It’s not just what we eat. It’s what our gut microbiome can handle

We often associate a healthy gut microbiome with greater bacterial diversity. But emerging research suggests that what our gut bacteria actually do may be just as important as how many different species we have.

A 2026 systematic review published in Nutrition Reviews examined 48 human studies investigating how grains and pseudograins such as oats, barley, wheat and quinoa influence our gut microbiome.

The findings revealed something interesting:

• 41 of 48 studies reported changes in microbial composition, meaning the types or relative abundance of bacteria living in the gut.
• Only 4 of 29 studies measuring microbial diversity found significant increases.
• 12 of 28 studies reported changes in short-chain fatty acids (SCFAs), compounds produced when gut bacteria ferment certain carbohydrates. These compounds play important roles in nourishing our intestinal cells, maintaining the gut barrier and regulating inflammatory responses.

So what does this tell us?

Grains can influence the gut microbiome without necessarily increasing its overall diversity. Some of these changes involve bacteria with the capacity to produce compounds that support important aspects of gut health.

But there’s another side to this research that I find particularly relevant in clinical practice.

A food that supports beneficial microbial activity isn’t necessarily a food that everyone can comfortably digest.

For someone experiencing IBS, persistent bloating or digestive dysfunction, introducing large amounts of fermentable fibre may increase discomfort, even when that fibre has potential microbiome benefits.

This raises two important considerations: what our gut bacteria are capable of doing and what our digestive system can comfortably tolerate.

And that’s why I believe we need to look beyond microbial diversity alone.

It’s not just about diversity. It’s about function.

Think of your gut microbiome as a garden.

You could have 30 different plant species growing in that garden, but what if half were invasive weeds competing for nutrients and disrupting the ecosystem?

Compare that with a garden containing 20 carefully balanced species, each contributing something valuable.

Some plants enrich the soil, others attract pollinators and others protect neighbouring plants.

It’s not simply the number of species that makes a garden healthy. It’s how they function together.

The same principle applies to our gut microbiome.

Some microorganisms break down dietary fibres, others produce metabolites that nourish our intestinal cells and others help regulate immune responses.

This cooperation is known as microbial cross-feeding.

One bacterial species produces compounds that another uses as fuel, creating a network of metabolic interactions.

For example, certain bacteria produce acetate and lactate, which other microorganisms can use to produce butyrate.

This is particularly interesting because butyrate is involved in maintaining the intestinal barrier and regulating inflammatory pathways.

And this brings us to some of the specific bacteria identified in the research.

What did the research find, and why does it matter?

1. Bifidobacterium: Supporting the bacteria that feed other bacteria

Interventions involving oats and wheat reported increases in Bifidobacterium adolescentis, B. bifidum and B. catenulatum.

Why is this important?

Bifidobacteria help ferment certain complex carbohydrates and produce acetate and lactate.

These compounds can then be utilised by other microorganisms to produce butyrate, one of the most important short-chain fatty acids in the colon.

Butyrate has several important biological functions:

• Gut lining: Provides a major energy source for colon cells, helping maintain a healthy intestinal barrier.
• Immune regulation: Influences inflammatory signalling and helps regulate immune responses.
• Gut environment: Helps maintain conditions that favour beneficial anaerobic microorganisms.

This is why supporting fibre-fermenting bacteria may have benefits beyond digestion.

Oats also contain beta-glucan, a soluble fibre associated with lowering LDL cholesterol and providing a fermentable substrate for certain gut microorganisms.

However, the quantity and type of fibre still matter.

Someone accustomed to a low-fibre diet may experience bloating when suddenly increasing fermentable fibre intake.

Gradually increasing portions can help some people build tolerance without overwhelming their digestive system.

2. Roseburia: Supporting intestinal barrier function

Some barley interventions reported increases in Roseburia, a bacterial genus containing important butyrate-producing species.

Why does this matter?

Our intestinal barrier acts as a selective filter, allowing nutrients to pass into circulation while helping prevent unwanted substances from crossing into the bloodstream.

Butyrate supports this barrier by providing energy to intestinal cells and influencing proteins involved in maintaining the connections between them.

It also helps regulate inflammatory pathways, making butyrate-producing bacteria an important area of research in gastrointestinal and metabolic health.

However, increasing Roseburia does not automatically mean inflammation has decreased. That requires direct measurements of inflammatory markers and clinical outcomes.

And again, we need to consider the individual.

Barley contains fermentable carbohydrates, including fructans, which can aggravate symptoms in some people with IBS.

So although barley may support certain beneficial microbial activities, it isn’t necessarily the best starting point for everyone.

3. Bacteroides uniformis: An emerging area of microbiome research

One small quinoa intervention reported an increase in Bacteroides uniformis.

This species is attracting scientific interest because certain strains can metabolise complex carbohydrates and influence metabolic and immune pathways.

Experimental research has investigated its potential effects on:

• Intestinal barrier integrity
• Inflammatory signalling
• Glucose and lipid metabolism

These findings are promising, although much of the mechanistic evidence comes from animal and laboratory studies.

Quinoa also offers a practical alternative to wheat and barley for people who need to limit certain fermentable carbohydrates.

However, individual tolerance and serving size still matter.

