What 3 Foods Are Bad for Your Gut?

The Worst Foods for Gut Health, and Diets That Help

What you eat has so much impact on your gut and overall health that the effects cannot be overestimated. Food can help or harm your gut microbiome — the huge collection of bacteria, yeasts and other microbes in your gut that influences everything from your immune system to your mental health. 

The full overview of your diet is by far more important than worrying about specific “superfoods” or occasional missteps in your diet.

In this article we’ll consider specifically what 3 foods are bad for your gut flora and gut health and also take a broad look at the foods and dietary patterns that help or harm wider gut and general health.

what 3 foods are bad for your gut: Various healthy food ingredients

A Healthy Gut Diet Is Highly Individual 

Before we go into the foods that are bad for pretty much everyone, it’s worth mentioning that the diet that keeps your gut healthy may not work for someone else. 

Though a general principle applies that eating unprocessed, real food and including plenty of veggies brings health benefits, there is much variation within this. 

For example, while one person may be able to consume dairy products or gluten without any gut issues, in other people, these foods can trigger irritable bowel syndrome (IBS) [1 Trusted SourcePubMedGo to source, 2 Trusted SourcePubMedGo to source].

Over time, the foods you may be sensitive to and that can cause inflammation in your digestive tract can change. They’ll also be different for different people.

In particular, prebiotic food and supplements (fibers that can feed friendly bacteria) are often touted for their gut health benefits. But for people who have imbalances like small intestinal bacterial overgrowth (SIBO), they can actually be problematic as they can also feed the wrong sort of bacteria.

A study that looked at giving prebiotics while treating SIBO with antibiotics found that they were less effective than giving probiotics with antibiotics [3 Trusted SourcePubMedGo to source]. 

Why Ultra-Processed Foods Are Bad for Everybody

Ultra-processed foods can be defined as those that are made “hyper-palatable” through the use of chemicals that add color, flavor, and texture. This processing generally increases the caloric density and flavor intensity of the food while stripping away the fiber, vitamins, and nutrients [4]. 

Many foods are processed (even natural yogurt and whole grain bread), but ultra-processed foods are on a different level in terms of how far they are removed from their “whole” state.

But, there’s a more specific problem — a diet rich in ultra-processed foods has been linked in several studies with reduction in the diversity and health of the gut microbiota, leading to inflammation [5 Trusted SourcePubMedGo to source, 6 Trusted SourcePubMedGo to source, 7 Trusted SourcePubMedGo to source].

The consumption of ultra processed foods is associated with: 

What 3 Foods Are Bad for Your Gut?

If we were to pick the absolute three worst foods for your health, particularly your gastrointestinal and gut bacteria health, what would they be? 

There are a number of candidates for this dubious “prize,” but three that score badly time and time again according to scientific evidence are: 

The first two of these are regularly present in processed and ultra-processed foods, while alcohol is something of a double-edged sword. Small amounts can be neutral or arguably even beneficial, but large amounts can cause great harm to your digestive health and general health.

Let’s look at these three more closely:

1. Added Sugar/Refined Carbohydrates

The issue with added sugar and refined carbohydrates (e.g. white flour, white rice, chips, cookies, and fries) is they provide virtually no nutritional value while also actively harming the beneficial bacteria in your gut. For example, research shows that added sugar and carbohydrates can:

  • Disrupt the gut microbiome. Higher intakes of carbohydrates (sugary beverages, bread, beer, snacks made of refined grains, starch, and added sugar) feed bad bacteria and reduce overall microbiome diversity [17 Trusted SourcePubMedGo to source].
  • Trigger IBS symptoms. A diet high in added sugars, along with processed foods, alcohol, and poor quality fats, can aggravate IBS symptoms [18 Trusted SourcePubMedGo to source].
  • Encourage bacterial and fungal overgrowths. Diets high in carbohydrates and sugar are linked to higher levels of Candida fungus and methane-producing microbes that are typically found in IBS-C (constipation) patients [17 Trusted SourcePubMedGo to source].
  • Cause inflammation. Sugar directly spikes inflammation levels. In a small human study, a 50-gram dose of fructose caused a spike in inflammatory markers within half an hour [19].
  • Throw off blood sugar balance. Diets that are heavy on refined carbs and sugar can raise blood sugar and create a vicious circle of insulin resistance and /or obesity, gut bacteria imbalance (dysbiosis), and inflammation (as illustrated in the infographic below) [20 Trusted SourcePubMedGo to source].
what 3 foods are bad for your gut: Illustration showing the effects of refined carbs on blood sugar

How Much Sugar Is Too Much?

