6 Signs of Gut Imbalance

Signs of gut imbalance can show up well beyond digestion, as cravings you cannot explain, skin that flares, catching every cold going round, aching joints or a flat mood. Researchers call this state dysbiosis, and most of what links it to those signs comes from studies that found an association rather than a cause.

If you are eating reasonably well, sleeping when you can and still feel off in ways nobody can quite explain, this is a reasonable place to look.

What is gut imbalance, and why does it matter?

Gut imbalance means the community of bacteria living in your gut has shifted in a way that is associated with poorer health. Researchers call it dysbiosis. It is rarely about one bad bacterium. Most of the organisms involved live in healthy guts too, and what changes is the balance between them.

Your gut microbiome balance matters because your gut bacteria are not passengers. They break down parts of your food that your own body cannot, and the compounds they produce in the process travel well beyond the gut. When the community that makes those compounds shifts, the signals it sends shift too.

At the moment, there is no single measure of a balanced gut, and no bacterial profile that counts as healthy for everyone because everyone’s gut microbiome is different. Instead, a useful definition of a dysbiotic gut is one when, compared with healthy people, it has lost some of the bacteria associated with good health, has more of the bacteria that can cause harm when they overgrow (which researchers call pathobionts), or has less variety overall. The three can happen at the same time.[1] Healthy guts also differ a great deal from one person to the next, so what counts as balanced depends on who you are compared with.[2] The most useful reference points are people who live and eat much like you, and your own gut over time.

How does your gut affect the rest of your body?

The bacteria in your gut microbiome affect the rest of your body mostly indirectly, by making compounds that act as signals. Some act on the gut lining and the cells around it, and some are absorbed into your blood and carried to your liver and the rest of your body. Three groups of compounds carry most of that traffic.

• Short-chain fatty acids. Made when gut bacteria ferment the fibre your own body cannot digest. Butyrate, one of them, is the main fuel for the cells lining your colon, so most of it is used where it is made. Acetate, another, passes into the blood in the largest amounts and reaches tissues around the body.[3] These compounds also act on immune cells and prompt gut cells to release hormones involved in appetite and blood sugar.[4][5]
• Secondary bile acids. Your liver makes bile acids to help digest fat, and gut bacteria reshape them into different forms. Most are reabsorbed and carried back to the liver. Those altered forms act as signals in how your body handles fat and glucose.[6]
• Tryptophan metabolites. Made from an amino acid in your food. They act on the gut lining and on immune cells. Some are also absorbed and can be measured in the blood.[7]

There is also a direct line. The vagus nerve runs from the gut to the brainstem, and signals from gut cells and from these compounds travel along it.[8] So the gut has both a chemical route, through the bloodstream, and a nerve route to the brain.

This is why a change in the gut community can show up somewhere that has nothing obviously to do with digestion.

What are the signs of gut imbalance beyond digestion?

Six signs of gut imbalance, or dysbiosis, come up most often in research. They are cravings, skin flare-ups, frequent infections, weight that will not shift, aching joints, and low mood, tiredness or poor sleep. None of them is specific to the gut, and each is described below with what has actually been studied.

Cravings you find hard to control

Appetite is partly regulated by hormones your gut releases, and short-chain fatty acids from fibre are one of the things that prompt their release. Two of those hormones, GLP-1 and PYY, signal fullness.[5]

What this does not show is that your gut bacteria are causing a particular craving. Sleep, stress, how much protein and fibre you eat and simple habit all shape appetite too, and most of them are easier to change.

Skin that flares up

Researchers describe a two-way relationship between the gut and the skin, often called the gut-skin axis, and differences in gut bacteria have been found in people with conditions such as eczema, acne and psoriasis.[9]

These are observed differences rather than evidence that changing your gut clears your skin. If you have a persistent skin condition, it is worth seeing a doctor about it directly rather than treating it through diet alone.

Catching every bug going round

Immune cells in and around the gut wall are in constant contact with gut bacteria, and short-chain fatty acids are involved in keeping immune responses proportionate.[4]

How often you fall ill depends on far more than this, including how much you are around other people, your sleep, your stress and your vaccination history.

