The Microbiome Group

The Microbiome Group Microbiome Analysis with Viola Sampson BSc MCMA and Associates

One of the worst foods you can eat with an imbalanced microbiome might also be one of the best foods you can eat for a h...
04/06/2026

One of the worst foods you can eat with an imbalanced microbiome might also be one of the best foods you can eat for a healthy one.

Jerusalem artichokes are one of the richest dietary sources of prebiotic fibres inulin and FOS. Your gut bacteria break down prebiotics to produce health-promoting short chain fatty acids. They also produce gas.

For someone with a balanced microbiome, that gas is almost unnoticeable. Some is used up by other bacteria and the rest passes through the gut painlessly. For someone with significant microbiome imbalances, where certain bacterial species are depleted or others are overgrown, prebiotic-rich foods can trigger bloating, cramping, flatulence and pain. We often see this in clients with IBS and Long Covid, and those whose microbiome hasn’t recovered following antibiotics.

A well-designed human trial in healthy adults found that daily consumption of Jerusalem artichoke inulin significantly increased Bifidobacteria, along with a smaller increase in the Lactobacillus group. We find these bacterial populations are often depleted in those with chronic gut conditions.

Prebiotic foods are essential for microbiome health, so the goal is to repair the microbiome to the point where eating them becomes enjoyable once more. In practice, this looks like a client who couldn’t tolerate Jerusalem artichokes at the start of their treatment programme being able to eat a full portion without symptoms. The food hasn’t changed. Their microbiome has. That shift is one of the clear markers of progress we look for in clinic.

If Jerusalem artichokes, or other prebiotic foods like onions, garlic or beans, cause you problems, that’s worth listening to — not as a reason to avoid them, but as information about what your microbiome might need.

Share this post with someone who struggles with prebiotic foods.

✏️ 📸 by Viola

REFERENCES
Ramnani et al (2010) Prebiotic effect of fruit and vegetable shots containing Jerusalem artichoke inulin: a human intervention study. Br J Nutr 104: 233–240 https://doi.org/10.1017/S000711451000036X

IMAGE Viola’s hands holding fresh Jerusalem artichokes.

Fresh figs have always been one of my favourites, and I think they are underrated when it comes to gut health.They’re ri...
01/06/2026

Fresh figs have always been one of my favourites, and I think they are underrated when it comes to gut health.

They’re rich in dietary fibre and polyphenols, including flavonoids and anthocyanins, which feed and diversify the bacterial populations in the gut.

They have also been studied specifically for constipation. A randomised controlled trial found that fig paste supplementation over eight weeks significantly reduced colon transit time and improved stool consistency in people with functional constipation.

I threw together this salad for lunch this week to pair with my grilled barramundi: rocket, fresh figs, goats’ cheese, walnuts, olive oil and lemon. Delicious.

Tell me in the comments — are you a fig fan, and what do you do with them?

✏️ 📸 by Vicky

REFERENCES
Baek et al. (2016) Randomized, double-blind, placebo-controlled trial of Ficus carica paste for the management of functional constipation. Asia Pac J Clin Nutr 25(3): 487–496.
https://doi.org/10.6133/apjcn.092015.06


IMAGES: Two close-up shots of fresh figs, one whole and halved showing the gorgeous crimson interior, one cut face in detail, alongside an overhead shot of the finished salad with figs, goats’ cheese and walnuts.

27/05/2026

Who said hummus has to be made with chickpeas? I didn’t have any. I didn’t have lemons either, and I didn’t have much time. What I did have was a tin of butter beans, some raw cider vinegar, unhulled tahini, olive oil, garlic powder, salt, pepper and dried oregano.

Butter beans feed a range of beneficial gut bacteria, including Bifidobacterium. I only lightly strained them because the water also contains prebiotic GOS — specifically raffinose and stachyose. Most recipes tell you to rinse them away. If you’re managing IBS symptoms, you’ll probably want to do that to reduce the FODMAP content of the beans, but for everyone else, keeping some of that water is likely to support your microbiome health.

I included oregano partly because it tastes good with beans and partly because dried herbs are an underrated source of polyphenols that feed a wider range of beneficial gut bacteria. The raw cider vinegar adds acidity and live cultures. The unhulled tahini has more fibre than hulled tahini, as well as more polyphenols and more calcium and iron. The garlic powder was simply a time saver — I didn’t want to bother with peeling and crushing fresh cloves. It still contains some prebiotic inulin and FOS, just a bit less than fresh garlic.

