The Microbiome: What We Actually Know

When I first began working as a gut‑focused dietitian, my sessions with newly diagnosed coeliac clients centred on one goal; helping them feel confident and safe living a gluten‑free life. With my Crohn’s disease clients, my focus shifted to understanding fibre tolerance during flares and remission, while protecting overall nutrition. Over time, I realised something important was missing and that was a conversation about what a ‘healthy gut’ actually looks like when you are living with coeliac disease or Crohn’s disease.

Gut health has become one of the most talked about topics in nutrition, and also one of the most misunderstood. Between gut detoxes, miracle probiotics, and microbiome tests promising personalised answers, it is easy to feel overwhelmed. The truth is that the real science of the microbiome is far more grounded and far more interesting than the noise online.

One of the biggest misconceptions is that there is a single “perfect” microbiome we should all aim for. Your microbiome is shaped by your birth, environment, diet, medications, stress, geography, and health conditions. Two people can have completely different microbial communities and still be equally healthy, including those with coeliac disease or Crohn’s.

The idea of “good” and “bad” bacteria also oversimplifies things. Microbes do not operate in neat categories. Many “beneficial” bacteria can cause issues in certain contexts, and some that sound concerning can live harmlessly in healthy people. What matters is the environment they are living in. Inflammation, diet, medications, motility, and immune activity all influence how microbes behave. It is less about who is there and more about what they are doing; to put it simply.

In present times, function matters more than species. Different microbes can perform the same job, much like different employees can fill the same role in a workplace. Even if two people have very different microbial species, their microbiomes can still carry out similar tasks. This is why trying to “boost” one specific bacterium is rarely helpful. What matters is the overall functional capacity such as digestion, fermentation, immune support, and barrier protection The factor that shapes microbial function more than anything else is diet.

It is also important to remember that gut health is more than microbes. The gut barrier, immune system, liver, nervous system, and diet all interact with the microbiome in a tightly connected network. A healthy gut depends on an intact barrier, balanced immune activity, efficient digestion, microbial stability, metabolic regulation, and lifestyle factors like sleep, stress, and movement. When one part of this system is under strain from inflammation, gluten exposure, a flare the others feel it. This is why gut health is not solved by a single food, supplement, or test; it is a whole‑body process.

Even with rapid advances in microbiome research, we still cannot look at someone’s stool sample and reliably predict disease risk or diagnose a condition. We can identify patterns and associations, but not certainties. Microbiome testing can offer interesting insights, but it is not a diagnostic tool and should not be treated like one.

Based on current evidence, a healthy microbiome tends to be functionally capable, resilient, balanced, low in inflammatory activity, and supported by a varied, fibre‑rich diet. But there is no single “ideal” profile and that is normal. For people living with coeliac disease or Crohn’s disease, gut health is not about chasing perfection. It is about understanding your body, supporting your microbiome through food and lifestyle, and working with the disease rather than against it.

Win a personalised “One Gentle Gut Step” To celebrate gut health month I am giving away a personalised, safe, evidence‑aligned gut tip tailored to your current phase (coeliac, Crohn’s flare, or remission). To enter, simply type GUT in the comments section. The winner will receive a tailored suggestion you can try this week.

References

Van Hul M, Cani PD, Petitfils C, et al What defines a healthy gut microbiome? Gut 2024.

Pecora F, Persico F, Gismondi P, et al Gut Microbiota in Celiac Disease: Is There Any Role for Probiotics? Front Immunol 2020.

Ma X, Lu X, Zhang W, et al Gut microbiota in the early stage of Crohn's disease has unique characteristics. Gut Pathog 2022.