Speaking to NutraIngredients ahead of his presentation at this year’s conference in Dublin (Feb 11-13), Jens Walter, professor of ecology, food, and the microbiome at University College Cork (UCC), informed that his research into the NiMe (Non-industrialized microbiome restore) diet has changed his whole mindset on gut health.
Inspired by the microbiomes of non-industrialized populations in Papua New Guinea, the clinically researched NiMe diet focuses on vegetables and fruits, whole grains and healthy plant and animal proteins. It is designed to reduce the risk of chronic disease by restoring gut microbiome features disrupted by the industrialization of food.
After years of working in biotics supplement research, Walter said it was a ‘hard lesson’ to realise this whole diet intervention was ‘in a league of its own’ when it came to health outcomes.
“I’ve worked on biotics my entire career and nothing comes close the effects of this NiMe diet, it’s in a completely different league.”
He added: “The effect of these whole foods and the fibre being embedded in three-dimensional structures, it’s just a completely different thing to fibre supplements. That doesn’t mean that supplements can’t be helpful in certain areas but I don’t think supplements will ever be able to fix the bad diet we are consuming in industrialized nations.”
The NiMe project began as a concept to see if the Lactobacillus lineage observed in Papuan populations could be re-established. In 2025, research results showed the diet successfully reversed several microbiome effects linked to industrialization.
Interestingly, overall microbial diversity decreased in participants, yet gut community stability and interconnectedness increased, fiber fermentation capacity improved, pro-inflammatory microbes declined, and health-promoting bacteria became more abundant. The diet further led to broader cardiometabolic benefits, reduced risk markers for non-communicable diseases, modest but significant weight loss, lower cholesterol measures and improved insulin sensitivity.
The team behind the NiMe (Non-industrialized Microbiome Restore) Diet have since partnered with a ready meal service in Ireland to deliver clinically validated meals across the country.
Yet, the Professor acknowledged that actually affecting public health change through diet was a huge challenge.
“It’s well recognized how hard it is to make people make healthy choices,” he added, noting he will use the Probiota platform to ask what might be the actionable strategies for making people healthy.
Fermented foods under the spotlight
Speaking alongside Walter within the ‘microbiome diets and fermented foods’ pillar of the conference programme, Paul Cotter, head of food biosciences and head of microbiology at Teagasc and SeqBiome, will provide a presentation on advances in fermented food research.
The academic will display his work which has improved our understanding of the microbial communities within different fermented foods (FFs).
His team’s large-scale genome-wide analysis demonstrated that closely related Lactic acid bacteria (LAB) strains occur in both food and gut environments, providing unprecedented evidence that fermented foods can be regarded as a possible source of LAB for the gut microbiome.
He further co-authored a 2024 review which summarized current knowledge about FFs, concluding that since microorganisms are exposed to similar environmental pressures in some FFs as they are in the human gut, traditional FFs might be a source of novel probiotic strains, able to survive the gastrointestinal passage.
Cotter will use the Probiota platform to discuss new gut research technologies helping to position FFs as sustainable contributors to human health, such as Nimble’s ingestible capsule which enables passive analysis of small bowel luminal fluid.
Gut research pioneer
Also joining Probiota as a winner of the event’s annual Pioneers competition, will be Boston-based MedTech startup Microvitality. The firm aims to transform gastrointestinal health through precision microbiome diagnostics. The company’s core innovation is a non-invasive ingestible capsule that samples the small intestine to provide accurate microbiome and immune biomarker data, unlocking insights previously inaccessible with traditional stool tests or invasive procedures such as endoscopies.
Multi-omic approaches
The esteemed expert will discuss the opportunities to advance knowledge through multi-omic research—combining data from genomics, transcriptomics, proteomics, metabolomics.
“Metagenomics gives you the identity and the functional potential, the genetic potential of the microbes that are present in these foods,” he explained, “but there hasn’t been so much done in terms of meta transcriptomics, which allows you to look at gene expression to see which genes are really switched on.”
“Then there’s probably even less research again in the field of meta-proteomics where you see not only which genes are switched on, but which transcripts are then converted into protein,” he added.
Cotter has contributed to advancing meta-transcriptomic analysis of fermented foods, most prominently through a 2023 co-authored review which highlights both methodologies and real-world applications. The review discussed how meta-transcriptomic analyses have been applied to kefir to investigate which microbial genes are activated during fermentation—linking these to flavor, fermentation efficiency, and bioactive metabolite production. This demonstrates how meta-transcriptomics captures the functional output of microbial communities, beyond mere presence.
“Some microbes present in low abundance can actually have a very major contribution because they have genes that are very highly expressed and they produce a lot of proteins,” he said.
Discussing gaps in knowledge, Cotter emphasized a need to understand the specific health benefits of fermented food metabolites in order to be able to create microbial communities within fermented foods with targeted health goals.
However, he noted several challenges with this concept when it comes to producing products at scale.
“These are made in a manner that’s designed to simplify the food so that you can make a consistent product that will taste the same today, tomorrow, next year, but quite often that involves such a simplification of the foods that some microbes that play an important role in texture or flavour get lost along the way,” Cotter said.
“I see there being a middle ground, whereby you harness the key attributes of the artisanal foods and the key approaches for producing on an industrial scale, to strike that balance where you can have the best of both.”
Probiota 2026 promises three days of engaging, inspiring and informative sessions covering a wide array of topics including: postbiotics, ‘from gums to gums’, the gut-brain axis, microbiome diets and fermented foods, next-gen biotics, strain optimization, regulation, and more. For more information and to purchase tickets. visit the event website here.
