Antimicrobial Peptides from Commensal Next Generation Probiotics

Current trends in maintaining and improving health are centered on disease prevention rather than treatment. This requires personalized health solutions seamlessly integrated in individual´s lifestyle. Gut microbiota is both a major contributor to and indicator of an individual’s general health. Besides the metabolic role, gut microbiota is an important barrier- and immune-modulator contributing to the prevention of metabolic and inflammatory diseases. The balance between gut bacterial species also contributes to exclude pathogenic bacteria, decreasing the risk of bacterial infections and the need for antibiotics.
This is particularly relevant considering the worldwide crisis of resistance development to classical antimicrobials, with the consequent need for molecules with new targets and modes of action. The 2030 Agenda for Sustainable Development strategy defines infectious diseases (e.g.: tuberculosis, viral infections) as a priority. To find such diverse compounds, namely from microbial sources, there is an increasing search for understudied environments as a promising alternative to discover new compounds. Among these, the gastrointestinal tract appears as an uncommon yet highly appealing environment for the search of novel candidates. Indeed, in situ postbiotics production, namely, antimicrobial peptides (AMP), is regarded as a valuable strategy to aid gut microbiota modulation and several classical probiotic bacteria are known AMP producers. Indeed, probiotic bacteria play a key role in the gut health modulation ecosystem. Emerging as next generation probiotic candidates (NGP) are some commensal bacteria, which have proven beneficial effects to the host and are generally considered intrinsically safe, as they are part of the normal host’s microbiota. Several studies have been performed to characterize several NGP and the nature of their interaction with other commensal bacteria and the host. However, the usual microaerophilic to strictly anaerobic metabolism and fastidious growth nature of these bacteria represents a challenge in terms of culturability and handling procedures. Thus, in this project, we propose the application of culture-independent techniques to ensure and maximize the expected outcomes in terms of screening and production of AMP. A genome mining approach in parallel with an advanced methodology for transcriptomics analysis will be employed to identify putative production of antimicrobial compounds that may participate in the defense against pathogenic bacteria. Providing that these peptides might not always be produced under standard culture conditions, and to overcome the handling issues inherent to the nature of their producers, herein, we intend to heterologoulsy express the putative biosynthetic clusters in a suitable host, that has been previously engineered and applied as a probiotic strain. This system will allow AMP production and their characterization, structure elucidation, and possibly future gene manipulations. Candidate AMP will be identified/characterized and purified using optimized chromatography and mass spectrometry approaches, for bioactivity screening, toxicity evaluation and mode of action studies.
Such AMP can have a true market application impact either as preservatives for food matrices or as coadjuvants in probiotic treatments, namely, in the protection against gut colonization by pathogenic bacteria. This hypothesis driven proposal intends to provide a pipeline that can be generally applied to NGP and gut microbiota for AMP detection and production, providing innovative biopreservation solutions, value-added probiotic/postbiotic formulations, and efficient, cost competitive, optimized methodology to be applied to strictly anaerobic NGP, exceeding state-of-the-art technologies.
This project represents an important advance for science at the international level contributing i) to the knowledge of AMP, particularly regarding the unexplored gut environment and the context of next generation probiotics, whose biosynthetic clusters are still poorly studied and, therefore, promise exciting results; ii) with novel bioactive natural peptide alternatives with intended applications mainly intended for human welfare, fulfilling the goals of UN 2030 Agenda.