What decides which microbes live inside an animal’s gut? Scientists have wondered about this question for years.
Gut bacteria help digestion, protect against disease, and even support the immune system. But the body must also control which microbes stay and which get removed.
Scientists at the University of East Anglia in the United Kingdom explored this mystery by studying a tiny bird living on a remote island.
The work focused on the Seychelles warbler, a small songbird found only on Cousin Island in the Seychelles. This bird helped researchers uncover how immune genes shape the gut microbiome and influence health.
Island birds reveal gut microbes
Cousin Island in the Indian Ocean offers a rare opportunity for scientists. The island is small and isolated, and the warblers never leave it. Because of this, researchers can follow the entire bird population for many years.
“Cousin Island is small, isolated, and the warblers never leave it,” said Professor David Richardson from the University of East Anglia.
Every bird on the island wears colored leg rings so scientists can identify individuals. Researchers can track behavior, health, genetics, and reproduction throughout each bird’s life.
“This offers scientists an exceptional opportunity to study life-long biological processes in the wild,” noted Professor Richardson.
Scientists track birds for years
Although scientists collect detailed data, the birds still live naturally in the wild. The warblers eat natural food and interact with the environment as they normally would.
“It gives us the best of both worlds,” said Professor Richardson. “We can study animals living natural lives, with natural diets and gut bacteria, while still being able to collect detailed data from known individuals.”
Researchers began monitoring this population in the 1980s. Today the island hosts about 320 birds living in more than 100 territories. Nearly every bird has been identified and studied across its lifetime.
Bird droppings reveal gut bacteria
To study gut bacteria, researchers collected faecal samples from the birds. These samples allowed scientists to analyze the gut microbiome, which includes the many bacteria living inside the digestive system.
Dr. Chuen Zhang Lee carried out the fieldwork as part of his PhD research. Scientists used advanced DNA sequencing to examine both the types of bacteria and the genes those microbes carry.
The study involved hundreds of samples collected from many birds over several years. Researchers also collected small blood samples to analyze the birds’ immune system genes.
This information helped scientists explore how immune genes and gut microbes interact.
Immune genes influence gut microbes
The study focused on a group of immune genes called the major histocompatibility complex, or MHC. These genes help the immune system recognize harmful microbes and infections.
Scientists discovered that differences in these genes influence which bacteria can live inside the gut. Some gene variations allow certain microbes to thrive while others disappear.
“What we found is that immune genes help shape the gut microbiome in wild animals, with potential beneficial impacts on health and survival,” noted Dr. Lee.
Professor Richardson also described the two-way relationship. “In simple terms, an animal’s immune system may help determine which microbes can live in its gut, while those microbes in turn help support and train the individuals immune system.”
Changes in bacteria inside the gut
The research revealed that certain immune gene patterns changed the types of bacteria living inside the birds.
For example, some genes reduced the presence of bacteria such as Lactococcus lactis while increasing others like Staphylococcus lloydii.
Another specific immune gene variant also influenced bacteria. When that gene appeared, some microbes decreased while others such as Escherichia coli increased in the gut.
These shifts suggest that the immune system carefully controls which microbes remain inside the body.
Scientists also discovered that immune genes did not simply change which microbes exist. The genes also influenced what those microbes actually do.
How microbes support the body
The researchers looked beyond the list of bacteria and studied their functions. Some microbes help digest nutrients. Others protect the body from infections.
“We also looked at what those bacteria are actually doing,” said Dr. Lee. “For example, whether they are involved in metabolism, nutrient processing, or defence against viruses and other infections.”
The results showed an interesting pattern. Birds with greater diversity in certain immune genes had more microbial defence genes but fewer genes linked to metabolism.
This suggests a trade off. Strong immune control may reduce some helpful digestive functions while increasing protection against disease.
Why this discovery matters
The findings show that immune genes and gut microbes evolve together. The immune system shapes microbial communities, and microbes influence immune responses in return.
“Our work suggests a two-way relationship. Immune genes influence the gut microbiome, and the microbiome feeds back to influence immune function,” Dr. Lee explained.
Although this study focused on birds, the same biological systems exist in humans and many other animals.
Understanding how immune genes shape gut microbes could help scientists study health, immunity, and disease in the future.
The research involved several organizations including the Centre for Microbial Interactions and the Quadram Institute.
The study is published in the journal Microbiome.
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