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Allergy Today: What are Short Chain Fatty Acids and why should we care?

The term ‘short chain fatty acids’ is increasingly seen in research related to food allergy. Our Allergy Advisor decided to investigate why.

Science tells us that Short Chain Fatty Acids (SCFAs) are produced by bacteria in the gut during the digestion of fibre from plant foods, such as cereals, fruit and vegetables. Studies have also shown that SCFAs are linked to health-promoting effects including a reduced risk of inflammatory diseases.

Bacteria are part of the collection of microbes that make up our individual microbiomes, along with fungi, viruses and their genes. They are a part of us, living naturally in our bodies and on our skin, and are vital to our health and wellbeing. Among other things, they help our immune systems to develop and function.Human Microbiome-911

The make-up of each person’s microbiome is unique. The core is formed in the first few years of a person’s life; but can change over time in response to things like diet, medications, stress and environmental factors. Many studies are now looking at how these differences in the microbiome may lead to some people being more susceptible to developing conditions, such as diabetes, obesity, cardiovascular diseases, inflammatory bowel disease and allergies.

The Hygiene Hypothesis

A study published in 1989, by David Strachan, a lecturer in epidemiology at the London School of Hygiene and Tropical Medicine, was the catalyst for much of the research into what became known at the time as the Hygiene Hypothesis. In his study, he reported an association between larger household size and decreased allergic disease. He proposed that the lower incidence of infection in early childhood, due to smaller family sizes (e.g. not so many older siblings spreading infection to younger ones), could be an explanation for the rise in allergic diseases such as asthma and hay fever during the 20th century.

This lead to a theory that suggested a young child's environment can be "too clean" to effectively stimulate or challenge the child's immune system to respond to various threats during the time a child's immune system is maturing.

Subsequent research supported the hypothesis that reduced exposure to a diversity of microbes in a child’s early life increases their risk of developing allergies. This included studies that found children growing up on farms had lower rates of allergic diseases than those growing up in cities; and those born by elective caesarean section had a higher risk of developing allergies than those born by natural birth.

Other external factors that have been identified include exposure to cigarette smoke. For example, a Swedish study found that children had an increased risk of asthma in the first six years of life if their grandmothers smoked during early pregnancy, independent of whether the mother smoked.

However, it was not until the late 1990s that the human microbiome came to be recognised and its importance in health was acknowledged. More recent research now suggests that it is not just the early exposure to a reduced diversity of microbes that influences the risk of allergies in children, but also that this is likely to be mediated by a human microbiome which itself has changed due to losses of specific bacterial species from our ancestral microbiota, as passed on from mother to baby. These losses are likely to have happened over many generations, as the human microbiome has adapted to changes in environment and lifestyle, particularly since the industrial revolution and in relation to westernisation.

Where are we at now?

Research is ongoing to understand the microbiome and is now being conducted by many parties and with multiple stakeholders with various objectives. Overall, an understanding of what a healthy microbiome is and how to modify or replenish those in living humans, may help effectively treat, and even prevent, many diseases.  

This includes research into whether manipulating the intestinal microbiota may be able to treat or prevent allergies and other immune-related conditions. Various approaches are under investigation, including into the use of probiotics (live micro-organisms found in yoghurt and other fermented food) and prebiotics (special plant fibres that help healthy bacteria grow in your gut), and even faecal transplants.

Prebiotic dietary fibres fuel the activities of beneficial bacteria which produce SCFAs. There is now evidence that gut microbiome-derived SCFAs produced from a high-fibre diet may help protect against food allergy. However, there are a range of bacteria which produce different types of SCFAs, with many important roles in the gastrointestinal tract, including in relation to the immune system.

While research is ongoing to understand the role of SCFAs, it is known that many of us don’t have the diversity of bacteria, and therefore of SCFAs, in our microbiome, due to our westernised diet including the consumption of processed foods.

Until we have some definitive answers, we can probably help ourselves and possibly future generations by improving our diet through increasing the intake of dietary fibres. This may also contribute to improved health overall – and won’t do harm.

The New Zealand Nutrition Foundation advises the recommended amount per day (RDA) is 25g for women and 30g for men. Their tips for eating more fibre include:

  • Aim for at least five or more servings of fruit and vegetables each day. Leave the skin on, as it contains much of the fibre. Fruit and vegetable juices contain little or no fibre.
  • Choose wholegrain varieties of bread, cereals, rice and pasta. When baking, try substituting half of the white flour with wholemeal flour.
  • High-fibre breakfast options include porridge or muesli. Increase the fibre further by adding oat bran or wheatgerm, nuts, seeds (sunflower, sesame, pumpkin) and fruit (fresh or canned).
  • Try adding chickpeas, kidney beans or lentils to soups and casseroles.
  • If you are eating more fibre-rich foods, drink more water than usual as fibre absorbs water in the body.

Fibre | NZ Nutrition Foundation

Penny Jorgensen

Allergy Advisor

Allergy New Zealand


Grandmaternal smoking increases asthma risk in grandchildren: A nationwide Swedish cohort - Lodge - 2018 - Clinical & Experimental Allergy - Wiley Online Library

Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring | Nature Communications

What Are Short-Chain Fatty Acids And Why Should You Care? (

The Microbiome and Food Allergies | Food Allergy Research & Education

Weaving together genetics, epigenetics, and the microbiome to optimize human nutrition (

Allergy Today, October 2021