The one thing runners never track (and probably should)

You’ve done the training plan. You’ve got the shoes. But your 5K time is stuck, and your gut may be the reason.

Not your gut feeling. Your actual gut, which, it turns out, scientists now think plays a much bigger role in how your muscles perform than anyone realised. They have a name for it: the gut–muscle axis. And it might be the most underrated topic in recreational running.

So what is the gut–muscle axis, exactly?

Think of your gut and your muscles as being in a constant back-and-forth. Your gut bacteria do not just handle digestion, they produce compounds that travel through your body and appear to play a role in how your muscles work.

When gut bacteria break down fibre from food, they produce molecules that researchers believe act as both fuel and signals for muscle cells. The more fibre-munching bacteria you have, the more of these molecules are available and early research suggests this could matter for how your body responds to training.

The science is still developing, but the direction is clear: your gut is involved in a lot more than just what happens in the bathroom.

The stool sample that changed sports science

Here’s where things get properly interesting. In 2019, researchers studying Boston Marathon runners found something unexpected in their post-race stool samples.

Elite marathon runners had significantly higher levels of a bacterium called Veillonella compared to sedentary people. What makes this bacteria interesting is what it does: it appears to take lactate, the thing that makes your legs feel like concrete near the end of a hard run, and convert it into something muscles might be able to use again.

What actually helps

If you’re running regularly, here’s what the research currently points toward:

Eat more plants, more variety. Your gut bacteria eat fibre. The more diverse your plant intake, legumes, oats, garlic, leeks, onions, loads of veg, the more diverse your microbiome tends to be. Diversity seems to be what matters most.

Don’t chronically under-eat. Fuelling properly isn’t just about energy on the run, it also matters for what’s happening in your gut between runs.

Include fermented foods. Kefir, kimchi, yoghurt, sauerkraut. The evidence around fermented foods and helps to build your gut diversity.

Respect recovery. The research suggests extreme or prolonged training without adequate recovery is suggested to be associated with gut stress.

Pay attention to what your gut is telling you. Bloating, urgency, cramping around runs, these aren’t just inconvenient. They’re your gut communicating. Tracking your digestive patterns consistently gives you something to actually work with, rather than just hoping race day goes better than last time.

Your gut is data. Most runners aren’t reading it.

Here’s the thing about training: most runners track everything except what’s actually happening inside them. Pace, distance, heart rate, sleep score, all logged. Gut? Completely ignored until it becomes a problem on race day.

But your digestive patterns are one of the most consistent signals your body produces. What’s happening in your gut before, during, and after a run reflects how well you’re fuelling, how your body is handling training load, how your recovery is going, and even how stressed you are. It’s all connected.

The runners who improve fastest aren’t always the ones training hardest. They’re often the ones who’ve figured out what their body is actually telling them and adjusted accordingly. Your gut is part of that conversation. Probably a bigger part than you’ve been giving it credit for.

Gut symptoms that show up consistently around training aren’t bad luck. They’re a pattern. And patterns, once you can see them, can be changed.

The short version

A faster 5K isn’t only about more miles. Researchers increasingly think gut health is part of the picture, how your body handles fatigue, responds to training, and even how motivated you feel to show up.

Most runners have never thought about any of this. That’s the gap.

Now you have.

Safe is boring. Gutsi is not.

Sources

Mohr AE et al. (2024). Physical Exercise and the Gut Microbiome: A Bidirectional Relationship Influencing Health and Performance. Nutrients, 16(21), 3663. https://doi.org/10.3390/nu16213663

Mailing LJ et al. (2025). Exercise, the Gut Microbiome and Gastrointestinal Diseases. Gastroenterology. https://doi.org/10.1053/j.gastro.2025.01.236

Scheiman J et al. (2019). Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. Nature Medicine, 25, 1104–1109.

Dohnalova L et al. (2022). A microbiome-dependent gut–brain pathway regulates motivation for exercise. Nature, 612, 739–747. https://doi.org/10.1038/s41586-022-05525-z

Martinez-Guryn K et al. (2025). The gut-muscle axis: a comprehensive review. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2025.1695448

Mach N, Fuster-Botella D. (2017). Endurance exercise and gut microbiota: A review. Journal of Sport and Health Science, 6(2), 179–197.