I made a plate with a rainbow of colours that indicate a diverse range of polyphenols to support a diversity of gut bacteria. I added some fermented beet sauerkraut for more colour, taste, plant diversity and live bacteria.

Save this for when you need a quick lunch idea.

✏️ 📸 by Viola

VIDEO: Five images: butter beans and ingredients before blending, blending with a stick blender, finished hummus on a white plate, with raw salad veg and fermented beetroot.

Barbecues are mostly a meat occasion. They don’t have to be.Your gut microbiome thrives on veg. These are simple: courge...
22/05/2026

Barbecues are mostly a meat occasion. They don’t have to be.

Your gut microbiome thrives on veg. These are simple: courgette, aubergine, asparagus on the grill, laden with crushed garlic. Nothing you haven’t seen before, and the garlic and asparagus both provide prebiotics to feed beneficial gut bacteria. But the lentil salad brought some more nourishment for my gut microbiome:

🖤 Black lentils for resistant starch, prebiotic fibre and polyphenols.
♥️ Pomegranate molasses for more polyphenols.
💚 Fermented gherkins for live bacteria.
Three different routes to supporting my microbiome health in one dish.

I added the herb robert flowers, not only because they are pretty but because they contribute a surprising, pungent flavour.

If you’re firing up the barbecue this Bank Holiday weekend (and a heatwave) in the UK, try making the veg the main event and show your microbiome some love.

Share your favourite combinations in the comments to inspire me and others reading this!

✏️📸 Viola

Image: A white bowl of black lentils topped with grilled asparagus, courgette and aubergine, scattered with bright pink flowers, held beside a hot barbecue grill.

I got some probiotics for my tomato seedlings! The science behind them is fascinating. These discs apparently contain my...
19/05/2026

I got some probiotics for my tomato seedlings! The science behind them is fascinating. These discs apparently contain mycorrhizal fungi and nitrogen-fixing bacteria. There are greenhouse and field trials showing mycorrhizal fungi can improve tomato yield and fruit quality, and evidence that nitrogen-fixing bacteria support growth under reduced fertilisation.

But the label on this product just says “beneficial bacteria [that] act to fix nitrogen from the air.” No species or strain information for the bacteria or fungi. In my clinical practice, species and strain details are the baseline for recommending any probiotic — that’s how we match them to clinical trial evidence for specific health benefits.

The soil and gut microbiomes are interconnected ecosystem, and soil health is something I care about deeply. I nearly went down a very different path shortly after I graduated from my degree in medical biosciences, when I seriously considered a PhD position with a leading soil microbiologist. Instead, I ended up campaigning to keep Genetically Modified crops out of the UK, driven in large part by concerns about the impact of industrial farming practices on soil microbial communities, and the importance of farming practices that support soil health. Two decades later, that work shapes how I think about the microbiome today, both in our gut and the soil, as ecosystems worth protecting and nurturing.

I’ll let you know how my tomatoes turn out in a few weeks!

Have you tried probiotics for your garden? Let me know in the comments.

✏️📸 Viola

REFERENCES
In comments

Image: Viola’s hand holds a brown disc above a pot containing fresh compost, next to a small tomato seedling on patio paving.

As the weather gets colder in Melbourne the mushroom season begins.Mushroom season is one of my favourite times of year,...
14/05/2026

As the weather gets colder in Melbourne the mushroom season begins.

Mushroom season is one of my favourite times of year, because so many different varieties become available. If you want to find the best variety head to farmers markets or the local markets in country towns.

Mushrooms contain several compounds with well-documented effects on the gut microbiome, including beta-glucans, a type of prebiotic fibre that feeds beneficial bacteria and drives the production of short-chain fatty acids.

Different mushrooms contain different beta-glucan profiles, and these structural differences appear to influence which bacterial populations they support.

🟡Oyster mushrooms are a rich source of beta-glucans, with lab studies suggesting their particular profile has an effect comparable to inulin, selectively promoting the growth of Bifidobacterium species.

🟤Shiitake are also a rich source of beta-glucans and contain a well-studied compound that helps regulate immune function.

⚪Lion’s Mane contains compounds which may help stimulate neuronal growth, repair and maintenance.

🟠Chestnut mushrooms are high in beta-glucans and support microbial diversity

Regularly including a wide range of mushrooms may help create a more resilient and diverse gut ecosystem over time. They are also easy to prepare as they can be added to soups, pastas or simply roasted or sauteed.

