Eczema + Problem Skin ConditionsJun 5, 202610 min read

How Your Microbiome Shapes Your Skin: The Gut-Skin Axis Explained

The short answer

Your gut microbiome and your skin are in constant conversation. The trillions of bacteria, fungi and other microbes living in your gut help train your immune system, calm inflammation and produce compounds (like short-chain fatty acids) that travel through the bloodstream and influence how your skin behaves. When the gut microbiome is out of balance, a state researchers call ‘dysbiosis’, the skin often pays the price. We see this most clearly in eczema, where children and adults with atopic dermatitis tend to have less diverse gut bacteria and lower levels of the helpful microbes that produce soothing metabolites.

The gut and the skin are not separate systems. They are two ends of one long conversation.

One important note before we go further. The science of the gut-skin axis is still evolving. What follows is my best read of the current peer-reviewed literature, but nothing is black and white. New research keep changing the picture, and I’ll keep updating this article as they do.

Why I’m writing this

I had eczema as a child. It went quiet in my mid-twenties, then came roaring back during each pregnancy. During my second pregnancy, my OB told me to take probiotics. Honestly, at the time, I didn’t fully understand why. I just knew I felt better when I took them, and the patches on the back of my knees calmed down a little.

Looking back, that throwaway piece of advice was based on a growing pile of research linking the maternal gut microbiome to infant skin. The probiotics weren’t really for me. They were predominantly for the baby growing inside me. I took them again during my third pregnancy.

This is the part I think about a lot. My eldest was born before I knew any of this, and I didn’t take probiotics during her pregnancy. Her eczema still needs to be actively managed today - she's 15 for reference. My two younger children, the babies of the pregnancies where I did take probiotics, both flare but less often and less severely. It's not proof of anything. But it does line up with the published trials, and I cannot pretend it doesn’t influence how I think about this.

I wrote this article for the version of me who stood in the chemist holding a probiotic bottle and wondering ‘why on earth do my insides have anything to do with my outsides?’ Quite a lot, as it turns out. Let me walk you through what the science actually says, and where it stops short.

If you want the flipside of this conversation, i've written a seperate article on how your skin affects your gut microbiome is the other half of the puzzle. The gut-skin axis runs both ways, and that surprised even me.

What is the gut-skin axis?

The ‘gut-skin axis’ is the term researchers use to describe the two-way communication between your gut microbiome and your skin. A 2026 review in the journal Gut Microbes describes it as a ‘bi-directional, microbiota-driven relationship with therapeutic potential’, which is a fancy way of saying that what happens in your gut shows up on your skin and the other way round.

The conversation happens in three main ways:

Immune signalling. About 70 percent of your immune system lives in and around your gut. Microbes there constantly train immune cells, which then circulate to every other tissue, including your skin.
Metabolites. Gut bacteria ferment the fibre you eat and release compounds called short-chain fatty acids (SCFAs), mainly butyrate, propionate and acetate. These compounds enter the bloodstream and have measurable effects on skin cells.
Barrier function. A healthy gut lining and a healthy skin barrier are made of similar things. When one is leaky, the other often follows.

If any one of these channels is out of balance, the skin can react. For people with sensitive or eczema-prone skin, all three are usually a little wobbly at once.

The microbes living in your gut (a 30-second tour)

You are home to roughly 38 trillion microbes, most of them in your large intestine. The big bacterial groups include Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. Within those, helpful ‘commensal’ bugs like Bifidobacterium, Lactobacillus, Akkermansia and Faecalibacterium prausnitzii do a lot of the heavy lifting. They:

Ferment fibre into SCFAs.
Compete with less friendly microbes for space and food.
Produce vitamins (B vitamins, vitamin K).
Reinforce the gut lining.
Calm the immune system.

When this community is diverse and well-fed, the immune system tends to be calmer. When diversity drops, often after antibiotics, illness, a low-fibre diet or chronic stress, the immune system gets twitchy. Twitchy immunity is bad news for skin that is already reactive.

How a wobbly gut shows up on the skin

Researchers have now linked gut dysbiosis to a long list of skin conditions. The strongest evidence sits with eczema (atopic dermatitis), acne, psoriasis, rosacea and chronic hives. The pattern is consistent: less diverse gut bacteria, fewer of the SCFA-producing ‘good guys’, and the skin tends to be more reactive.

This is an association rather than a one-to-one cause. Plenty of people with calm skin still have dysbiosis, and some people with eczema have a relatively diverse gut microbiome. The research describes a tendency, not a guarantee.

The four mechanisms (peer-reviewed, in plain English)

This is the part I wish someone had explained to me back when my GP first said ‘take probiotics’. The picture is still being filled in by researchers, but four mechanisms keep coming up across the literature.

