The dark microbiome

We have been missing a large number of the microbes that live in our body, and we have no idea how they affect our health.

In recent years, we have come to understand that our microbiomes – the microbes that live in our guts and elsewhere – may affect everything from armpit smell to obesity. This realisation has prompted groups around the world to begin developing therapies that target our microbiomes in an effort to treat a range of conditions.

But it appears that microbiome studies have been missing many species. “We might be overlooking a huge number of microbes that we cannot see with standard methods,” says Christine Moissl-Eichinger at the Medical University of Graz in Austria.

Moissl-Eichinger has been investigating species we know very little about because they aren’t easy to detect or grow in the lab. Her interest began when she was involved in checking if microbes were present on spacecraft destined for other planets. She found cells belonging to the group known as archaea. These look just like bacteria, but are a different branch of life.

Moissl-Eichinger has also found archaea in hospitals, prompting her to realise that they must come from people – even though few archaea have been discovered in or on the human body.

To identify microbial species, researchers usually look for a particular gene that acts as a genetic barcode for bacteria and archaea. Different species have subtly different DNA sequences in this gene, so reading the sequence can tell you what microbes are present in a sample.

Moissl-Eichinger and her colleagues have shown that the standard sequencing method often detects no archaeal species, or just one, in samples taken from people’s bodies. But when her team used a version of the sequencing method optimised to detect archaea in the same samples, it revealed that there were in fact dozens of these species present.

Each part of the body seems to be home to characteristic species of archaea, as with bacteria.

For example, the gut has many archaea that produce methane, while the main archaea on the skin break down ammonia, a process that might help determine skin pH and skin health (bioRxiv, doi.org/cq3z).

What’s more, in the nose and appendix, individual archaea cells outnumbered those of bacteria. “We did not expect that,” says Moissl-Eichinger. Because we have only just discovered them, we don’t know what most of the archaea in our bodies do. Finding out won’t be easy because it is very difficult to grow archaea in the lab for detailed studies.

While many kinds of bacteria cause infections and diseases, no archaeal species is known to do so. That might change now we are finding so many more of them in our bodies.

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