Gut dysbiosis: symptoms, causes and how to fix it

Author: Simone Jeffries
Qualified Naturopath | BHSc(N) | ANTA, BSSM

Last reviewed: July 7, 2026

We have billions of bacteria living in our digestive tract, tucked into the mucous membranes – a huge garden of microbes. We have evolved alongside these bacteria, they are essential to our health, and we cannot live without them.

A balanced gut microbiome matters for nearly every part of our health, and many fields – microbiology, neurobiology, immunology, nutrition – now recognise how much our microbes do for us. Gut bacteria ferment the food we eat, break down the fibres we cannot digest, and make extra nutrients in the process. Some researchers argue the microbiome should be treated as a vital organ.

Those microbes influence mood, energy, weight, clear thinking, immunity, skin, joints and how well you feel overall. When the balance tips, we can feel off. That imbalance is called dysbiosis.

Why does gut dysbiosis happen?

Gut flora can shift quickly^1,2, but dysbiosis usually builds up over time. The most common driver is a diet low in fruit and vegetables – the prebiotic fibre gut microbes feed on – so species and numbers dwindle. Gut bacteria thrive on fibrous fruits, vegetables, grains and beans.

Think of a garden. If the main plants are removed or struggling, weeds take over fast. The gut works the same way: disruptive microbes multiply when there is not enough competition to keep them in check.

Antibiotics are a big one – even a single course can sharply reduce gut diversity, and it does not always bounce back fully.⁵ Other things that can deplete or unbalance the microbiome include some medicines, sweeteners, laxatives, and preservatives and additives in processed food, along with very restrictive diets, ongoing stress, constipation or diarrhoea, and digestive tract infections.

How gut dysbiosis affects your health

Most often, dysbiosis shows up as digestive trouble – bloating, gas, diarrhoea and constipation. Plenty of other conditions can mimic it, though, so it is wise to have your symptoms checked by an experienced practitioner rather than assume.

The effects reach well beyond the gut, because we lean on these bacteria for so much.

Immunity and inflammation

Much of your immune system sits around the gut. When bacteria ferment fibre they make short-chain fatty acids, which help train and calm the immune system and keep inflammation in check. Lose the microbes that make them and that steadying influence drops away, which is one way dysbiosis is linked to inflammatory conditions.³

Mood and the gut–brain axis

The gut and brain are in constant two-way conversation, and gut microbes are part of it, helping produce and regulate chemicals that affect mood, stress and clear thinking. It is a big reason an unhappy gut can leave you feeling flat or frazzled.⁴

Metabolism, skin and more

Gut microbes also help make certain vitamins, antioxidants, fatty acids and neurotransmitters, and they influence how sensitive you are to insulin, how you handle fat, and how your skin behaves. When the community is off, any of these can wobble too.

The gut and the vaginal microbiome

There is a plausible link between the gut and the vagina, though the direct evidence is still emerging rather than settled. One of the clearest threads is oestrogen: a set of gut bacteria known as the estrobolome helps recycle oestrogen, and a low-diversity, dysbiotic gut can lower how much active oestrogen circulates.⁷ Oestrogen is what keeps vaginal tissue plump and feeds the protective bacteria there, so gut health and vaginal health are connected through hormones.

Researchers also describe a broader crosstalk between the gut and genital-tract microbiomes, partly through those same short-chain fatty acids and immune signals, but this is early-stage work and not yet something to draw firm clinical conclusions from.⁸ In practice, looking after the gut is a sensible part of looking after the whole system.

How to restore a healthy gut microbiome

The reassuring part is how responsive the gut is – helpful changes can begin within days of eating differently.¹ The broad strokes are simple, and they are worth doing before anything fancier.

Eat a wide variety of plants – fruits, vegetables, beans, grains, herbs and spices – so there is plenty of fibre to feed a diverse microbiome.²
Add fermented foods, which can increase microbial diversity and lower markers of inflammation.⁶
Consider a probiotic, matched to your situation.
Only use antibiotics when you really need them, and support your gut afterwards.
Look after sleep and stress, since both feed back into the gut.

If symptoms are ongoing or you are not sure what is driving them, a naturopath, herbalist or other experienced practitioner can put together an individualised plan – herbal medicine, food and targeted pre- and probiotics – rather than guesswork.

Getting support for gut dysbiosis

To work out what is going on, I will first test your microbiome using functional testing, microbiome mapping (GI Map), and if it is relevant, vaginal microbiome mapping. From there I use herbal medicine, food and pre- and probiotics to rebuild your gut microbiome and ease the uncomfortable symptoms.

If you are dealing with vaginal symptoms too, improving your overall microbiome often helps settle the vaginal one as well. Book an appointment here.

Frequently asked questions

What are the symptoms of gut dysbiosis?

Most commonly, digestive symptoms like bloating, gas, diarrhoea and constipation. Because the microbiome touches so much, it can also show up as low mood or energy, skin flare-ups, or feeling generally run down. Other conditions can look similar, so it is worth getting checked rather than self-diagnosing.

Can gut dysbiosis affect your vagina?

Possibly, mainly through oestrogen. Gut bacteria help recycle oestrogen, and a dysbiotic gut can lower how much circulates, which in turn affects the vaginal tissue and its protective bacteria. The direct gut–vagina evidence is still emerging, but supporting your gut is a reasonable part of caring for your vaginal health.

How do you fix gut dysbiosis?

Mostly by feeding a diverse microbiome: a wide range of plants and fibre, some fermented foods, sensible antibiotic use, and attention to sleep and stress. For stubborn or unclear cases, an experienced practitioner can test and tailor a plan rather than leaving it to trial and error.

This article is general information and not a substitute for personalised medical advice. If your symptoms are ongoing or you are worried about them, please see an experienced practitioner.

References

David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–563. https://pmc.ncbi.nlm.nih.gov/articles/PMC3957428/
Leeming ER, Johnson AJ, Spector TD, Le Roy CI. Effect of diet on the gut microbiota: rethinking intervention duration. Nutrients. 2019;11(12):2862. https://pmc.ncbi.nlm.nih.gov/articles/PMC6950569/
Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16(6):341–352. https://www.nature.com/articles/nri.2016.42
Cryan JF, O’Riordan KJ, Cowan CSM, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99(4):1877–2013. https://journals.physiology.org/doi/full/10.1152/physrev.00018.2018
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4554–4561. https://pubmed.ncbi.nlm.nih.gov/20847294/
Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137–4153.e14. https://pubmed.ncbi.nlm.nih.gov/34256014/
Baker JM, Al-Nakkash L, Herbst-Kralovetz MM. Estrogen–gut microbiome axis: physiological and clinical implications. Maturitas. 2017;103:45–53. https://pubmed.ncbi.nlm.nih.gov/28778332/
Amabebe E, Anumba DOC. Female gut and genital tract microbiota-induced crosstalk and differential effects of short-chain fatty acids on immune sequelae. Front Immunol. 2020;11:2184. https://pmc.ncbi.nlm.nih.gov/articles/PMC7511578/