Balancing Gut Health and Muscle Mass

Balancing gut health and muscle mass: what the science actually says

When we are aiming to build or maintain muscle mass, most people think they need to increase protein intake – but for many people, this comes with an unexpected side effect: bloating, sluggish digestion, or changes in bowel habits.

Sometimes these symptoms are compounded by embarrassing, rotten egg-y wind. As high protein diets and protein supplements become increasingly popular, a new 2026 review in Nature Reviews Gastroenterology & Hepatology sheds light on what actually happens to protein inside the gut, and how to support both muscle growth and digestive health.

What happens to protein in the gut?

Your small intestine is remarkably efficient at digesting and absorbing protein, but not always completely. Even in healthy adults, up to 20 grams of undigested protein makes its way into the colon each day, more if total protein intake is high or digestion is impaired.

Once in the colon, microbes ferment leftover protein and generate metabolites such as hydrogen sulfide, ammonia, phenols, and indoles. In small amounts, these may not be a problem, but in higher concentrations, they can irritate the gut lining, impair gut barrier function (leaky gut), and contribute to inflammation.

High-protein diets can stress the gut (as well as your kidneys)

Modern high-protein diets, especially those high in red or processed meat, tend to generate more sulphur and nitrogen-based metabolites. Observational studies have reported links between these compounds and increased ulcerative colitis flares or risk of colorectal cancer.

The issue isn’t necessarily the protein itself, but the combination of excess protein, type of protein and low fibre intake. Many high-protein diets unintentionally reduce fermentable carbohydrates and dietary fibre, which shifts gut microbes towards less favourable protein fermentation a far less favourable metabolic pathway.

But protein is important for muscle growth

Athletes and active individuals genuinely benefit from higher protein intakes. Research supports 1.4–2.0 g/kg of ideal bodyweight/day to optimise muscle protein synthesis, recovery, and training adaptations. Higher intakes don’t offer any added muscle benefits for
most people. The challenge is achieving these intakes without overwhelming the gut or altering the microbiome in unfavourable ways.

Protecting your gut while optimising muscle mass

The good news: you can absolutely fuel muscle growth without harming gut health.

1. Choose more digestible protein sources
   Choose fish or plant-based proteins instead of red and processed meats or heavily processed protein foods, which produce more harmful metabolites. Whey isolate, soy and pea protein isolates are efficiently absorbed and less likely to reach the colon.

2. Prioritise fermentable fibre
   Fibre, especially resistant starch, inulin, and FOS — diverts microbial metabolism away from protein and towards SCFA production. This protects the colon and improves microbial balance. Fibre is the buffer that makes high-protein diets gut-friendly.
3. Don’t cut carbs
   Many bodybuilding diets drastically cut carbs. This removes fibre and prebiotics, increasing proteolytic fermentation and its consequences
4. Spread protein evenly throughout the day
   Having some protein at each meal improves absorption efficiency and reduces colon “spillover.” A protein-carb snack immediately post training maximises muscle gain while preserving optimal balance of your gut bacteria
5. Keep plants on the plate
   Plant proteins naturally come with fibre and protective phytochemicals and produce fewer harmful metabolites when fermented. Even partial replacement of animal protein with plant sources improves fermentation patterns.

Here’s some ways to have the best of both:

• Whey or plant protein smoothie
• Overnight oats with yoghurt (or protein powder)
• Chia pudding with nuts or nut butter
• Baked beans (solo or on grain toast)
• Pearl barley salad with haloumi and herbs
• Potato salad with eggs and olive oil dressing
• Unripe banana pikelets (banana, oats, egg)
• Tofu and soba noodle salad
• Up and Go (low sugar)

Based on https://www.nature.com/articles/s41575-026-01173-0 (Nature Reviews
Gastroenterology & Hepatology, 2026)

Help Yourself Dietitians are all PhD qualified, ensuring evidence like this is matched to your
eating preferences and habits in an empathic and empowering way that suits your lifestyle.

Written by Dr Kerith Duncanson (APD, PhD)