1. Short-chain fatty acids (SCFAs) talk to your skin cells

When your gut bacteria ferment fibre, they release SCFAs. Butyrate is the star of the show. Butyrate:

Promotes the differentiation of regulatory T cells (Tregs), which are the calming side of the immune system.
Strengthens the lining of the gut, which keeps the immune system from over-reacting.
Has been shown in mouse and human studies to support skin barrier integrity by influencing how keratinocytes (the cells that make up the outer layer of your skin) mature.

A 2022 paper in Mucosal Immunology showed that gut-derived SCFAs directly improved skin barrier integrity by changing how keratinocytes use energy and differentiate. Translation: what you feed your gut bacteria changes how well your skin holds water and keeps irritants out.

2. Treg cells (the peacekeepers)

Regulatory T cells (Tregs) are the immune cells that say ‘enough, settle down’. People with eczema and other allergic conditions tend to have fewer functional Tregs. SCFAs from a healthy gut microbiome help generate Tregs. Fewer SCFAs, fewer Tregs, more inflammatory skin reactions. It really is that direct.

A 2023 study in early-life infant microbiomes found that an imbalance between pro-inflammatory CD4+IL17+ T cells and anti-inflammatory Tregs in the gut may be a ‘key determinant of early eczema development’. That study is one of several pointing in the same direction.

3. Gut permeability (‘leaky gut’) and skin reactivity

When the gut lining is compromised, undigested food particles and bacterial fragments can cross into the bloodstream. The immune system flags them, releases inflammatory signals, and those signals don’t stay local. They travel to skin, joints and lungs. For people with a genetic predisposition to atopic skin, this background hum of immune activation can make flares more likely.

This is not the same as the ‘leaky gut’ wellness industry hype. Increased intestinal permeability is a real, measurable thing, and it is linked to skin reactivity in peer-reviewed research, just not in the dramatic ‘cleanse to cure’ way it sometimes gets sold.

4. The vitamin D and aryl hydrocarbon receptor (AhR) pathways

This one is more recent science but very interesting. Gut bacteria produce compounds (like indole derivatives from tryptophan) that activate something called the aryl hydrocarbon receptor in skin cells. AhR signalling helps the skin barrier mature and helps the skin tolerate environmental irritants. People with eczema often have lower AhR activity. Several gut bacteria, including certain Lactobacilli, produce compounds that boost AhR. Another quiet, beautiful example of inside-out skin biology.

These four are the cleanest mechanisms we have so far. Researchers are also looking at vagus nerve signalling, hormone metabolism and circulating bacterial vesicles. Expect this list to grow.

What about probiotics?

This is the question I get most often. Honestly, the research is promising but specific, not magical.

What the evidence shows:

Maternal probiotic supplementation in late pregnancy and early breastfeeding (especially Lactobacillus rhamnosus GG) reduced the risk of eczema in infants in several large trials. A 2022 meta-analysis in American Journal of Clinical Dermatology confirmed a meaningful protective effect when probiotics are taken in the perinatal period.
Probiotics in already-established eczema show more mixed results. They may help some people, particularly children, but they are not a cure.
Strain matters. ‘Probiotics’ is not one thing. Lactobacillus rhamnosus GG, Lactobacillus reuteri and certain Bifidobacterium strains have the most evidence behind them for skin outcomes.

So when my OB told me to take probiotics during my second and third pregnancies, the science behind it was the maternal-microbiome-to-baby transfer pathway. The bacteria that colonise a baby’s gut in the first months of life come largely from mum. If mum’s gut is in better shape, baby’s gut microbiome tends to start in better shape too. The probiotics were predominantly for the babies, not for me.

I didn’t take probiotics with my eldest. She has chronic eczema today. My two younger kids, both born after probiotic pregnancies, have eczema that flares but less often and less severely. That’s an n of three in one family. It would never pass as evidence on its own. But it is consistent with the published trials, and it’s a pattern I think about every day.

The science is still evolving. New trials may sharpen or soften the effect size we currently see. If you’re pregnant or planning to be, talk to your GP, obstetrician or a microbiome-aware dietitian or naturopath about whether perinatal probiotics make sense for you.

What I’d change if I could rewind

If I could give my younger self one piece of advice, it would be: stop looking only at the rash. Look at the whole system. The skin is a window into what’s happening inside.

