20/09/2025
I’ve got two highlights from Day 2 of the 13th Probiotics, Prebiotics, and New Foods Conference.
The first is from Professor Lens Walter’s (University College Cork) excellent presentation on his attempt to restore the microbiome of city-dwelling Canadians.
Previous research has found that the microbiome of Westerners is substantially lacking in diversity when compared to hunter-gatherer populations, like the Hadza in Africa, the Yanomami in Brazil & Venezuela, and the highlanders of Papua New Guinea. The Yanomami, for example, have recently been found to carry over 250 previously unseen species in their ecosystems. According to the “Missing Microbes” hypothesis, the loss of microbes in Westerners, species we’ve carried in our guts for millennia until recently, is a driver of the chronic inflammatory diseases we face in Western nations. Accordingly, there is great interest in restoring the diversity of the microbiome in Western populations, in addition to improving its composition.
Inspired by the diet of the Papua New Guinea highland tribes, Prof. Walter’s team developed a dietary protocol to do just this. It was designed around foods that could be found in Western supermarkets, but contained a similar amount of fiber and fiber types to the PNG traditional diet, including 45 grams per day of fiber. The PNG highlanders do not eat wheat or dairy, but typically have 1 serving per day of animal protein (chicken, fish, or pork only). The Restore dietary protocol followed these rules, too.
The team tested their dietary protocol in a randomized, crossover feeding trial in 30 healthy, urban-living Canadians. Subjects followed the Restore diet for 3 weeks (or their usual diet), then had a 3-week wash-out period before switching to the alternate diet for another 3 weeks (for the microbiota to return to baseline composition).
Blood and stool samples were taken throughout each dietary period. All meals and snacks were provided to the subjects to last them the 3 weeks.
So, what did they find?
Interestingly, they found a decrease in microbiome diversity after the Restore diet. This occurred within 4 days of starting the diet and then stabilized. This was an unexpected finding, and at odds with their hypothesis.
They did, however, find increased levels of beneficial anti-inflammatory microbes - 3 species of Bifidobacterium, 4 species of Faecalibacterium, and 2 strains of Roseburia were found to increase on the diet. The latter species being an important butyrate producer. At the same time, there were reductions in populations of Bilophila (a key hydrogen-sulphide gas producer) and Mediterraneibacter torques (a key species involved with the degradation of our protective mucin layer).
During the Restore diet period, subjects had significant reductions in body weight, BMI, total cholesterol, LDL cholesterol, blood glucose, CRP, and fecal calprotectin. Additionally, they noted significant decreases in the amount of bacterial-produced mucin-degrading enzymes in the stool.
In conclusion, the Restore dietary protocol significantly improved microbiome composition and a wide range of metabolic and inflammatory parameters, but did not improve ecosystem diversity. In fact, over a 3-week consumption period, diversity decreased. So why the latter finding? Reductions in populations of some microbes may have occurred due to the lowered pH (due to increased SCFA production) of the colonic environment, which we know suppresses the growth of some microbes (generally pro-inflammatory species), as well as reductions in levels of bile- and protein-consuming microbes (due to the reduction in animal protein and fat consumption levels vs their usual diet).
If you want to learn more about the specific diet used in the study, its rationale, and even the recipes used, Professor Walter’s team has created a free resource: https://pressbooks.openeducationalberta.ca/nimediet/
My second highlight was from a presentation by Professor Koren (Bar Ilan University). He had a fascinating presentation looking at the impact of antibiotics on aggressive behaviours. His research is following up on earlier 2017 research that found low doses of penicillin, when given to soon-to-be mother mice or their offspring soon after birth, induced persistent microbiome alterations, brain inflammation, and ongoing aggressive behaviour that persisted into adulthood. He was able to replicate the finding in his updated study, in that antibiotics given to pregnant rats induced persistent aggressive behaviour in their offspring and persistent alterations in brain gene expression.
He followed this up with a study where they took fecal transplants (FMT) from human babies given antibiotics in their first 24 hours of life and gave them to mice at 5 weeks old. These mice displayed increases in aggressive behaviour from the time of FMT onwards compared to those who had FMT from non-antibiotic-exposed babies.
While this is obviously very preliminary research, the potential implications of these findings are immense. Professor Koren (and hopefully others) will be following up on these findings over the coming years, so watch this space! In the meantime, we have yet another potential reason to restrict antibiotic use to when it is truly necessary, and more data reinforcing the importance of the gut-brain axis.
