The rumen microbiome: an underexplored resource for novel antimicrobial discovery

Linda Oyama ,Florence Privé,Jennifer Richards,Mei Zhou,Fionnuala T Lundy,Joan E Edwards,Matthias Hess,Hilário Cuquetto Mantovani ,Marc Maresca,Hannah Vallin ,Olga V Golyshina,Kai Hilpert,Susan Elizabeth Girdwood ,Alan Cookson ,Josette Perrier,Christopher J Creevey,Mandy Wootton,Peter N Golyshin,Ralf Mikut,Yu Luo,Toby Wilkinson ,Narcís Fernández-Fuentes ,Sharon Huws

doi:10.1038/s41522-017-0042-1

Abstract

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.

Highlights

The global increase of multi-drug resistant (MDR) bacteria, combined with the decreasing number of novel and effective antibacterial agents being developed for the market, poses a serious global threat to human health.[1,2] Urgency is required with respect to discovery and development of novel antibiotics, alongside antimicrobial stewardship and development of rapid tools to detect MDR bacteria.[3]
A metagenomic library consisting of 8448 fosmids from the plantattached rumen microbiome[15] was screened for antimicrobial activity by a combination of agar-based functional screening, sequencing of positive clones and bioinformatic prediction of Antimicrobial peptides (AMPs) sequences
Antimicrobial properties of rumen microbiome test the antimicrobial activity of fosmid clones, lawns of pathogens including methicillin-sensitive Staphylococcus aureus (MSSA) RN4220, Escherichia coli K12, Salmonella enterica serovar Typhimurium SL1344, Listeria monocytogenes NCTC 11994 and Enterococcus faecalis JH2-2 were inoculated on appropriate agar medium and the clones were gently transferred on top using multichannel pin replicators

Summary

Introduction

The global increase of multi-drug resistant (MDR) bacteria, combined with the decreasing number of novel and effective antibacterial agents being developed for the market, poses a serious global threat to human health.[1,2] Urgency is required with respect to discovery and development of novel antibiotics, alongside antimicrobial stewardship and development of rapid tools to detect MDR bacteria.[3] Antimicrobial peptides (AMPs), cationic AMPs, are promising alternatives to currently available antibiotics, due to their broad spectrum activity against. Gram positive and Gram negative bacteria, and their rapid mode of action on the cytoplasmic membrane, which results in a decreased rate of resistance being developed by the targeted pathogens. Depending on availability of resources, bacteria in communities can either be symbiotic with one another or live in competition.[5]. Synthetic generation of AMPs has produced very few if any viable AMPs for medical use, there is a need to further prospect from nature.[4]

Methods

Results

Conclusion