Teen Microbiome Shifts May Determine Acne Risk

Teenage skin undergoes dramatic changes, and so does the bacterial ecosystem living on it.

Researchers at the Massachusetts Institute of Technology (MIT) analyzed the skin microbiomes of children and their parents to track how specific bacterial strains behave over time. They found that a species linked to acne settles in during adolescence and rarely changes in adults.

The study was published in Cell Host & Microbe.

How skin bacteria and acne are linked during adolescence

Acne is one of the most common skin conditions, especially during adolescence, but we still don’t fully understand why it only affects some people. A key suspect is Cutibacterium acnes (C. acnes), a bacterium that lives deep in facial pores. It’s found on nearly everyone’s skin, yet only some people develop acne, leading researchers to suspect that not all C. acnes strains behave the same way.

The facial skin microbiome is dominated by two species: C. acnes and Staphylococcus epidermidis (S. epidermidis). Together, they make up ~80% of the skin’s bacterial population in adults. Each person carries a mix of strains, and some may trigger inflammation, while others may help suppress it.

Recently, the use of topical probiotics – live, “beneficial” strains of C. acnes – to prevent or reduce acne has started to be explored. However, many treatments don’t lead to long-term changes in the skin microbiome. Early studies haven’t shown lasting effects, and researchers are unsure how to get these strains to stick or when they might be most effective.

Previous studies relied mostly on DNA from skin swabs, which can’t reliably distinguish closely related strains. There is a lack of clear data on how skin bacteria move between people, how often new strains arrive or what makes some strains persist.

That leaves key questions unanswered: When do new strains arrive? Can they outcompete resident strains? Does age impact your risk of colonization?

The new study traces how C. acnes and S. epidermidis lineages move, compete and persist, focusing on the teenage years, when acne risk is highest.

“We wanted to know if these communities were truly stable, and if there could be times where they weren’t stable. In particular, if the transition to an adult skin like microbiome would have a higher rate of acquisition of new lineages,” said corresponding author Dr. Tami Lieberman, an associate professor at MIT.

When and how skin bacterial strains settle

Lieberman and colleagues collected facial skin samples from 30 children, ages 5–15 years, and 27 of their parents. Over a 1.4-year period, they sampled 4 areas of the face: the forehead, nose, cheek and chin. The team cultured over 4,000 individual bacterial colonies and used high-resolution metagenomic sequencing to identify and track them at the strain level.

The full genomes of individual bacterial cells were sequenced so that the bacteria could be grouped into lineages – sets of strains that differ by fewer than 100 single-nucleotide mutations. By doing this, they could monitor how specific strains of C. acnes and S. epidermidis spread, how long they stayed and whether people in the same household shared them.

Across all samples, the researchers identified 89 C. acnes and 78 S. epidermidis lineages, with some individuals hosting up to 11 of each at once.

They found that C. acnes behaved in a stable and selective way. Most people pick up new C. acnes strains during adolescence, when oil production increases and pores become more hospitable.

After that, new strains are rarely established. Adult skin seemed to resist newcomers, even after direct contact.

“For C. acnes, what we were able to show was that people do get strains throughout life, but very rarely. We see the highest rate of influx when teenagers are transitioning to a more adult-like skin microbiome,” said Lieberman.

“If we had a strain that we knew could prevent acne, these results would suggest we should make sure we apply them early during the transition to adulthood, to really get them to engraft,” she added.

Multiple strains often coexisted on one person, usually seeded by multi-cell transmission events.

 

S. epidermidis showed a different pattern. Strains came and went quickly, typically lasting around two years. New strains appeared regularly across all ages.

Despite this, the participants still maintained distinct communities, even family members in close contact didn’t fully share their strains.

“That suggests that something is preventing homogenization between people. It could be host genetics or host behavior, or people using different topicals or different moisturizers, or it could be active restriction of new migrants from the bacteria that are already there at that moment,” said Lieberman.

Previous work suggested that the skin microbiome was stable over time, but the team found that while the species stay constant, the specific strains within them can change significantly.

Teenage skin creates a window for microbiome treatments

The results suggest that the early teenage years may be the only reliable window for introducing new strains. Once the microbiome stabilizes in adulthood, new strains are unlikely to stick. Applying topical treatments for acne and other skin conditions too late may therefore limit their effectiveness.

The study shifts attention to adolescence, a period often overlooked in microbiome research. During this period, oil production on the face increases sharply, creating conditions that support the expansion and settlement of new C. acnes strains.

Future work needs to track immune responses to new strains and test interventions in larger, more diverse groups.

“We want to understand why we each have unique strain communities despite the fact that there is this constant accessibility and high turnover, specifically for S. epidermidis. What’s driving this constant turnover in S. epidermidis, and what are the implications of these new colonizations for acne during adolescence?” said Lieberman.

 

Reference: Baker JS, Qu E, Mancuso CP, Tripp AD, Conwill A, Lieberman TD. Intraspecies dynamics underlie the apparent stability of two important skin microbiome species. Cell Host Microbe. 2025. doi: 10.1016/j.chom.2025.04.010

 

This article is a rework of a press release issued by the Massachusetts Institute of Technology. Material has been edited for length and content.