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Gut Bacteria Strongly Influence the Aging Genome in Flies

Stress response and innate immunity genes are the most affected.

Gut bacteriaGut bacteria

Most of the genetic changes associated with increasing age disappear in the absence of gut bacteria, according to a new fruit fly study [1]. It’s a pretty surprising finding, and while there are some important implications, it’s also a bit challenging to interpret.

A flat aging line

The experiment itself was relatively straightforward. A team at the US National Institutes of Health sequenced RNA from fruit flies grown under normal conditions and in axenic conditions – that is, with antibiotics in the growth medium. Their goal was to understand more about how the bacteria in the gut contribute to aging, building on earlier studies showing that the absence of gut bacteria extends the lifespan of nematodes and fruit flies, depending on growth conditions.

The analysis was somewhat more involved. The idea was to identify systematic changes in gene expression that happen as the flies age and use these as a baseline against which to measure the difference in axenic conditions. To accomplish this, they first used a machine learning algorithm to identify genes that consistently changed their expression level over the life of the conventionally raised flies, which they call ‘classifier genes’. This selected 1628 genes out of the 15,034 measured, and these were used to make a model that predicted age based on gene expression. The researchers then used this model to predict the age of the axenic flies – basically, comparing their biological and chronological ages.

The result was quite a surprise. All of the axenic flies aged 10-45 days had a gene expression profile like that of 30-day-old conventionally grown flies. In other words, the expression profile of 10-day old axenic flies was about 20 days older than them, while that of 45-day old flies was about 15 days younger. It also turned out that about 70% of the changes in expression that happened in the conventionally raised flies disappeared in the axenic ones.

Stress-free flies

It turned out that this was due to a dramatic change in how the expression of genes throughout the genome changes during aging. When the researchers looked at the types of genes that changed expression in axenic and conventional conditions, they found some striking differences. In flies raised in axenic conditions, two major age-related classes of genes did not change with age: stress response genes and innate immunity genes.

In conventionally raised flies, stress response genes were elevated earlier in life, but this didn’t happen in the axenic flies. Likewise, older conventionally raised flies had lower levels of innate immunity genes, but expression of these genes remained high in 45-day-old axenic flies. Genes belonging to several other processes continued to change with age – olfaction, metabolism, and circadian rhythm – but stress response and innate immunity genes make up a bulk of the age-associated changes, and both processes are considered hallmarks of aging.

The team then verified the physiological relevance of these changes by challenging conventional and axenic mice of different ages with stressors and parasites. They also used several different tests to confirm that these changes were due to the absence of gut bacteria rather than the presence of the antibiotic. Overall, these analyses all supported the main findings, and it’s worth noting that there was also an increase in the lifespan of the axenic flies.

Finally, the researchers repeated their assessment of the ‘gene expression age’ of the axenic flies, but this time, they only used genes that changed their expression levels in both the conventionally raised and axenic flies – that is, they left out the stress response and innate immunity genes. This time, the analysis didn’t tag all of the axenic flies as 30-day-old conventional flies. Instead, the model showed a slower rate of transcriptional aging in the axenic flies, so they generally seemed younger than their conventional counterparts, which matches well with the observation that they had a longer lifespan.

Lifespan is limited both by intrinsic decline in vigor with age and by accumulation of external insults. There exists a general picture of the deficits of aging, one that is reflected in a pattern of age-correlated changes in gene expression conserved across species. Here, however, by comparing gene expression profiling of Drosophila raised either conventionally, or free of bacteria, we show that ~70% of these conserved, age-associated changes in gene expression fail to occur in germ-free flies. Among the processes that fail to show time-dependent change under germ-free conditions are two aging features that are observed across phylogeny, declining expression of stress response genes and increasing expression of innate immune genes. These comprise adaptive strategies the organism uses to respond to bacteria, rather than being inevitable components of age-dependent decline. Changes in other processes are independent of the microbiome and can serve as autonomous markers of aging of the individual.


This is a really fascinating paper. (It’s also open access, so go read it if you want to know all the details that were left out in this summary!) The results are pretty clear, but it’s tough to say exactly what’s going on. It’s certainly not as simple as “gut bacteria cause 70% of genetic aging”, and it would be incorrect to conclude that getting rid of gut bacteria would decrease aging or increase lifespan. That happened in the sterile conditions that these flies were raised in, but it would probably be a terrible idea in the wild.

The main takeaway is that our gut bacteria are intimately involved in how stress response and innate immunity change over the course of our lives. The authors contend that this means these changes “are not inevitable features of aging, but rather […] a series of strategies to respond to the challenges of its normal microbial environment.” The microbiome is a vital part of who we are and how we have evolved, so understanding how it modulates these processes will be invaluable in learning how to control aging.

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[1] Shukla, AK et al. Common features of aging fail to occur in Drosophila raised without a bacterial microbiome. iScience (2021), doi: 10.1016/j.isci.2021.102703

About the author
Sedeer el-Showk

Sedeer el-Showk

Sedeer became a professional science writer after finishing a degree in biology. He also writes poetry and sff, and somehow juggles an ever-growing list of hobbies from programming to knitting to gardening. Eternal curiosity and good fortune have taken him to many parts of the world, but he’s settled in Helsinki, Finland for the moment. He hopes he’ll never stop learning new things.
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