There aren’t hard and fast rules as to what level of carbs and sugars you can tolerate, as it depends on what sort of shape your gut health is in. The section below gives some guidance on choosing a balanced diet that will support your gut health and healing.

The World Health Organization suggests we should get less than 5% of our energy intake from added sugars [21]. U.S. guidelines are more lenient at less than 10% of energy intake [22]. However I’d caution against eating any sugary foods, especially those with added sugars, while you are in the early stages of trying to calm inflammation and bacteria imbalances in your gut.

2. Additives

Additives are chemicals added to foods to help preserve it and prevent food poisoning but also to create texture, hold in moisture, add color, and generally make processed food seem more appealing.

A growing amount of research in animals and some in humans, suggests that too many additives should be avoided, as they can cause gut bacteria imbalances that impact our health. For example, research has found that: 

  • 2019 research at Australia’s Sydney University found that titanium dioxide, used as a food color, affected gut bacteria activity and promoted undesirable biofilms (bacteria that stick together), which could lead to diseases such as inflammatory bowel diseases and colorectal cancer [23 Trusted SourcePubMedGo to source].
  • In mice, the emulsifiers carboxymethylcellulose and polysorbate 80 created dysbiosis and overgrowth of mucus-degrading bacteria (potentially leading to increased intestinal permeability or a leaky gut) [24 Trusted SourcePubMedGo to source, 25 Trusted SourcePubMedGo to source].
  • In another mouse study, polysorbate 80 and carboxymethylcellulose also induced
    • Low-grade inflammation
    • Obesity
    • Metabolic syndrome (obesity combined with high blood sugar, high blood pressure, and high cholesterol)
    • Colitis in animals predisposed to this disorder [26].
  • The artificial sweeteners saccharin, aspartame, sucralose, and aspartame have variously been linked with alterations in gut bacteria and the metabolites that they produce as well as an uptick in intestinal and liver inflammation [27 Trusted SourcePubMedGo to source, 28, 29, 30]

How Many Additives Are Too Many?

Although, individually, additives must be proven non-toxic for humans [31] few studies have been done on humans consuming several additives together. It makes sense to minimize your intake of them. For people with robust gut health, a few additive-containing ultra-processed foods won’t do any harm, but cutting them out as strictly as you can when your gut health is poor could pay dividends. 

3. Alcohol

what 3 foods are bad for your gut: Different types of alcoholic drinks in bottles and glasses

There’s no reason why most people can’t enjoy a drink in moderation. According to the American Heart Association a modest amount of alcohol can increase HDL (good) cholesterol, while some drinks, such as red wine, contain healthy antioxidants [32]. But alcohol is bad news for gut health when it’s consumed in excess, or if you currently have a sensitive gut. 

Here are the main reasons why we’ve included it as one of the worst foods for your gut:

  • Too much alcohol disrupts the production of digestive enzymes, so your gut will be less likely to efficiently break down, digest, and absorb nutrients from your food [33].
  • A high alcohol consumption can cause inflammation in your gut, increasing the chance that your gut could become permeable (or “leaky”). Leaky guts can allow undigested food particles, bacteria or allergens into the bloodstream, stimulating autoimmune conditions [33].
  • Like sugar and additives, long-term alcohol consumption also can cause health changes in the composition of the gut microbiome, or gut dysbiosis [33, 34 Trusted SourcePubMedGo to source].

How Much Alcohol Is Too Much?

The 2020-2025 Dietary Guidelines for Americans say that for adults, the maximum recommended amount is no more than two drinks a day for men or one drink or less a day for women (pregnant and breastfeeding women should avoid it completely) [35].

However this is for people with good gut health — it’s a good idea to largely stay away from alcohol while addressing gut health problems, though a little when you’re socializing with friends is fine!

