Children on farms are less likely to develop allergies. A new study suggests that exposure to certain bacteria associated with animals in the first few weeks of life may explain this pattern.

Scientists have identified infancy as a critical window for both gut microbiome diversity and immune system development. However few studies have focused on gut bacteria diversity in the first few weeks of life and compared it to allergy development later on.

The study, led by researchers from the University of Gothenburg in Sweden, took infant faecal samples starting at three days of age up until 18 months and compared the gut microbiomes in children on farms, with pets, or neither. Three and eight years later, they followed up with the children and assessed whether they had allergies.

Gut microbiomes are known to change or “mature” over time. At first, facultative bacteria that prefer an oxygen-rich environment dominate. But as the faculatives consume oxygen, less oxygen-tolerant anaerobes begin colonising the infant gut.

Eventually, these anaerobes create a complex ecosystem that outcompetes the original faculatives, marking a more mature gut microbiome. One metric of gut microbiome maturity is the ratio of anaerobes to faculatives.

Remarkably, the Swedish researchers found that children on farms had a seven-fold higher ratio of anaerobes to faculatives compared to children not on farms by one week of age.

While children with pets did not have this higher ratio, they did show earlier colonisation by three different anaerobes (Bifidobacterium, Clostridium, and Lactobacillus) in the first four months compared to children without pets.

Even though many of the microbiome differences between cohorts disappeared as they aged, microbiome characteristics from the first weeks of life were clearly associated with allergies in the same individuals at age eight.

The results support the finding that early colonisation of anaerobes provides protection from allergy development in children.

However, this study was a relatively small cohort study involving 65 children, so larger studies are needed to confirm the results.

The research is published in the journal, PLOS One.