Antibiotics Can Damage These Gut Dwellers
By: Sam Westreich
Tags: Health, Medicine, Food, Science, Diet

A recent study just suggested that, when we take antibiotics, we may cause more long-term changes to our gut microbiome than we previously suspected — and also that our most common method of looking at the gut microbiome may not be complete enough to see these effects.

Researchers from the Hans Knöll Institute in Germany looked at a group of individuals in the three months after they took doses of antibiotics, using a combination of different genetic sequencing technologies to monitor changes to their gut microbiome.

Inside our digestive tract is a collection of bacteria, fungi, and other species, constantly competing with each other for limited resources. This group of different micro-organisms is known collectively as the gut microbiome, and it has many effects on its host, and has come to be regarded as our newest discovered organ.

When we first started looking at the gut microbiome, we spent most of our energy focused on the bacteria that are present. But now, this paper suggests that we need to pay attention to the fungi and other species that are present — and we may be missing long-term impacts of our medical treatments on this part of our bodies.

A More Complete Look at the Gut Microbiome

Remember, the gut microbiome is the term given to all of the different organisms that live in our small and large intestine. The majority of these organisms are bacteria, but there are also fungal, archaeal, and viral species present as well.

When we first started studying the gut microbiome, we did so using a method called 16S ribosomal RNA sequencing. This method of sequencing looked at a specific region of a specific bacterial gene, which we could use to identify the bacterium from which it came.

When I talk to non-scientists, I like to describe 16S rRNA sequencing as barcoding; just like how the barcode on a box at a grocery store tells the checkout machine what price to ring up, the 16S region lets us identify the bacterium from which it came.

However, 16S rRNA sequencing only works on bacteria; fungi and other organisms have different ribosome sequences, which won’t be pulled out by this method.

In order to see the fungi, archaea, and viruses that are also present, we need to sequence everything, which is called metagenomics (and is a lot more expensive and needs a lot more computing power to analyze).

In this paper, the authors used the more intense, more expensive, and more complete metagenomics “sequence-everything” approach to look at the activities of fungal species in the gut, after they took a course of antibiotic drugs.

Fungi in Our Gut?

Although most of the species in our gut are bacterial, we also see some fungal species present.

Some of these fungal species seem to be able to peacefully coexist with us, but other species of fungi can cause negative effects for us. Fungal infections can cause inflammation of our gut by provoking an aggressive response from our immune system, and can also increase the severity of some allergies.

Remember, in our gut environment, there are limited resources and niches available. Because of this, there’s plenty of competition between different species in our gut as they fight for their spot. Some bacteria, in fact, defend their niches by secreting molecules that inhibit the growth of fungi, slowing down their competition so that the bacteria can flourish.

Thus, when we take an antibiotic and wipe out the bacteria in our gut, we open up the playing field for fungi to move in. This is where this study focused on investigating, looking at the long-term effects of briefly giving fungi an open window to stake their claim.

Study Results — Long-Term Fungal Shifts

Published in the peer-reviewed BMC Microbiome, the study is titled “Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria”, by a group of researchers out of Hans Knöll Institute in Germany.

When they examined the gut microbiome communities after antibiotic treatment, they found that the bacterial community quickly rebounds to approximately the same as before the treatment. We’ve seen this with other studies.

When looking at the fungi, however, the researchers found that there were long-term shifts in the number and the activity level of the fungi present.

Shortly after the antibiotic consumption, the number of different fungal species spiked as they seized on niches previously occupied by bacteria.

As bacteria re-colonized the gut, the number of fungal species present dropped back down.

As the fungi try to re-stabilize, their activities switched from cooperative to competitive, battling for territory.

Even by three months later, the fungi were still expressing competitive proteins, and had not resumed their symbiotic relationships with bacteria.

Putting it all together, it seems that, while antibiotic consumption causes short-term disruption of our bacterial microbiome, it has a delayed but longer-lasting disruptive effect on the fungi in our gut.

“Doc, I know these will help my bacterial infection, but what will they do to the little fungal partners living inside my intestine?” Photo by Mark Fletcher-Brown on Unsplash

Should We Stop Taking Antibiotics?

Overall, this study shouldn’t be enough to make us stop taking antibiotics. If we have a serious bacterial infection, most of us would much rather have some gut inflammation than die from the infection.

However, this study does suggest that we should follow up on better methods to repair our gut after we disrupt it with antibiotics — and we should look wider than just the bacteria. Although this study was small (only 14 participants), it highlights that we need to consider how altering the bacteria in our gut can affect the rest of the system.

Currently, we don’t have treatments for specifically restoring our gut after we take antibiotics — most probiotics only contain a couple of bacterial strains and don’t replicate our natural gut environment. But if we look for a method of gut restoration, we may want to include fungal species that live in happy symbiosis with the bacteria we add.