At this year’s IPA World Congress + Probiota in Dublin, Dr. Paul Cotter, head of food bioscience at Teagasc and head of microbiology at SeqBiome Ireland, challenged the idea that all fermented foods are inherently good for us.
He highlighted that while most fermented foods are health-promoting, production methods can alter microbial composition and therefore the associated health outcomes.
Fermentation can also lead to unwanted changes, such as spoilage or gas and alcohol production. This is more common in fermented foods made at home, given that artisanal approaches are inherently inconsistent.
This lack of consistency is causing challenges when it comes to European health claims. Indeed, EFSA has only approved one health claim associated with fermented foods despite hundreds of applications.
Researchers, like Dr. Cotter, are now focusing their efforts on substantiating these claims by using new technologies, such as omics, to allow the full potential of these foods to be harnessed.
What is the definition of a fermented food?
The International Scientific Association for Probiotics and Prebiotics (ISAPP) defines fermented foods as “foods made through desired microbial growth and enzymatic conversions of food components.”
The ‘desired’ aspect is crucial, Dr. Cotter noted, given that fermentation can lead to undesirable outcomes. Importantly, this process does not always involve adding something in. For example, fermenting dairy products can remove lactose to make these products suitable for people who are lactose intolerant.
However, contrary to popular belief, fermented foods are not technically classified as a source of probiotics. This is because probiotics, by definition, must confer a health benefit to the host. And while fermented foods often contain living microbes, studies investigating whether these microbes are responsible for a health benefit remain to be done.
He explained that quite often when a probiotic is said to be present in a fermented food, it has been added, and quite often that microbe has come from the gut.
“Most of the probiotics we have are from the gut rather than fermented foods,” he said. “I think that’s something that we can rebalance because there really is great potential among these microbes to be further developed, but we just don’t have the clinical data and the clinical studies.”
However, by using metagenomics, Dr. Cotter’s lab has uncovered hundreds of ‘SGBs’ (bacterial species) in fermented foods that were previously unknown. By researching 2,500 food metagenomes, the team discovered 613 known SGBs, 211 partially unknown SGBs (those that were known to exist, but have not yet been successfully grown) and 320 completely unknown SGBs that bioinformaticians had never come across before.
“This is somewhat surprising,” Dr. Cotter said. “There was an assumption that because we’ve been studying fermented foods for so long and we think we can grow most of them on agar plates […] that there’s no reason to be applying metagenomics. But most of the culture-based approaches we use are somewhat biased. The microbes that grow best take over. The ones that take a little bit longer to grow take some time, and sometimes, we’re not patient enough to see that they’re there.”
Dr. Cotter said the discovery of 320 completely unknown SGBs was “startling”, as this means there are hundreds of species that the general population are consuming daily, but researchers don’t know whether these microbes are contributing to health or whether they are potentially detrimental.
To exemplify this point, Dr. Cotter highlighted new research by Samuel Breselge, a researcher at Teagasc, who analyzed the microbial content of fermented water kefir grains from all around the world. Breselge et al. uncovered 18 potentially novel bacteria, including novel genera.
“It wasn’t just like finding Bifidobacterium longum for the first time, it was like finding Bifidobacterium full stop for the first time,” Dr. Cotter said. “It’s amazing to me as a microbiologist to find all of these microbes under our nose.”
Looking ahead
When it comes to the future of ‘Fermentbiome’ research, Dr. Cotter said new multi-omics approaches have the potential to redefine the field. For example, metaproteomics (the large-scale identification and quantification of proteins expressed by microbiomes) is allowing researchers to see not only which microbes are present, but their relative contribution to functional outcomes.
New technologies which help to better measure food intake also have the potential to be a game-changer when it comes to clinical research. In a recent paper, Cotter et al. developed and validated a new fermented food intake questionnaire (FFIQ) to better capture dietary intake, but his team are now also exploring a more objective measure which utilizes glasses with in-built cameras.
“The challenge is not the recording but developing the AI tools to blur all of the things that we don’t want to see – their passwords and bank account details and whatnot,” he said. “We’ve used this together with Atlantia [Clinical Trials] and that’s been a fantastic experience. That data and those publications will be generated soon.”
Establishing guidelines for researchers assessing fermented food intake in clinical trials would also be helpful to ensure there is sufficient information on exactly what form of fermented foods are being used in clinical trials and their microbial compositions, he said.
