The rumen microbiome: an underexplored resource for novel antimicrobial discovery

Linda B. Oyama, Susan E. Girdwood, Alan R. Cookson, Narcis Fernandez-Fuentes, Florence Privé, Hannah E. Vallin, Toby J. Wilkinson, Peter N. Golyshin, Olga V. Golyshina, Ralf Mikut, Kai Hilpert, Jennifer Richards, Mandy Wootton, Joan E. Edwards, Marc Maresca, Josette Perrier, Fionnuala T. Lundy, Yu Luo, Mei Zhou, Matthias Hess, Hilario C. Mantovani, Christopher J. Creevey, Sharon A. Huws

Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, Lynronne-2 and Lynronne-3) were effective against numerous bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.