Balancing Diet Variety and Potential Sensitivities

You may have heard that the wider variety of foods you eat, the better for your microbiome. For example, the American Gut Study found that people regularly eating more than 30 different types of plant foods each week had a significantly more diverse microbiome than those eating 10 or fewer different plant foods a week [36]. 

While eating a wide variety of foods is ideal, you may find it hard to tolerate if you’re dealing with an imbalance, infection, or overgrowth in your gut. Still, as you heal, you should be able to increase your dietary variety over time. 

What’s the Best Healthy Gut Diet? 

The diet that works best for resolving your own gut-related symptoms will be personal to you. But there are common goals for a new diet:

  • Feed good gut bacteria and correct imbalances in your microbiome
  • Reduce gut and systemic inflammation
  • Identify and eliminate foods you may be sensitive to, which could worsen your symptoms

I’d always advise starting with the least restrictive diet and only cutting out foods if and when you need to.

The Paleo Diet 

For many people, a Paleo-style diet works well to improve gut health and is generally a good healthy eating plan to start with. 

Paleo regimens provide whole, unprocessed foods and a variety of healthy plant foods and lean protein. But they minimize or remove gluten-containing grains, and dairy, which are two of the most common food intolerances that could be adding to your gut health woes. Research has shown that the Paleo diet can help to calm inflammation by minimizing your exposure to foods that provoke an immune response [37 Trusted SourcePubMedGo to source]. 

what 3 foods are bad for your gut: Chart showing what and what not to eat on the Paleo diet


If a Paleo diet doesn’t alleviate symptoms after a week or two, you might want to try a low FODMAP diet. The low FODMAP diet helps to reduce bacterial overgrowth by temporarily cutting out fermentable carbs and natural sugars (such as those in legumes, dairy, onions, honey and wheat). It has scientifically validated benefits for:

Microbiome Superfoods and Supplements

While it may seem we’ve focused a lot on the foods that you might not be able to eat, there are also many gut-friendly foods that can be added into your diet for a gut health boost.

Fermented Foods

For example, you can support your gut health with a variety of fermented foods that have mildly probiotic actions. These include:

  • Kimchi
  • Kombucha
  • Kefir and natural live yogurt (most of the lactose in these is converted into lactic acid, but still take care if you are highly dairy intolerant)
  • Tempeh and miso (if no soya allergy)
  • Sauerkraut

There’s an important caveat to note here however  — though fermented foods are great for most people, they can be problematic for those with histamine intolerance. If you have or suspect you may have histamine intolerance, go carefully.


Polyphenols found in several colorful plant foods are also very gut friendly and safe to eat for most people. While they are not in themselves probiotics, they are still microbiome-friendly foods that encourage beneficial bacteria while discouraging bad bacteria (such as Clostridium species, Staphylococcus and Salmonella) [45 Trusted SourcePubMedGo to source, 46 Trusted SourcePubMedGo to source].

Polyphenol-rich foods include:

  • Berries of all types
  • Black and green tea
  • Red and black grapes 
  • Spinach and other darky leafy greens
  • Cocoa and high-cocoa (low-sugar) chocolate

Probiotic Supplements

Infographic detailing how probiotics work

For the most powerful benefits, probiotic supplements will bring better results than probiotic foods (given their much higher concentrations of bacteria). Research shows that effective probiotic supplements can: 

I’ve seen the best results with my patients when they combine Lactobacillus and Bifidobacteria blends with Saccharomyces boulardii (a beneficial yeast) and soil-based probiotics (usually Bacillus species). This trio usually gives optimal results and the best symptom relief. In IBS, for example, systematic reviews and meta-analyses have shown a multistrain probiotic approach is best [55 Trusted SourcePubMedGo to source, 56 Trusted SourcePubMedGo to source].

The Bottom Line

Eating too many sugary and additive-laden processed foods and drinking too much alcohol is bad for virtually any person’s gut. Fresh, whole, unprocessed foods and probiotics are good for almost all. 

Beyond that, a gut healthy diet is personal to you and the food that your system can tolerate. Listen to your body and find out what works for you.

Working with a functional health specialist can help resolve more complicated gut issues, so reach out to me or someone else on my team if you need further, personalised support.

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