Why isn’t higher microbial diversity always better?

Higher microbial diversity can be associated with better health, but diversity alone doesn’t tell us how well the microbiome is functioning.

Two individuals may have very different bacterial populations but similar abilities to ferment dietary fibre and produce short-chain fatty acids.

This is known as functional redundancy, where different microorganisms perform similar biological functions.

A more diverse microbiome may offer greater resilience in some circumstances, but the presence of more species isn’t automatically beneficial.

And importantly, we need to distinguish microbial diversity from dietary diversity.

While eating a wide variety of plant foods is generally encouraged, someone experiencing significant digestive symptoms may not tolerate a sudden increase in different fermentable fibres.

The long-term goal may be greater dietary variety, but the starting point needs to reflect the individual’s digestive tolerance.

For some people, that means beginning with smaller portions of a limited number of well-tolerated fibres and gradually expanding their diet.

I’m currently creating a Gut Reset & Repair Program for people who need to start here, with a focus on digestive tolerance and gradually rebuilding dietary variety.

For others, temporarily reducing particular fermentable carbohydrates may help manage symptoms before foods are systematically reintroduced.

A systematic review and network meta-analysis involving 944 patients with IBS found that a low-FODMAP diet was effective for improving overall IBS symptoms and bloating compared with several other dietary approaches.

However, the researchers also highlighted the need for more evidence on food reintroduction and personalisation.

Dietary restriction shouldn’t automatically become the long-term solution.

It’s not just what we eat. It’s what our gut can handle.

As both a clinical nutritionist and chef, this is where I believe nutrition research has another important question to explore.

We’ve studied the nutritional composition of grains extensively, but the way we prepare them can also change their properties.

Traditional methods such as soaking, sprouting, fermentation and cooking can influence:

• Mineral availability: Certain preparation methods can reduce phytate, a compound that binds minerals such as iron and zinc.
• Digestive tolerance: Preparation can alter food structure and some fermentable carbohydrates.
• Resistant starch: Cooking and cooling certain starchy foods can increase resistant starch, which may become available for fermentation by gut microorganisms, essentially providing them with food.

But preparation doesn’t guarantee digestive tolerance.

For example, increasing resistant starch may provide more fermentable substrate for gut bacteria, but it may also increase gas production in susceptible individuals.

Similarly, soaking or sprouting doesn’t necessarily make every grain suitable for someone with IBS.

The systematic review did not directly establish whether soaking or sprouting improves microbiome outcomes.

However, it raises an important question:

Could the way we prepare grains influence their effects on our gut bacteria and digestive health?

I believe this deserves further investigation, particularly in people with digestive dysfunction who struggle to tolerate a broad range of plant fibres.

My takeaway

Rather than chasing the highest possible microbial diversity, perhaps we should focus more on supporting a gut microbiome that functions well.

That means considering the types of fibre we consume, the metabolites our bacteria produce and how our digestive system responds.

For people experiencing bloating or IBS, increasing fibre without considering digestive tolerance can sometimes make symptoms worse.

A healthy diet isn’t necessarily the one containing the greatest variety of fibres today. It’s one that supports nutritional adequacy, digestive comfort and the gradual development of a more varied diet where possible.

The goal isn’t simply to eat more grains.

It’s to understand how to include nutritious foods in ways that work for the individual.

Bringing the science into the kitchen

If you or your patients struggle to digest grains, legumes, nuts and seeds, I’ve created my Prep Like a Pro guide to help you understand traditional preparation methods that may improve digestibility and nutrient availability.

Because it’s not just what we eat. It’s how we prepare it and what our bodies and microbes can do with it.

Grab your copy here 👉 Prep Like a Pro guide

Love your guts,

Chef Leilani | Clinical Nutritionist & Gut Health Educator

Research references

1. Primary systematic review (2026)

Gonen-Colak B, Turan-Demirci B, Buyuktuncer Z.

Modification of Gut Microbiome by Cereal and Pseudocereal Consumption: A Systematic Review.

Nutrition Reviews, 2026.

Read on PubMed

Research quality: Peer-reviewed systematic review of 48 human intervention studies involving 1,960 participants.

Conflicts of interest: None declared.

Funding: Hacettepe University Scientific Research Projects Coordination Unit.

The review followed PRISMA reporting guidelines, although its protocol was not prospectively registered. The included studies varied in design, duration and interventions, limiting how confidently individual grain effects can be compared. 

2. Supporting systematic review and meta-analysis (2022)

Black CJ et al.

Efficacy of a low FODMAP diet in irritable bowel syndrome: systematic review and network meta-analysis.

Gut, 2022.

Read on PubMed

Research quality: Systematic review and network meta-analysis of 13 randomised controlled trials involving 944 patients.

Conflicts of interest: None declared.

This supports the discussion about fermentable carbohydrate tolerance and IBS symptoms. 

3. Supporting research on microbial cross-feeding (2019)

Alessandri G et al.

Bifidobacterial Dialogue With Its Human Host and Consequent Modulation of the Immune System.

Frontiers in Immunology, 2019.

Read on PubMed

4. Supporting research on butyrate (2021)

The Immunomodulatory Functions of Butyrate.

Read on PubMed