Biology subjects

Gillings, M.

Publications and source records attributed to Gillings, M..

3 recordsLinked to original sources

bioRxiv2026

Discovery of novel antimicrobial resistance genes in food and fertiliser using a high-throughput gene capture and functional screening platform

Integrons are genetic elements that drive bacterial adaptation by capturing and expressing mobile gene cassettes. They play a key role in dissemination of antimicrobial resistance (AMR) genes, particularly in Gram-negative bacteria. In addition to known AMR determinants, integron gene cassettes carry a vast reservoir of novel genes whose functions are largely uncharacterised, making it diNicult to assess their full contribution to the resistome. Contributing to this are limitations in current sequence-based prediction methods which often lack the ability to identify unknown AMR or other adaptive genes with novel mechanisms. To address this, we developed an integron gene cassette capture system, a functional screening platform that captures environmental gene cassettes for direct phenotypic testing. Using this system, we recovered previously unknown AMR determinants while also providing insights into the prevalence of known clinical AMR genes in a range of environmental samples, including food items. Here we provide experimental data on multiple novel bleomycin resistance genes and a stress response gene conferring gentamicin and tobramycin resistance. Our sequence analysis of the captured library also highlighted the diversity of the environmental cassette pool, with 656 unique cassettes recovered, the majority of which encoded proteins with unknown functions. The cassette capture system is a powerful tool for accessing hidden elements of the resistome and discovering novel adaptive genes that may go undetected using current sequence-based approaches. Environmental implicationAntimicrobial resistance (AMR) genes are hazardous biological contaminants, yet the vast majority of environmental integron gene cassettes remain functionally uncharacterised. This study addresses this sequence-to-function gap by deploying a novel functional capture platform directly on realistic environmental matrices, including agricultural fertilisers, coastal seawater, and commercial food products. By characterising these cassettes, we uncovered hidden reservoirs of both novel and clinically established AMR genes circulating in critical exposure pathways. This work reveals the true hazardous potential of the mobile environmental resistome, validating a proactive One Health surveillance tool for monitoring emerging biological threats.

microbiology↗

bioRxiv2025

Agriculture alters protein evolution of nitrogen cycling genes in soil bacteria at a global scale

Humans are the worlds greatest evolutionary force. Yet, our impacts on the evolution of Earths microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2,500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase were specific to Burkholderiales, a major group of denitrifying bacteria. We provide evidence that agriculture is driving evolution of protein regions implicated in substrate access to the enzymes active site, possibly resulting in increased rates of nitrate reduction. We hypothesise that increasing substrate turnover would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant denitrifiers globally, such evolutionary consequences of agriculture on this lineage could have cascading ecological impacts. These findings indicate that anthropogenic selection can alter protein-level evolution of vital microbial biogeochemical processes.

microbiology↗

bioRxiv2020

Red fox viromes across an urban-rural gradient

The Red fox (Vulpes vulpes) has established large populations in Australias urban and rural areas since its introduction following European settlement. Foxes cryptic and highly adaptable nature allows them to invade cities and live among humans while remaining largely unnoticed. Urban living and access to anthropogenic food resources also influences fox ecology. Urban foxes grow larger, live at higher densities and are more social than their rural counterparts. These ecological changes in urban red foxes are likely to impact the pathogens that they harbour, and foxes could pose a disease risk to humans and other species that share these urban spaces. To assess this possibility, we used a meta-transcriptomic approach to characterise the viromes of urban and rural foxes across the Greater Sydney region in Australia. Urban and rural foxes differed significantly in virome composition, with rural foxes harbouring a greater abundance of viruses compared to their urban counterparts. In contrast, urban fox viromes comprised a greater diversity of viruses compared to rural foxes. We identified nine potentially novel vertebrate-associated viruses in both urban and rural foxes, some of which are related to viruses associated with disease in domestic species and humans. These included members of the Astroviridae, Picobirnaviridae, Hepeviridae and Picornaviridae as well as rabbit haemorrhagic disease virus-2 (RHDV2). This study sheds light on the viruses carried by urban and rural foxes and emphasises the need for greater genomic surveillance of foxes and other invasive species at the human-wildlife interface. ImportanceUrbanisation of wild environments is increasing as human populations continue to expand. Remnant pockets of natural environments and other green spaces in urban landscapes provide invasive wildlife such as red foxes with refuges within urban areas, where they thrive on the food resources provisioned by humans. Close contact between humans, domestic species and foxes likely increases the risk of novel pathogen emergence. Indeed, the vast majority of emerging infectious diseases in humans originate in wild animals. Here, we explored potential differences in viromes between urban fox invaders and their rural counterparts. Viromes of foxes and their ectoparasites comprise a diversity of viruses including those from the Astroviridae, Picobirnaviridae, Hepeviridae, Caliciviridae and Picornaviridae. Microbial surveillance in foxes and other urban wildlife is vital for monitoring viral emergence and for the prevention of infectious diseases.

microbiology↗