; Nogueira, Teresa. "Are Virulence and Antibiotic Resistance Genes Linked? A Comprehensive Analysis of Bacterial Chromosomes and Plasmids". Antibiotics 11 706 (2022): https://doi.org/10.3390/antibiotics11060706.
Celia P. F. Domingues; Joao S. Rebelo; Francisca Monteiro; Nogueira, Teresa; Dionisio, Francisco. "Harmful behaviour through plasmid transfer: a successful evolutionary strategy of bacteria harbouring conjugative plasmids". Philosophical Transactions B (2021): https://doi.org/10.1098/rstb.2020.0473.
Pathogenic bacterial genomics and food safety
We study the genomes of human foodborne pathogenic bacteria, such as Listeria monocytogenes, Campylobacter sp., Salmonella sp., and others. We are interested in understanding their distribution in environmental microbiomes, such as aquaculture production environments, linked to the food chain. In this context, we aim to understand which genetic traits are involved in their adaptation to the food production environment-
We also seek genomic evidence for the persistence of the Listeria monocytogenes phenotype in food processing environments.
Recent projects:
Representative publications:
Azevedo, I.; Barbosa, J.; Albano, H; Nogueira, T.; Teixeira, P. Lactic Acid Bacteria isolated from traditional and innovative alheiras as potential biocontrol agents. Food Microbiology 2023, 104450. https://doi.org/10.1016/j.fm.2023.104450
Ribeiro, M.; Maciel, C.; Cruz, P.; Darmancier, H.; Nogueira, T.; Costa, M.; Laranjeira, J.; Morais, R.M.S.C.; Teixeira, P. Exploiting Potential Probiotic Lactic Acid Bacteria Isolated from Chlorella vulgaris Photobioreactors as Promising Vitamin B12 Producers. Foods 2023, 12, 3277. https://doi.org/10.3390/foods12173277
Joana Inês Bastos Barbosa; Helena Albano; Beatriz Silva; Maria Helena Almeida; Nogueira, Teresa; Paula Teixeira. "Characterization of a Lactiplantibacillus plantarum R23 isolated from arugula by whole-genome sequencing and its bacteriocin production ability". International Journal of Environmental Research and Public Health (2021): https://doi.org/10.3390/ijerph18115515.
Science education and outreach
We actively contribute to the development of educational games and other activities to disseminate scientific knowledge about biological evolution and, particularly, the evolution of microbial genomes and their zoonotic transmission.
Recent projects:
Representative publications:
Mavrikaki, E.; Realdon, G.; Aivelo, T; Bajrami, A.; Bakanay, C.D.; et al. Evolution in European and Israeli school curricula - a comparative analysis. International Journal of Science Education 2024. https://doi.org/10.1080/09500693.2023.2293090
de Lima, Joelyn; Adnadevic, Tanja; Barstad, Johan; Georgiou, Martha; Holm, Sile; Kenig, Bojan; Martinelli, Lucia; et al. "Developing non-formal learning activities focused on increasing evolutionary knowledge and scientific literacy". zenodo (2023): 1-63. https://doi.org/10.5281/zenodo.7711038.
Sá-Pinto, Xana; Realdon, Giulia; Torkar, Gregor; Sousa, Bruno; Georgiou, Martha; Jeffries, Alex; Korfiatis, Konstantinos; et al. "Development and validation of a framework for the assessment of school curricula on the presence of evolutionary concepts (FACE)". Evolution: Education and Outreach 14 1 (2021): http://dx.doi.org/10.1186/s12052-021-00142-2.
Adnadevic, Tanja; Milosevic, Tamara; Radovcic, Davorka; et al. "Exploratory study of evolution-themed, non-formal education in Europe". (2020): https://doi.org/10.5281/zenodo.3712725.
Pedro H C David; Xana Sá-Pinto; Teresa Nogueira. "Using SimulATe to model the effects of antibiotic selective pressure on the dynamics of pathogenic bacterial populations". Biology Methods and Protocols (2019): https://doi.org/10.1093/biomethods/bpz004.