Most of us have heard the five-plus-a-day message for fruit and vegetables. But new research into gut health suggests that advice may soon need tweaking.

At Kiwi scientist Rob Knight’s laboratory at the University of California, San Diego, the shit isn’t so much hitting the fan as filling a knowledge vacuum. Poo sample swabs arrive here by post daily from all over the world: 42 countries, 15,000 samples, and 11,000 people so far. The information Knight and his team are gleaning from them is changing the world’s thinking on gut health.

Knight, a professor of paediatrics and computer science and engineering, is co-founder of the American Gut Project, in which each participant pays US$99 to have their stool sample scrutinised. Launched in 2012, it’s the world’s largest citizen-science project to investigate and map the human microbiome – a system so complex and so important to our health it’s been called our second brain. In its first report last year, Knight’s team revealed one of its most exciting discoveries to date: that the greater the variety of plants in the diet, the greater the diversity of bacteria in the gut.

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“So far, the advice about what you should eat for your microbiome has been very generic,” Knight told the Listener. “It’s been mostly explaining stuff that your grandmother knew already – that you should eat your vegetables, avoid too many potatoes if you don’t want to get fat, that kind of thing. And there’s been some understanding that eating fibre is good because of your microbiome, but it’s stuff that’s been known for generations that people don’t really want to do.”

What is different now, says Knight, is that genetic results are enabling scientists to individualise advice – understanding, for example, that one person should eat tomatoes and another should avoid them, and what foods might help an individual to achieve better blood-sugar control. The differences are not only in our genome and microbiome, but in how each individual metabolises what they eat, and the chemical by-products that result. “You personally might be better off eating the cheapest white bread at the supermarket, or you might need fancy wholegrain bread, but for some people, the fancy wholegrain is bad for them.”

The study found that no matter what diet participants preferred – vegetarian, vegan or omnivore – those who ate more than 30 different types of plants a week (including herbs and spices) had more diverse gut microbiomes than those who ate 10 or fewer types. Numbers in each of those groups were small (about 40), but still statistically significant. There were also differences at less extreme levels, where participants numbered in the thousands.

Variety is the key

Knight says the information suggests that if you want to positively reshape your gut bacteria, “you shouldn’t just eat a big plate of broccoli, but rather eat a lot of different kinds of plants, including fruits and spices. In terms of what your microbiome looks like overall, you can be a vegan who eats vegetables or a vegan who mostly eats chips and biscuits. That’s going to have a much bigger effect on the microbiome than sometimes eating meat.”

Greater diversity of gut bacteria has been associated with better gut health, although the mechanisms are still not well understood. Less diversity has been linked to conditions including irritable bowel, diabetes and obesity.

For Knight, the biggest question is finding out, at a chemical level, what is in our food. “A chemical analysis of any new food will find thousands of molecules and no one will know what they are, what they do, or what effect they have on our bodies.” The second question is how food interacts with our microbiome, and our genetics, to positively or negatively affect our health – and how we can then predict which diet might work best. It’s unlikely research will discover a single new food “hero”. “If there was a hero that worked for everybody, we would know about it already.”

The project also found that antibiotics fed to animals, such as chickens and cows, could be detected in human stool samples and could potentially alter the gut microbiota.

Knight will discuss the latest findings in a keynote speech at the Foodomics 2019 conference in Auckland, hosted by the High-Value Nutrition National Science Challenge. The challenge is a Government-funded, $83 million, 10-year programme launched in 2014 with the aim of finding food-based solutions to some of our commonest maladies, including obesity and diabetes, gut problems, asthma and infant malnutrition.

The meeting has attracted leading local and international investigators in the field, including Australia’s most-cited researcher, Nicholas Talley, a professor of medicine and of epidemiology, known in scientific circles as the godfather of functional gastrointestinal disorders worldwide. Research both here and abroad into possible dietary causes of – and solutions to – gut ill-health are expected to dominate proceedings, but Talley will focus on the likely precursors: genetic predisposition and the triggering role of infection.

It’s not in the mind

Talley and his team from the University of Newcastle were the first to discover a genetic contribution to some cases of irritable bowel syndrome (IBS) and indigestion, disproving the notion that functional gut problems with no obvious pathology were “all in the mind”. “Even now, there are a lot of gastroenterologists and doctors you will talk to who will say it’s just psychological. It doesn’t help at all, because there is no cure for that and you just suppress symptoms. So, we have gone from that paradigm to knowing there is probably real pathology set off by various processes that are potentially able to be interrupted and are therefore curable. There’s a long way to go to prove it, but it is certainly exciting.”

Talley believes a subtle inflammatory process is at play in people with IBS and other common gut disorders, set off when the gut bacteria break down food to release substances that produce an immune response. It’s a complex process, a combination of what the bacteria produce, how they interact with each other and the immune system, and whether the body is then able to suppress or change the immune reaction. “That ends up driving whether you end up ill when your neighbour eating the same thing is perfectly well.”

One of the obvious dietary candidates is wheat, and the role of proteins including gluten, and various fermentable carbohydrates (Fodmaps). But people must usually have a genetic predisposition for them to be a problem, Talley says. “If you are not set up to have an abnormal immune response to the food antigens, you’ll be fine.”

Gut problems and bacteria

Talley believes research will lead to the identification of certain gut bacteria that actively cause harm, such as Helicobacter pylori, which is a strong risk factor for stomach cancer, rather than problems being caused by the interaction of multiple bacteria. “Lots of other things change with Helicobacter, but the only thing that matters is Helicobacter. We are coming at it from that angle and it’s a little bit controversial.” Asked if the importance of gut diversity has been overemphasised, Talley says it isn’t clear. “Correlation and association doesn’t mean cause and effect.”

In New Zealand, some of the most detailed research teasing out the links between diet, gut bacteria and gut problems such as IBS is being done in a High-Value Nutrition National Science Challenge collaboration involving AgResearch, the University of Otago, Christchurch, the Riddet Institute, Massey University, the Malaghan Institute, Plant & Food Research and the University of Auckland, led by principal scientist Nicole Roy. Christchurch gastroenterologist Richard Gearry co-ordinates the clinical arm of the research. Says Roy: “People think about their gut as a long tube that food goes through and some nutrients are absorbed, but it’s an incredibly complex system and it is very difficult to define what a healthy gut actually is.” The work aims to identify foods capable of improving gut function, the metabolic pathways that can help scientists understand what is going on, and for biomarkers to be picked up in blood tests to diagnose the conditions. “If we can identify a molecule in their blood, faeces and even breath, we can better understand how the gut is working and which foods might improve their symptoms and quality of life.”