Eating for Your Microbiome? More Plants Can Help

New studies highlight the benefits of plant-forward and non-industrialized diets for the gut microbiome.

What’s on the menu for a healthy microbiome? High-fiber foods, like broccoli and lentils are key –– according to two new studies with two vastly different approaches published in Cell and Nature. As the debate about the role ultra-processed plant-based meat substitutes should play in a healthy diet rages on, these new studies focused on a more balanced, plant-forward approach, finding that a diet high in plants (fruits, vegetables and legumes) is good for a healthy gut. In addition to reducing climate emissions then, adapting a plant-forward diet can help to create a balanced gut microbiome, which in turn can reduce inflammation and risk of developing chronic diseases. 

Each of our microbiomes is a nexus of bacteria, specific to factors like our environment, stress and age. Microbiomes can be vastly different among people –– and even twins –– that they’re often likened to a microbial fingerprint of sorts. But we know that diet plays a large role in forming healthy gut bacteria. An Italian team of researchers set out to identify if there are signature microbiomes for vegans, vegetarians and omnivores (people who eat both plants and meat) out of a group of nearly 22,000 people living in the United States, the United Kingdom and Italy. And, as it turns out, there is a pattern of key bacteria associated with each dietary cohort.

How Much Does Diet Affect Your Microbiome?

“As more and more people adopt vegan and vegetarian diets, we wanted to find out how different their microbiomes are and which microorganisms are responsible for these differences,” Gloria Fackelmann, postdoctoral researcher at the Department of Cellular, Computational and Integrative Biology, University of Trento, said in a press release. According to the paper, published in Nature, vegan and vegetarian diet signatures were associated with a healthy cardiometabolic system and production of beneficial fatty acids. 

“Our data showed that omnivores on average ingest significantly fewer healthy plant-based foods than vegetarians or vegans,” the researchers wrote, adding that “optimizing the quality of omnivore diets by increasing dietary plant diversity could lead to better gut health.” Omnivores had strong signals of bacteria like A. putredinis, associated with meat consumption, which the paper links to inflammatory bowel disease and an increased risk of colon cancer. However, an important caveat — Fackelmann notes that they didn’t measure health markers of these specific participants, they instead looked to the scientific literature of what is known about these bacteria (They did, however, study stool samples – more on this in a bit).

That doesn’t mean that excluding animal products automatically equals a healthy microbiome. Here’s where that balanced diet comes back in. A varied diet of fiber-rich foods like plants is key. “Avoiding meat or dairy products does not necessarily have a positive effect if it does not come with a variety of quality plant-based products,” Nicola Segata, research lead on the paper, said in a press release. 

For the microbiome, a critical ingredient is fiber. “Your microbiota is tuned towards digesting fiber predominantly, so eating a largely plant based diet gets more of those nutrients to them,” Eric Martens, a professor of microbiology and immunology at University of Michigan Medical School, who was not involved in the studies, tells Sentient.

There was less bacterial diversity in vegetarians and vegans than in omnivores, but another important detail is that diversity doesn’t always equal an optimal microbiome. On the one hand, a diverse microbiome means more bacteria, so more opportunity for defense against infections and ability to break down various food types. But that’s assuming those bacteria are beneficial and not all bacteria are. A person could have a diverse array of harmful microbes, which would negate the whole concept. So while diversity is important, of more importance is what bacteria are present, rather than how many. “When people hear diversity, we hear about it in the context of biodiversity and always more diversity is better. But for the gut…higher diversity wouldn’t exactly equate to having a more favorable microbiome composition,” Fackelmann tells Sentient.

In the Nature study, the participants’ stool samples were analyzed using shotgun metagenomic sequencing, which yields highly specific information about the species of gut bacteria present. Interestingly, they found that vegans had more soil-derived microbes and omnivores more dairy, highlighting that gut bacterial members may come directly from the food we eat. 

Looking To a Non-Industrialized Diet for Answers

In a different vein, a team of microbiologists based in Ireland tested the effects of a non-industrialized diet on the microbiome — in other words, mostly plants and low in processed foods. “Industrialization has drastically impacted our gut microbiome, likely increasing the risk of chronic diseases,” Jens Walter, a professor of Ecology, Food, and the Microbiome at University College Cork, tells Sentient. Walter and his colleagues developed a diet — called the NiMe diet (Non-industrialized Microbiome Restore) — high in plants and fiber and low in meat and processed foods, based on the eating habits of rural Papua New Guineans. 

In a strictly human controlled trial, 30 participants followed this diet and consumed L. reuteri, a beneficial bacterium found in the gut of rural Papua New Guineans but rarely found in industrialized microbiomes. Unlike the Nature study, Walter and his colleagues directly measured the health risk factors of participants and found that after just three weeks, the diet had decreased low-density lipoprotein (LDL) cholesterol by 17 percent, reduced blood sugar by 6 percent and reduced levels of a protein associated with heart disease. Martens put more emphasis on the findings of this paper, as the authors both staged a dietary intervention and measured the health effects, rather than finding correlations with the scientific literature.

The magnitude of the findings was surprising, Walter tells Sentient. “I didn’t think a three-week study would be enough to improve blood glucose or cholesterol,” he says. Another surprise was that participants lost weight even though the calories were the same as their usual diet. The researchers are sharing their “NiMe diet” with the public via online free recipes on Instagram. 

In practice, shifting to a non-industrialized diet may be difficult. We are increasingly consuming more ultra-processed foods and less whole foods than we were just two decades ago. Misleading food marketing claims and the rise of various dubious “wellness” trends also make grocery shopping for a healthy diet that much harder. Keep it simple, Martens says. He recommends supplementing your diet with plant-based fiber from whole sources as opposed to picking up the quick-fix fiber snack bar.

The Bottom Line

No matter the specific details of your diet, the microbiome is crucial in all stages of life to maintain health. Research shows food and lifestyle changes can bolster protection against chronic diseases, although this tends to be challenging for most Americans just based on what we actually eat. Small incremental changes towards eating more plants may feel like a less daunting prescription. These studies, among others, act as a signal that dietary tweaks and increased intake of high fiber food like plants can reap significant microbiome and health benefits.