Five things chickens have taught us about gut health

17th March 2023

More than a food source or pets, chickens have helped us learn about gut health. PhD Student Bushra Schuitemaker explains five things chickens have taught us about gut health.

A young woman smiling holding a chicken

Chickens were domesticated 7,000 – 10,000 years ago, with our human fascination for the animal recorded as far back as ancient Egyptians and Aristotle. Since the 16th century, chickens have helped to modernise human physiology. It was the first bird to have its full genome sequenced, in the early 21st century. Chickens have been teaching us about human health for thousands of years, but what have they taught us about gut health?

Factors affecting gut health

What we eat can impact what microbes live in our gut, but there other factors that play a role in our gut health too.

In both chickens and humans, genetics and our environment can have a huge influence on the structure and function of our gut microbiome.

Differences in our gut microbiomes can be seen all over the world. Where we live can affect our microbiome composition.

It is also worth considering how we live. By studying chickens, we have learnt more about how the environment affects microbiomes. Commercial chickens kept in strictly managed flocks have different microbes than the chickens kept in back gardens.

Have you ever had stomach issues when feeling stressed? This happens to chickens too! When chickens are stressed, such as when they sense danger or are too hot, this can upset their gut. As well as having less of an appetite, chickens can have worse nutrient digestion and absorption and stress can even weaken their immune system making them more susceptible to disease.

Where gut bacteria comes from and how it changes over time

The first microbes to grow in the chicken gut and how the microbiome develops throughout a chicken’s life has been well studied by scientists.

Early life exposure to microbes has long lasting effects on a chicken’s microbiome. The bacteria that first grow in the gut, don’t necessarily continue living in the gut. But these microbes influence the future microbiome development.

Chickens don’t receive any initial microbiome transfer from live birth or breast-feeding like humans do. Instead, chickens receive their first microbes from the outside of the egg as they break through their shell when hatching, their nest and from the feathers of the hen that sits on top and keeps them warm. In a commercial environment, farmers can use a spray on the outside of the egg prior to hatching to mimic the natural process of initial colonisers.

Scientists often find Lactobacilli and Enterococci bacteria in the chick’s gut from the first day of hatching, which are largely from the environment.

Alongside these, up to one week after hatching, you start to see bacteria that quickly grow such as Escherichia/Shigella or Streptococcus. These bacteria help to develop the chicken’s immune system. After one week, we see fast growing microbes in the gut which are Ruminococcus-like, such as Clostridium.

Finally, after two weeks, a stable bacteria population establishes with Firmicutes and Bacteroidetes bacteria, the common microbes living in the gut.

Thanks to the research from the likes of Professor Lindsay Hall, we can observe similar development and changes in the gut microbiome of human babies. Just as we see in chickens, the early human infant microbiome is a key health regulator, associated with long-term health.

Antibiotics and Antimicrobial Resistance

Antibiotics are important to prevent and control diseases. However, global overuse in human medicine and industrial food production has resulted in concerning antimicrobial resistance genes that stop effective use of antibiotic treatment.

The first use of antibiotics in chickens was in 1951 as a routine feed inclusion against coccidiosis. Coccidiosis is an intestinal tract infection caused by a microbe called coccidia.

Mass medication of chickens was intended to curb disease and increase productivity. Continuous use of low-dose antibiotics in chicken feed, known as antimicrobial growth promoters (AGPs), was thought to protect against disease-causing bacteria.

In 2006, the EU banned the use of AGPs in the feed of all livestock animals due to global concerns of antimicrobial resistance.

How AGPs work to protect against disease were unclear. But they were believed to be suppressing the chickens’ microbiome to allow a greater uptake of nutrients by chickens allowing a greater weight gain in chickens.

Following the ban, the poultry industry saw an increase of intestinal health issues such as necrotic enteritis and a 5% decrease in overall productivity. This also had a substantial economic impact and alluded to the importance of maintaining the microbiome for good gut health.

To overcome these issues, other measures were needed like providing enhanced care and welfare, and a focus on hygiene, diet, and reducing stress. Even for humans, there has been a reduction in the use of antibiotics, with a greater emphasis on looking at diet and stress when treating diseases.

Now, over a decade later, all preventative antibiotics have stopped in the UK, with only the highest priority antibiotics, that are critically important for humans (e.g., treating pathogens that cause foodborne disease and will affect human consumers such as Salmonella), are being used as a last resort in chickens. Due to global reform and important legislations, there has been a global reduction in the use of antibiotics in the poultry industry but differences in reporting make it challenging to quantify exactly how much this has reduced.

Research into the use of antibiotics in chickens has led us to better understand the transfer of antimicrobial resistance, and the importance of maintaining high welfare in animal farming.


Probiotics are live organisms that provide a health benefit. The chicken gut microbiome is a diverse population of bacteria, fungi, and viruses. These microorganisms create a ecosystem. We can even influence our own gut health and the gut health of our chickens by using probiotics and prebiotics.

The microbes interact with each other as well as their host, the chicken, all along the digestive track. These microbes do a range of activities that help with immunity, digestion, and nutrient absorption. If we can identify the helpful microorganisms, particularly bacteria, we can make new probiotics.

Lactobacilli are ‘good ’ and ‘safe’ bacteria, and Lactobacilli probiotics are the most studied. In chickens, bacteria from the Lactobacillus genus are present in the gut from the first day of hatching.

In humans, Lactobacilli are also a dominant good bacteria and are often found in breast milk. There are already many Lactobacilli probiotics commercially available for both human and chicken health.

In fact, probiotics such as Lactobacilli can be found in fermented foods such as yoghurts, kimchi and sauerkraut. These foods can be just as beneficial to the gut health of chickens as they are for the gut health of humans.

Competitive exclusion

Dr Ella May Barnes

Competitive exclusion is a specific phenomenon where species with identical niches can’t live together because they compete with one another. This idea was pioneered in poultry by Dr Ella May Barnes at the Institute of Food Research, the predecessor of the Quadram Institute, back in the 1970s.

In the gut, healthy bacteria colonise the intestine to prevent disease-causing bacteria from establishing. Competitive exclusion was first described in chickens as an initiative to prevent the disease-causing bacteria Salmonella as an early coloniser in commercial poultry production. It can be a specific strategy for probiotics too.

There are a variety of ways competitive exclusion work. Some bacteria can directly attack and damage others with acids and antimicrobial molecules. Commonly, bacteria need to compete for resources such as nutrients or places to live inside the gut. Bacterial communities can physically block access to other bacteria by forming biofilms. Another way bacteria can exclude their competition is to stimulate the host’s immune system and clear out any harmful microbes.

Competitive exclusion is now used as a common probiotic strategy for improving human, and animal, health.

Chickens are a global protein source and economically influential and with 75% of all land-reared animals being chickens , this is an internationally important animal that still has a lot to teach us. The future of agriculture depends sustainable practises and high welfare with the gut microbiome providing an assortment of research targets to investigate.

My research is aiming to find new ways to monitor the gut health of poultry to predict disease resistance, performance and, stress but perhaps I will also discover more lessons for the human gut along the way.


Related People

Related Targets

Targeting antimicrobial resistance

Antimicrobial Resistance

Targeting food safety

Food Safety

Targeting the understanding of the microbiome

Understanding the Microbiome

Related Research Groups

Narbad group

Arjan Narbad

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