Community structure
How do microbial communities differ between shorebirds and poultry, and which environmental or host factors explain those differences?
Project 02-C
HU-RIZON
Metagenomics and AMR ecology across wild birds, poultry and human-influenced environments.
Developing programme
Wildlife does not sit outside the One Health system.
Migratory birds move through coastlines, agricultural landscapes, urban spaces and waste-associated environments. Their microbiomes can therefore reveal how ecological connectivity and human activity shape microbial communities and antimicrobial resistance.
HU-RIZON compares metagenomic data from shorebirds and poultry to investigate taxonomic composition, resistance genes, mobile elements and recoverable microbial genomes. The programme asks not only which genes are present, but which ecological processes best explain their distribution.
MetagenomicsWild birdsPoultryAMR ecology
C1
Research questions
From resistome differences to transmission hypotheses.
Resistance ecology
Which antimicrobial resistance genes and mobile elements are enriched in human-influenced systems?
Genome recovery
What can metagenome-assembled genomes reveal about poorly represented species, lineages and host associations?
Connectivity
Do shared genes, genomes or mobile elements support exchange between wildlife, livestock and environmental reservoirs?
Methods
Which analytical workflows provide robust, reproducible comparison across complex host-associated metagenomes?
Surveillance value
Can wildlife microbiomes act as sentinels of environmental exposure and emerging resistance?
Planned outputs
A connected publication programme.
The project is structured to support a central ecological analysis alongside focused work on methods, resistance, non-bacterial reads and recovered microbial genomes. This avoids forcing every result into a single overloaded paper while preserving a coherent scientific narrative.
Flagship ecology paper
Community, resistome and ecological contrasts between poultry and wild birds.
AMR and mobile elements
Resistance gene context, sharing and human influence.
MAG catalogue
Genome recovery, novel diversity and host association.
Methods and surveillance
Practical recommendations for wildlife and One Health metagenomics.
Connected story
Wild birds and the rise of resistance.
A previous population-genomic study showed that proximity to humans was associated with greater lineage and resistance diversity in wild-bird Campylobacter. HU-RIZON widens that lens to the entire microbial community.
Read behind the paper