Which mushrooms are your favourite?

REFERENCES
Contato et al (2025). Lion’s Mane Mushroom (Hericium erinaceus): A Neuroprotective Fungus with Antioxidant, Anti-Inflammatory, and Antimicrobial Potential—A Narrative Review. Nutrients, 17(8), 1307.
https://doi.org/10.3390/nu17081307

Mitsou et al (2020), Effects of Rich in β-Glucans Edible Mushrooms on Aging Gut Microbiota Characteristics: An In Vitro Study, Molecules, 25(12), 2806. https://doi.org/10.3390/molecules25122806

Zhao et al (2023) The benefits of edible mushroom polysaccharides for health and their influence on gut microbiota: a review. Front. Nutr. 10:1213010.
https://doi.org/10.3389/fnut.2023.1213010

✏📷 by Vicky

Research suggests that a more Mediterranean-style diet may support both gut health and mental wellbeing. This means mor...
12/05/2026

Research suggests that a more Mediterranean-style diet may support both gut health and mental wellbeing.

This means more vegetables, fruit, whole grains, beans, nuts, fish, and olive oil - and fewer ultra-processed foods and sugary drinks.

Why does this matter?
Your gut microbiome helps with digestion, immune function, and the production of compounds that may influence the gut-brain axis.

That means that small, everyday food choices can do more than support digestion - they may also help create a healthier environment for your gut microbes.

Below are some simple ways I help to support to support my microbiome:

✅Eat a wide variety of plant foods, including seasonal foods like wild garlic.

✅Aim for more fibre each day (this might mean adding a seed mix or a tablespoon of flaxseed to my morning muesli).

✅Include fermented foods if you enjoy them (e.g. slightly warm sauerkraut - delicious).

✅And cut back on highly processed foods where possible (it is possible to change your sweet tooth!)

And lastly focus on consistency, not perfection.

A healthy gut doesn’t come from one “superfood” or one supplement. It comes from a pattern of eating that feeds your microbes well over time.

REFERENCES:
Jacka FN, O'Neil A, Opie R, Itsiopoulos C, Cotton S, Mohebbi M, Castle D, Dash S, Mihalopoulos C, Chatterton ML, Brazionis L, Dean OM, Hodge AM, Berk M. A randomised controlled trial of dietary improvement for adults with major depression (the 'SMILES' trial). BMC Med. 2017 Jan 30;15(1):23. doi: 10.1186/s12916-017-0791-y. Erratum in: BMC Med. 2018 Dec 28;16(1):236. doi: 10.1186/s12916-018-1220-6. PMID: 28137247; PMCID: PMC5282719.

✏️Melody
📸 Melody (sweet potato with spicy yoghurt, pomegranate seed and mint), rose harrisa chickpeas, fresh and sundried tomatoes) and quinoa with feta

05/05/2026

Each year I make this. It’s the end of wild garlic season and usually I would gather flowers a little earlier as the petals were already dropping from these. But this makes a wonderfully pretty infused vinegar and will set me up for some delicious salad dressings for the month ahead.

I like to use unfiltered, raw apple cider vinegar with the mother. This means any beneficial yeasts and bacteria are still present — mainly acetic acid bacteria but typically also lactic acid bacteria (including Lactobacillus species) and yeasts. Those that are still live won’t take up residence as part of my gut microbiome, but the bacteria and their cell components and products may have beneficial effects on the way through my gut.

It already smells amazing after a couple of days so I will start using it soon.

Wild garlic spreads through splitting bulbs and by seed so I always sparingly pick the flowers or seedheads in any patch.

✏️📸 Viola

REFERENCE
Trček, Mahnič & Rupnik (2016). Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing. International Journal of Food Microbiology, 223, 57–62. https://doi.org/10.1016/j.ijfoodmicro.2016.02.007

VIDEO:
White wild garlic flowers on a chopping board are transferred to a clip top jar and submerged in vinegar.

Recently, a few clients have asked me about postbiotics, so I decided to write a blog to share with them, as there are n...
01/05/2026

Recently, a few clients have asked me about postbiotics, so I decided to write a blog to share with them, as there are now several postbiotic supplements on the market proclaiming a benefit to the gut microbiome.

