Microorganisms circulating between animals and the environment play a significant role in ecosystem, animal, and human health. Understanding microbial population dynamics in farm animals and environment

helps identify key intervention points to mitigate public health concerns such as antimicrobial resistance. This

research applies next-generation sequencing (NGS), metagenomic, and transcriptomic approaches to investigate microbial communities in animal production systems and their surrounding environments. Sampling focuses on farms and related environmental sources, with particular attention to biofilms, to better

understand community diversity, distribution, and survival strategies. Following collection, genetic material is extracted and analysed using advanced molecular technologies to obtain comprehensive information on community structure and function. The resulting data are processed through bioinformatic pipelines to characterize composition, assess genetic diversity, and examine mechanisms of persistence in environmental matrices and biofilms. By integrating metagenomic and transcriptomic analyses, the project aims to clarify how microorganisms circulate and adapt at the animal environment interface, supporting improved surveillance, risk assessment, and One Health strategies.

Five publications related to the Researc topic for the candidate interview:

• Marcelino V.R., Wille M., Hurt A.C. et al. Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC Biology (2019), 17, 31. https://doi.org/10.1186/s12915-019-0649-1

• Luo A., Wang F., Sun D., Liu X., Xin B. Formation, Development, and Cross-Species Interactions in Biofilms. Frontiers in Microbiology (2022), 12:757327. doi: 10.3389/fmicb.2021.757327

• Zhang L., Chen F., Zeng Z., Xu M., Sun F., Yang L., Bi X., Lin Y., Gao Y., Hao H., Yi W., Li M., Xie Y. Advances in Metagenomics and Its Application in Environmental Microorganisms. Frontiers in Microbiology (2021), 12:766364. doi: 10.3389/fmicb.2021.766364

• Durán-Viseras A., Lindner B.G., Hatt J.K., Lai A., Wallace R., Ginn O., Brown J., Konstantinidis K.T. Metagenomic insights into the impact of litter from poultry Concentrated Animal Feeding Operations (CAFOs) to adjacent soil and water microbial communities. Science of The Total Environment (2024), 170772, https://doi.org/10.1016/j.scitotenv.2024.170772.

• Guéneau V., Rodiles A., Frayssinet B., Piard J.C., Castex M., Plateau-Gonthier J., Briandet R. Positive biofilms to control surface-associated microbial communities in a broiler chicken production system - a field study. Frontiers in Microbiology (2022), 13:981747. doi:10.3389/fmicb.2022.981747

Tutor: Prof. Andrea Laconi
e-mail address: andrea.laconi@unipd.it