What on Earth Is the Microbiome? (Explained as If We Were Having a Beer) 🍺

Imagine we’re sitting at a bar. You take a sip of your beer and ask:

“So, what exactly is the microbiome, and why does everyone keep talking about it?”

The shortest possible answer is this: you are not just you. You are you plus a huge community of microorganisms that live in and on your body. That includes bacteria, fungi, viruses, archaea, and others. All of them together, plus their genetic material, form what we call the microbiome.

Different parts of your body host different communities. The gut has its own “city” of microbes, the skin has another, and the vagina, mouth or lungs each host their own neighbourhood with their own rules. If you imagine your body as a country, the microbiome is the population: different regions, different customs, mostly peaceful coexistence, with the occasional troublemaker.

These Microbes Are Not Just Passing Through

The microbes that live with you are not temporary visitors that turn up randomly. You start acquiring them from birth, and they stay, adapt and change with you. You adapt to them as well, in a kind of long-term relationship: sometimes stable and balanced, sometimes a bit toxic.

When this relationship is in a good place, we talk about homeostasis: your immune system is reasonably calm, your gut works, and your tissues are not constantly inflamed. When that balance breaks, things get complicated. You might see more inflammation, changes in digestion, higher susceptibility to infections, or subtler shifts that we are still trying to fully understand.

What the Microbiome Does While You Drink Your Beer

While you’re relaxing, your microbiome is working quietly in the background.

One of its most obvious roles is in digestion. There are components in your food, especially certain types of fibre, that your own enzymes simply cannot break down. Microbes step in, digest those molecules, and in the process produce substances like short-chain fatty acids. These compounds help maintain the health of your gut lining and influence how your immune system behaves.

The microbiome also acts as a kind of training ground for your immune system. Your immune cells are constantly exposed to signals from these microbes and learn to distinguish between “this is part of normal life” and “this is a threat”. Without this constant education, the immune system would be much more likely to overreact to harmless stimuli or underreact to real dangers.

Another important role is competition with pathogens. When your resident microbes occupy the available space and resources, it becomes harder for harmful invaders to settle in and cause trouble. It’s similar to a bar that is already full of regulars: it is not so easy for a disruptive group to come in and take over the place.

On top of that, microbes produce a wide variety of molecules that can travel beyond the gut or the local tissue where they live. Some of these substances can reach the bloodstream and help shape inflammation, metabolism and, indirectly, the function of distant organs. This does not mean that your microbiome is “controlling your thoughts”, but it is clearly part of the web of signals that keeps your body running.

When the Balance Breaks

The mere presence of microbes is not the problem; the issue arises when the composition of the community shifts in an unfavourable way. This kind of imbalance is often referred to as dysbiosis.

Many factors can push your microbiome in that direction: repeated or inappropriate use of antibiotics, diets dominated by ultra-processed foods and low in fibre, chronic stress, lack of sleep, underlying diseases, hormonal changes and certain medications. When this happens, microbes that used to protect you may decrease, species that promote inflammation may become more abundant, and pathogens may find it easier to colonise your tissues. Your immune system might start reacting differently, either becoming too aggressive or not reactive enough.

In sensitive environments such as the gut, the vagina or the endometrium, these changes can have important consequences. They may influence how vulnerable someone is to particular infections, such as HIV, and how well certain preventive strategies, like vaginal rings for pre-exposure prophylaxis, actually work in real life.

Can You Actually “Fix” Your Microbiome?

People often hope for a simple answer here, something like a miracle probiotic that resets everything. Unfortunately, biology is rarely that kind.

There is no single “perfect microbiome” that everyone should aim for. Different individuals can be healthy with somewhat different microbial communities. What research does show is that certain patterns tend to be associated with better outcomes: for example, communities that support lower levels of chronic inflammation, or that are linked to better responses to specific treatments. Other patterns correlate with higher inflammation, greater susceptibility to infections or poorer treatment responses.

Still, some general principles seem to help many people: eating more varied, fibre-rich foods; relying less on highly processed products; avoiding unnecessary antibiotics; and maintaining basic habits like regular movement and decent sleep. These are not magical microbiome hacks, but they create conditions that tend to favour a more resilient and balanced community of microbes.

At the same time, it’s important not to turn the microbiome into a new form of superstition. Not every health issue can be blamed on it, and not every problem can be solved by “improving your microbiome”.

Why Scientists Care So Much About It

From the perspective of someone working in research, the microbiome is fascinating because it is relatively accessible and incredibly informative. We can sample it through stool, vaginal or skin swabs, respiratory samples and more. Its composition reflects aspects of your immune state and your level of inflammation. And, unlike your genome, it can change noticeably over time in response to diet, infections, medications, hormones and lifestyle.

All this makes the microbiome a promising tool. It may help us estimate the risk of certain diseases or infections, identify who might respond better to a particular therapy, or design interventions that deliberately shift the microbial community towards states that support better health. Of course, where there is potential, there is also hype, and not every microbiome-related product on the market is backed by solid evidence.

Before We Order Another Round

If you walk away from this imaginary bar conversation with just a few ideas, let them be these: you are an ecosystem, living in permanent partnership with a vast community of microbes; most of them are not enemies but collaborators, as long as the balance is maintained; and the microbiome is one important piece of a much larger picture that includes your genes, environment, lifestyle, infections and medical treatments.

In future posts, I can zoom in on more specific questions, such as the vaginal and endometrial microbiome, how it might affect HIV susceptibility and prevention, and how we actually study all this using bioinformatics and large datasets.

For now, let’s finish the beer. 🍺