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A delicate balance

A collaboration between Teagasc and the Agri-Food and Biosciences Institute is aiming to better understand viral-bacterial interaction in the poultry gut and its effect on food safety.

TResearch Summer 2023

The gut is home to a highly complex ecosystem comprising various microbiomes (microorganisms that live within a given environment, such as the human body or the digestive system), including bacterial, fungal, viral and bacteriophage, which are, to some extent, dependent upon each other and on the nutritional supply to the host.

Recent advancements in high throughput ‘omics’ technologies – which analyse and characterise the properties of microbiomes – have improved our understanding of the role of commensal and pathogenic bacteria in the immune system, but interactions with the virome is still unknown.

Researchers at Teagasc and the Agri- Food and Biosciences Institute (AFBI) in Northern Ireland are working together on a microbiome project to provide new insights into viral bacterial interaction in the poultry gut to determine potential dysbiosis, pathogen colonisation and its effect on broiler production.

Increase in harmful pathogens

Chicken meat continues to be one of the most consumed sources of protein worldwide, with demand expected to have increased significantly by the year 2050. With the ban of antibiotics as growth promoters in the European Union, enteric pathogens – microbes that can cause disease or infection – are becoming more frequently observed on broiler farms.

Strong pathogens such as Campylobacter, Escherichia coli and Salmonella can modify the chicken gut and cause intestinal and caecal dysbiosis – bacterial imbalance. Using advanced technology, we can better understand the interactions between the viruses and bacteria and therefore decrease the pathogen load in chickens, ensuring food safety.

The complex mechanism

Recent studies of gut microbes in humans and mammals have shown that viruses and bacteria interact to a much greater degree than was previously thought and in a variety of ways, both directly and indirectly, often enhancing pathogenesis.

Bacteria and viruses often occupy the same niches and the interactions are well characterised in humans – for example, influenza virus and streptococcus spp. It has been suggested that direct interactions largely favour virus pathogenicity while indirect interactions promote bacterial activity/pathogenesis.

One mechanism of viral/bacterial interaction in the chicken gut is through the action of bacteriophages, which plays an important role in shaping the composition and function of the gut microbiome. For example, the addition of a bacteriophage cocktail to the drinking water of broiler chickens causes changes in the gut microbiome, including an increase in the abundance of Lactobacillus (good bacteria).

Another mechanism is through the activation of bacterial virulence genes. Viruses can trigger the expression of virulence genes in bacteria, leading to increased pathogenicity. This has been observed, for example with Salmonella enterica, where the presence of viruses caused the upregulation of virulence genes.

However, the interactions are not always easily understood and similar studies may report contradictory results.

It is also possible that the presence of different bacteriophages or viruses in the chicken gut may have different effects on colonisation with pathogens such as Campylobacter, and that the gut microbiome composition may also play a role in these interactions.

Evidence-driven hypothesis

Guillain Barré syndrome is the most common cause of acute paralysis worldwide. The microorganisms mostly associated with Guillain Barré syndrome include Campylobacter jejuni, Zika virus and recently Coronavirus type-2.

There is evidence to support an autoantibody mediated immune process that is triggered by molecular mimicry between structural components of peripheral nerves and microorganism interaction. Moreover, it has been reported that the initial primary infection by bacteria provides the foothold for other secondary pathogens. The pathogenicity enhancing mechanism has also been demonstrated by reovirus and rotavirus, which are common enteric viruses in broiler chickens.

Research undertaken by the AFBI suggests that enteric viral infections and bacterial dysbacteriosis are underlying causes of observed growth issues in broilers. The Microbiome project between Teagasc and the the AFBI aims to provide a novel understanding of viral and bacterial interactions in the chicken gut, with a particular focus on their effect on Campylobacter proliferation and uneven flock growth in commercial chickens using advanced omics technology.


Jignasha Patel has received funding from Research Leaders 2025 programme, co-funded by Teagasc and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 754380.


Jignasha Patel, Research Leaders 2025 and Marie Skłodowska-Curie Fellow, Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin 15.

Victoria Smyth, Senior Scientific Officer, and Head of Avian Virology Department AFBI, Stormont, Northern Ireland.

Declan Bolton, Principal Research Officer, Teagasc Food Research Centre, Ashtown, Dublin 15.

Image credit: cottonbro studio/pexels.com.