Postbiotics differ from probiotics and prebiotics. Probiotics are live microorganisms and prebiotics are a type of fibre which feeds beneficial bacteria. While probiotics and prebiotics are generally considered beneficial for gut health, postbiotics are less well understood.

Postbiotic supplements contain bacterial products and cell fragments or even whole, inactivated or heat-killed bacterial cells that have are believed to have a therapeutic effect. The International Scientific Association for Probiotics and Prebiotics (ISAPP) defines a postbiotic supplement as 'a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host.'

One of the advantages of postbiotics is that they contain no live organisms. This may be helpful because they do not need to be refrigerated (like some probiotics do), and they could be safely consumed by immunocompromised clients who may not be able to take probiotics.

A good example of a postbiotic is butyrate, an important short chain fatty acid (SCFA) that plays a key role in maintaining gut wall integrity. We have been using butyrate in clinical practice for several years now, and the results have been consistently promising, with an excellent safety profile.

Postbiotics are also naturally found in fermented foods, including those that have been pasteurised or cooked. For example, sourdough bread includes beneficial acids produced during the proving process and of course the bacteria and yeasts introduced through the sourdough culture that don't survive the oven.

While postbiotics may play an increasingly important role in maintaining gut health in the future, our primary focus is always on nourishing the gut microbiome through food and targeted prebiotics first.

If you want to know more, my fully-referenced blog is now live!

✏📷 by Vicky

You have bitter taste receptors throughout your gut, not just in your mouth! The taste on your tongue is just the beginn...
28/04/2026

You have bitter taste receptors throughout your gut, not just in your mouth! The taste on your tongue is just the beginning of a much longer conversation between your food and your gut.

One significant role of these bitter receptors in the gut appears to be microbial surveillance: detecting when bacteria are organising, mounting an immune response before infection takes hold, releasing antimicrobial compounds and thickening the mucus lining. Bitter plant compounds activate the same receptors.

When those receptors are stimulated, a cascade follows. Specialised cells in the gut lining release signalling molecules including GLP-1, which regulates blood sugar and satiety, and cholecystokinin, which triggers bile release from the gallbladder. Bile emulsifies fats in your food for absorption, acts as an antimicrobial to control bacterial populations in the small intestine, and is metabolised by gut bacteria into secondary bile acids that shape microbiome composition and intestinal immune function. There is also emerging evidence that bitter receptors in the gut’s smooth muscle play a role in peristalsis, the muscular contractions that move food forward. A diet chronically low in bitter foods leaves this signalling system underactivated, with reduced satiety signalling, lower bile release, and wider metabolic and microbiome impacts.

There is a second reason bitter foods are important. Most polyphenols are bitter, and polyphenols feed beneficial gut bacteria, transforming them into bioactive compounds that shape microbiome composition and reduce inflammation. Bitter diversity in the diet is polyphenol diversity. And polyphenol diversity feeds a complex microbiome.

The third reason is one not often discussed. Industrial farming has systematically bred bitterness out of our food because it reduces sales. Supermarket lettuce, cultivated chicory, commercial apples are all significantly sweeter and lower in bitter compounds than their wild or heritage equivalents. Even people eating a varied plant-rich diet may be getting far less bitter stimulus than the gut’s signalling system expects.

This salad was my answer to that: wild dandelion leaves, chicory, radicchio and wild garlic mustard provided the bitterness I often crave at this time of year. I also added wild leek, kalamata olives (for polyphenols), fermented gherkins and cucumber, with brown rice and whole wheat grains.

REFERENCES
Jalševac et al. (2024) Profiling bitter taste receptors (TAS2R) along the gastrointestinal tract and their influence on enterohormone secretion. Gender- and age-related effects in the colon. Frontiers in Endocrinology 15:1436580. PMID 39512758
Rudolph et al. (2025) Bitter taste receptors in bacterial infections and innate immunity. Immunity, Inflammation and Disease 13(7):e70232. PMID 40709685
Sternini et al. (2025) Bitter taste receptors as sensors of gut luminal contents. Nature Reviews Gastroenterology & Hepatology 22(1):39–53. PMID 39468215
Camillo et al. (2025) Bitter taste receptors 38 and 46 regulate intestinal peristalsis. International Journal of Molecular Sciences 26(5):2092.
Osakabe et al. (2024) Sensory nutrition and bitterness and astringency of polyphenols. Biomolecules 14(2):234. PMID 38397471

✏️📸 Viola

Image: a brightly coloured salad in a square, white bowl on a wooden surface.

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