The line includes studies with the microbial cell in all its complexity: (i) identification/characterization of organelles, cellular structures and metabolic pathways involved in vital processes associated with physiology and interaction with hosts/environments; (ii) analysis of different aspects of microbial genetics and the control of gene expression.

The line includes the bioprospecting of microorganisms as well as bioactive molecules with potential application in different biotechnological processes in various sectors, namely: pharmaceutical industry, oil industry, agriculture, textile industry, as well as environmental, bioenergy and medical areas. The personal hygiene and cosmetics segments have also invested in innovative products of microbial origin. Enzymes, biosurfactants, biopolymers, antimicrobials and pigments, among other bioproducts, have been applied in these different areas. The microorganisms themselves can be used as probiotics and in microbiome studies.

Study of the occurrence, distribution, abundance and function of populations or communities of microorganisms in space and time. Understanding the intra- and interspecific relationships of microorganisms, their taxonomic position, as well as their relationship with the environment in which they live, aiming to discover how they influence and are influenced by them.

Study of the genetic, epidemiological, biochemical and molecular mechanisms of action and/or resistance to different classes of antimicrobial agents. Bioprospecting for new molecules with antimicrobial action, both of natural and synthetic origin, as well as new therapeutic strategies (e.g. drug repositioning, compound synergism), with special emphasis against resistant microorganisms, are contemplated in this line of research.

Study of the prevalence, incidence, distribution and transmission of infectious agents responsible for diseases in humans and/or plants of national and international relevance. These studies aim to develop methods to (i) prevent and avoid contagion, (ii) obtain prognosis and diagnosis, (iii) prevent (e.g.: development of vaccines) and treat infectious diseases caused by viruses, bacteria, protozoa and fungi. The mechanisms of aggression (e.g.: gene expression and production of potential virulence-related factors) to the host organism, which generate cellular/tissue/systemic lesions and dysfunctions, are also the target of this line of research.

To investigate the cellular and molecular mechanisms that govern the interactions between infectious agents (viruses, bacteria, protozoa and fungi) and their hosts (vertebrates, invertebrates, plants or even other microorganisms), seeking to elucidate different stages of the development of the infectious process. The infectious agent-host-environment triad, which controls genetic/biochemical plasticity as well as the formation of new patterns of infections and diseases, is studied in this line of research from a morphophysiopathological perspective.

This line of research includes the study of the body’s protective mechanisms against pathogens and oncogenic processes, as well as the role of inflammation in the pathophysiological processes of infectious, metabolic, degenerative, allergic, autoimmune diseases and cancer. The investigation of the role of the immune system in normal physiological mechanisms for maintaining homeostasis (e.g., interaction with the microbiota, generation of natural antibodies, organ function and metabolism) is also included in this line of research. This line of research represents an opportunity to identify targets for the treatment and prevention of diseases, as well as the development of cell therapies and vaccines.