18/09/2025
Fascinating human research on the negative effects a low fibre diet has on the gut microbiome in just 7 days! It also gives some evidence against the long term use of diets like the carnivore diet, strict low FODMAP diet, restricted phase of the Bi Phasic Diet. It’s also why I’m always working with my clients to expand their diet as soon as possible so we can feed their microbiome. Also interesting to note is they used food, not supplements, to increase fibre. So a food first approach has good outcomes!
One of my highlights from Day 1 of the 13th Probiotics, Prebiotics, and New Foods Conference came at the end of the day – 10 hours into the conference! Some attendees had left by this point, but this microbiome nerd could not leave until the end of all presentations! 🤓
Professor Desai, from the Luxembourg Institute of Health, did a deep dive into the impacts of a low fiber diet on microbiome composition. This is an area that has long been discussed by microbiome researchers, who have described it as one of the key issues with the Western diet – the starvation of our microbiome. The Western diet contains a low amount of fiber (often as little as 10-15g/day); whereas diets of hunter-gatherer societies have been found to consistently contain 50+ grams of fiber per day, with some, like the African Hadza, containing 100-150g per day. Animal studies have consistently shown low fiber diets to result in negative changes in the microbiome (i.e., induce dysbiosis), resulting in increased proportions of problematic, pro-inflammatory species and decreased numbers of beneficial, anti-inflammatory microbes. More specifically, such a diet favors growth of bacterial species that degrade the gut's protective mucus lining. Human epidemiological studies looking at long-term dietary patterns and microbiota composition have found similar results to these animal studies too. So, there is quite a lot of data in this area already. But to date, there has been little human data from interventional study designs, that have directly evaluated the impact of low fiber diets on the human microbiome in a more rigorous way.
In this study, forty healthy participants were randomly assigned to either a low- or high-fiber dietary intervention and then, following a washout period to reverse any microbiome changes, switched to the other diet type (i.e., a randomized, crossover trial where subjects essentially served as their own controls). During the low-fiber phase of the study, subjects consumed 14g/day of fiber. In the high-fiber phase, 40g/day. All meals were provided (3 meals per day for 1 week). Between each dietary phase of the study was a 1-week washout for the microbiome to return to baseline. It is important to note that the fiber came from consuming a wide-range of fruits, vegetables, legumes, whole grains, and mushrooms – not fiber supplements.
After just 7 days on a low fiber diet what changes did we see? We saw increased populations of mucus-degrading gut species (Mediterraneibacter gnavus and Mediterraneibacter torques) – species linked to inflammatory bowel disease, multiple sclerosis, and coronary artery disease. Additionally, there were blooms in Bilophila, a key hydrogen-sulphide gas producer, associated with visceral hypersensitivity in the gut, inflammatory bowel disease, cognitive impairment, and Alzheimer’s disease. They also observed increased signs of mucus degradation.
When consuming the high-fiber intake, we saw increases in populations of key butyrate-producing species, like Faecalibacterium and Dysosmobacter. These species are considered to be gut protective with anti-inflammatory activity (within and beyond the gut).
In summary just 7 days on a low-fiber diet induced harmful changes to microbiota composition, inducing the growth of mucin-degrading bacterial species and degradation of our protective gut mucus layer. So why does this matter? Degradation of our protective mucus layer leads to decreased gut integrity (i.e., leaky gut), with resultant increased translocation of bacteria, endotoxin (LPS), food proteins, and pro-inflammatory bacterial metabolites into the bloodstream. These are the key drivers of the chronic inflammatory disorders we see all around us in Western nations.
