For a long time, the large intestine was seen as little more than a waste-processing unit—an organ that prepared undigested food residues for elimination. We knew microbes lived there, but most of them could not be cultured (that is, grown in a lab), so they remained a mystery. Back then, gut health was judged by simple indicators such as regular bowel movements (anywhere from three times a day to once every three days) and appropriate stool consistency (not too hard, not too loose).
Everything changed with the arrival of new technologies that allowed us to identify microbes without having to grow them in a lab. Suddenly, the gut and its microbes became one of the most fascinating organs to study. Scientists realised that these microorganisms were interconnected with gut health and overall health in multiple ways. Today, we not only know which microbes are there (at least, the vast majority), but we’ve also learned a lot about what they do, and how they influence our digestion, immunity and even mental health.
A thriving gut community
The community of microorganisms in the gut behaves like an ecosystem. Think of your gut microbes like a rainforest. Just like a rainforest is home to a wide variety of trees, plants, animals, and microbes, your gut hosts trillions of microorganisms—bacteria, fungi, and viruses. These species don’t live in isolation; they interact, compete, and cooperate, forming a complex web of relationships. When the ecosystem is balanced, it supports the health of the whole forest. Similarly, a balanced gut microbiota helps digest food, produces vitamins, and protects against harmful invaders. If something disrupts this balance—like antibiotics or poor diet—it’s like cutting down trees in the rainforest: the entire system suffers.
The measurement dilemma
Here is the challenge: it remains very difficult to describe how such a balanced ecosystem in our gut should look like. There is no universal healthy microbiome; each person’s microbial community is unique, like a fingerprint. Although it has become feasible to analyse someone’s microbiota composition, we cannot say with certainty whether it is in good shape or not.
One idea is to look at what bacteria do, rather than who they are. Microbes produce a wide variety of metabolites, small molecules that can enter the bloodstream and influence organs like the liver or even the brain. These metabolites can be quantified in bodily samples like plasma or feces. Some of them are presumably beneficial for our health whereas others might be rather detrimental. Measuring profiles of metabolites in blood or stools might theoretically give clues about gut health. But here is where it gets complicated, these metabolite profiles not only depend on which microbes are present in your gut but also on what you eat and how you feed your bacteria. If you do not feed your bacteria the right food (think fiber-rich products), they will not be able to produce beneficial metabolites. Other factors, like when exactly the biological sample has been collected and how fast food moves through your gut, also play a role. Therefore, metabolite profiles may be helpful, but are far from perfect.
Attributes of a healthy gut microbiome
Researchers often describe a healthy gut microbiome through a number of key traits. First, it should be highly diverse – meaning that it contains many different species living together. Second, it needs resilience – the ability to recover quickly and completely after a perturbation (such as a course of antibiotics). Third, a healthy microbiome shows functional redundancy – which means that multiple species within the ecosystem can perform the same tasks, so that the system keeps working even if some species disappear. Finally, it should have metabolic flexibility, meaning that the microbes are capable of metabolising different food sources and adapting when the diet or environment changes. In this way, microorganisms are able to survive when nutrient availability changes.
As an individual, you cannot easily measure these traits in your gut microbiome. These qualities require tracking changes over time and multi-layered data rather than an static snapshot of species present. Scientists are working toward tools that combine microbiome data with metabolic and functional insights to create reliable ways to measure gut health.
However, if your digestion feels comfortable, your energy levels and immune health are good, you tolerate fiber and a variety of foods, and you live a healthy lifestyle (good sleep, moderate stress, regular exercise, healthy diet, no unnecessary antibiotics), your gut microbiome is very likely to be in good shape. You can implement these general, practical principles backed by microbiome research to date, helping you take care of your gut microbiome.