Things I now know matter for the gut-skin axis:

Fibre diversity. Try to eat 30 different plant foods a week. Different fibres feed different bacteria.
Fermented foods. Yoghurt with live cultures, kefir, sauerkraut, kimchi, kombucha. A small amount most days.
Sleep. The gut microbiome has its own circadian rhythm. Wrecked sleep wrecks the gut.
Stress. Chronic stress changes gut motility and microbial composition. Easier said than fixed, I know.
Antibiotics. Sometimes essential, but every course is a reset of the gut microbiome. Discuss with your GP whether probiotics during and after a course make sense for you.
Skip the wellness fads. Activated charcoal, restrictive ‘gut cleanses’ and parasite protocols are not the answer. Fibre, sleep, ferments and patience are.

Coming soon: I’m putting together a free Skin-ED Trigger Journal to help you spot patterns between food, stress, sleep, weather and flares. The microbiome piece is invisible, but its downstream effects on skin are often very visible. The journal will help you connect the dots. Keep an eye on the Skin-ED blog for the launch, or drop me a line and I’ll send it through when it’s ready.

How this shaped Salvida

Once I understood how much of the eczema story was happening inside the body, I made peace with something. Skincare alone will never fix gut dysbiosis. But here’s the flip side, and this is why I keep going.

Inflammation is bi-directional. When the skin is in a constant low-grade flare, the body is releasing inflammatory signals that can also worsen gut inflammation (that’s the focus of my companion article). So calming the skin from the outside is not vanity. It’s part of the system reset.

I designed Salvida with that in mind:

Barrier NPR+ balm is for the worst patches, the ones that won’t settle. It locks in moisture so the skin can stop losing water and start to calm and repair.
Bodyguard moisturising lotion is the daily layer. Fragrance-free, dye-free, essential-oil-free. The kind of moisturiser you can use on a six-month-old and a sixty-year-old without thinking about it.
Every Day Everywhere face and body wash is the one that swapped the foaming, fragranced wash that was making things worse with something that wouldn’t strip the skin.

None of these products fix the gut. Nothing topical can. But they remove one big source of irritation while you work on the inside, so your skin and your microbiome both get a chance to settle.

What I’d read next

One last thing

I’m not a doctor, a dietitian or a microbiologist. I’m an Aussie mum who has lived with eczema since I was little, who watched it return during pregnancy, and who has spent the last few years reading everything I can find about why this all happens. I made Salvida because I wanted products I could trust to use on my own family while I worked on everything else.

If you’re standing in the chemist holding a probiotic bottle and wondering ‘is this actually going to do anything?’, I get it. I’ve been there. Send me a message any time. I read every email and DM.

Jacqui x

Shop Barrier NPR+ | Shop Bodyguard | Shop Every Day Everywhere | Read more on Skin-ED

FAQs

Can a healthy gut really fix eczema?

Not on its own. Eczema is a complex condition involving genetics, the skin barrier, the immune system and the microbiome. A healthier gut microbiome can reduce flares for some people and may reduce the risk of eczema in babies when the mother takes probiotics in late pregnancy, but it is not a stand-alone cure. Think of gut health as one important lever among several.

What’s the best probiotic for skin?

The strains with the most peer-reviewed evidence for skin outcomes are Lactobacillus rhamnosus GG, Lactobacillus reuteri and certain Bifidobacterium strains. The best probiotic for you depends on your situation. I’d suggest talking to your GP, a dietitian or a naturopath who specialises in the microbiome rather than picking the loudest bottle on the chemist shelf.

Does diet really change my skin?

Yes, although usually slowly. Fibre diversity, fermented foods and lower ultra-processed food intake have the most consistent links to microbial diversity. Don’t expect a result in a week. The microbiome shifts over weeks to months, not days.

Are antibiotics bad for skin?

Antibiotics save lives, so they are not ‘bad’. But every course flattens gut diversity for weeks to months. If your skin tends to flare after antibiotics, that pattern is consistent with the gut-skin axis. Talk to your GP about whether probiotic support during and after a course is appropriate.

Why do babies born by caesarean section have higher eczema rates?

Vaginal birth seeds a baby’s gut with the mother’s bacteria. Caesarean birth changes that initial seeding. Several studies have linked caesarean delivery to a slightly higher risk of allergic conditions including eczema, although it’s just one of many factors. If your baby was born by C-section, please don’t catastrophise. There’s a lot you can do later that matters more.

Do prebiotics help skin?

Prebiotics are the fibres that feed your good bacteria. Foods like garlic, onion, leek, banana, oats, legumes, asparagus and resistant starches. There’s reasonable evidence that prebiotic-rich diets support a more diverse microbiome, which is linked to calmer skin. They tend to work better than supplements for most people.

Should I get a microbiome test?

Honestly, the consumer-level microbiome tests are not yet reliable enough to base big decisions on. They can be a fun snapshot, but the technology and reference ranges are still maturing. Save your money for fibre, ferments and sleep.

Eczema + Problem Skin ConditionsJun 5, 202611 min read

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