Microbiome quick guides series: Metabolites

Chances are, you already know about the diverse mix of microorganisms called the gut microbiota living in your digestive tract. And you may also know that these microorganisms affect your health in different ways. But to understand how they manage to influence the health of a human (or any other creature that hosts them), you need to know about the many kinds of molecules, called metabolites (muh-TAB-uh-lites), that are custom-made by the microbes.

What are metabolites?

Metabolites are molecules that are made—or changed—by microbes. They’re molecules that are produced as an end-product of microbial metabolism.

In other words, as microbes carry out the processes necessary for maintaining life, they end up producing a variety of molecules called metabolites. Sometimes specific microbes in your gut pair up with something from your diet to produce a metabolite.

Metabolites are also called small molecules, since they have a low molecular weight.

Thousands of types of metabolites exist in the human body, each with a specific chemical structure. Each metabolite is distinguished from other ones by (1) the chemicals that make it up, and (2) the 3-dimensional arrangement of the atoms. This chemical structure is important, because it determines what a metabolite does.

What is the metabolome?

The collection of metabolites in a certain place is called the metabolome (muh-TAB-uh-lome). For example, if scientists take a fecal sample and analyze all the metabolites contained in it, they’re examining the fecal metabolome. The blood metabolome and the urinary metabolome are also frequently studied in humans.

Knowledge about the metabolome of a living organism is part of describing its phenotype – a ‘snapshot’ of the organism’s entire physiology in its current state.

How are metabolites measured?

Metabolomics [muh-tab-uh-LOW-micks] is the study of metabolites, including scientists’ efforts to name and count metabolites from a biological sample.

When scientists want to undertake a metabolomic analysis, they can either analyze all the metabolites in a sample (untargeted metabolomics) or they can look for the presence of certain ones (targeted metabolomics). For the analysis, scientists usually use one of two basic techniques: nuclear magnetic resonance spectroscopy or mass spectrometry.

Some metabolites are not very stable, which means that they degrade or disappear quickly in a sample. This means scientists sometimes need to use special techniques to collect and store their samples (e.g. immediately putting a fecal sample into a -80°C freezer) in order to make sure the metabolites stay intact so they can eventually be measured.

What happens to metabolites after microbes produce them?

Many different things can happen to metabolites once they’re produced in your body. Some stick around in the same area where they were made (say, the gut) and do important jobs there. Others get converted to completely different metabolites. Still others circulate around the host’s body and find the correct receptors, where they fit like a key into a lock.

Because of this, when scientists look at the metabolites in a sample such as blood or fecal matter, it’s not the same thing as knowing the complete collection of metabolites that were produced in the first place within the host’s body. They only see the end result of many processes and interactions.

What do metabolites mean for health?

Thousands of metabolites are circulating in your body right now. Scientists have no idea what many of them do – but they are working to discover the specific mechanisms that link different metabolites to health and disease. In many cases, metabolites may act as ‘messengers’ between microbes and your body.

One family of metabolites, however, is already pretty famous for its effects on humans and other hosts: the short-chain fatty acids. The three most abundant and most studied types are butyrate, acetate, and propionate. These short-chain fatty acids are produced in the colon when microbes eat fiber that’s indigestible by the human body. Short-chain fatty acids feed the cells in the gut, and also circulate throughout the body and influence various processes—everything from metabolic health to the activities of different immune cells.