Weight that will not shift

Differences in gut bacteria have been found between people of different body weights.[10] In a study of 21 lean and obese adults whose calorie intake was changed under close monitoring, shifts in gut bacteria were linked to how much energy the lean participants absorbed from their food.[11] In another of 800 people, gut bacteria helped predict how far blood sugar rose after a meal.[12] This is the sign with the most research behind it and also the most tangled, because weight affects the gut community as well as the other way round.[13]

Joints that ache

Gut bacteria have been studied as a possible contributor to osteoarthritis, through low-grade inflammation that affects joint tissue. The mechanism is proposed rather than established, and the work is mostly in animals and in observational human studies.[14]

Low mood, tiredness or poor sleep

The gut and the brain are in constant two-way contact, and differences in gut bacteria have been found in people with depression[15] and with poor sleep.[16] The signalling runs along the vagus nerve, through immune pathways and through short-chain fatty acids.[8]

One correction worth making, because it appears nearly everywhere. Most of the body’s serotonin is made in the gut, but that serotonin does not cross into the brain, so it is not the explanation for how gut bacteria affect mood. Gut serotonin works mainly where it is made, helping to control how food moves through your intestines. What gut bacteria do influence is how much tryptophan, the raw material the brain uses to make its own serotonin, is available.[17]

Mood, tiredness and sleep also have many causes that have nothing to do with the gut, and they are worth talking to a doctor about in their own right.

What causes gut imbalance?

Most of what shifts the gut community is ordinary, and several of the causes are things you have some control over.

• Antibiotics. The clearest cause. In a study of twelve healthy men given a deliberately severe four-day course of three last-resort antibiotics, the gut community returned to near its starting composition within about six weeks, but nine species that every man carried beforehand were still undetectable in most of them six months later.[18] Antibiotics are often necessary. The point is that they are worth taking when they are needed rather than routinely.
• A diet low in fibre and variety. Gut bacteria that make short-chain fatty acids depend on fibre from plants. Diet shifts the community quickly, within a day of a big change reaching the colon.[19]
• Some medicines taken long term. Proton pump inhibitors, the medicines that reduce stomach acid, are one example. In an analysis of 1,815 people, those taking them had less varied gut communities, with differences across about a fifth of the bacterial groups measured.[20] This is an association found at one point in time, and it is a reason to review a long-standing prescription with your doctor rather than to stop one.
• Alcohol. Heavy drinking is associated with changes in the gut community and with a less well-sealed gut lining.[21]
• Poor sleep and sustained stress. Both are associated with changes in gut bacteria, and the relationship runs in both directions.[8][16]
• Gut infections. In a study of 99 people who had Campylobacter food poisoning, the 22 who still had bowel symptoms afterwards had less varied gut bacteria than those who recovered, and the differences were still there two months after the infection.[22]
• Ageing. The gut community tends to become less varied with age, though how much varies a great deal between people.[8][23]

How can you improve or maintain gut balance?

The changes with the best human evidence behind them are unglamorous and mostly about food. Here is what the research supports, and where it is weaker than people assume.

Eat fibre from a wide range of plants. People who eat a wider range of plant foods tend to have more varied gut bacteria, although that finding comes from observational data.[24] In a 17-week Stanford trial of 36 healthy adults, the group that ate more fermented food increased the variety of their gut bacteria and showed falls in inflammatory markers in the blood. The group that ate more fibre did not increase their diversity over the same period, although their gut bacteria did gain more of the enzymes that break fibre down, and their response depended on what their gut looked like to start with.[25] Fibre is still worth eating, for reasons beyond diversity. The finding is that fibre alone, over a few months, is not enough to broaden the community.

Add a daily serving of fermented food. In the same trial, larger servings had stronger effects. Yoghurt, kefir, kimchi, unpasteurised sauerkraut and kombucha are common options. Fermented foods that have not been cooked or pasteurised contain live microbes, which is not the same as containing probiotics, a term reserved for strains shown to give a specific health benefit.[26]

Keep moving and protect your sleep. Both are associated with gut composition, although the evidence is weaker than for diet.[16][27]

A word on probiotic supplements, which is where most people start. The evidence is strain-specific rather than general, meaning a result for one strain does not transfer to another.[26] Whether a strain settles in your gut also varies from person to person. In a study that sampled the gut lining directly, an 11-strain probiotic took hold in some people and was resisted in others, and its effect on the gut community was short-lived.[28] The same applies to every probiotic, AMILI’s included. A strain does not have to settle to do something useful as it passes through, but it does mean a probiotic is a habit rather than a fix.

If you are starting somewhere, start with one serving of fermented food a day and one new plant food a week. Both are small enough to keep up, and keeping it up is what matters.

Why these signs are hard to pin on your gut

Every sign in this article has several possible causes, and the gut is only one of them. Tiredness, low mood, skin flare-ups and aching joints all have more common explanations that are worth ruling out first, which is a job for a doctor rather than a reading list.

Some symptoms should send you to a doctor before you do anything else. Blood in the stool, unexplained weight loss, a persistent change in bowel habit, difficulty swallowing or iron deficiency without an explanation all need to be looked at properly.[29]

The useful move, once that is covered, is to stop guessing from symptoms. A gut microbiome test shows which bacteria are actually in your gut and how varied the community is, read against people living in Asia rather than a Western average. It is not a diagnosis, and it does not tell you that your gut is behind any particular symptom. What it gives you is a starting point of your own, so that when you change something you can see whether anything moved.