Paper towel or hand dryer? This simple question has sparked a fierce battle between the two industries, which have of course turned to that old PR strategy: Fund studies to show that the other side is gross and bad. Hand dryers spray bacteria all over place! Wet paper towels are soggy clumps of germs!

But there is a problem with these studies—and not just a kind of nitpicky “your method is bad” problem, so much as a big philosophical problem. They assume that bacteria are bad, and the fewer bacteria the better. With advances in microbiology though, scientists are mapping  the diverse communities of harmless and even beneficial microbes that live on healthy skin. Removing those bacteria can actually make room for pathogens. So what does it even mean to be “clean” if clean doesn’t mean bacteria-free?

In a thought-provoking preprint of a new paper titled, “Cleanliness in context: reconciling hygiene with a modern microbial perspective,” a group of University of Oregon scientists argue that hygiene studies need to rethink the definition of “clean.” The paper is, ironically, funded by Dyson (maker of jet hand dryers) but the authors don’t come down one side of the paper towel or dryer debate. Hygiene, they argue, can’t simply be about getting rid of as many microbes as possible.

Technology been driving the recent shifts in understanding of the skin microbiota. Historically, scientists have swabbed dirty hands and grown microbes from them on petri plates. But only 1 percent of microbes can actually grow on petri plates. More recently, DNA sequencing revealed the astonishing diversity of the other 99 percent. Different parts of the skin—the oily parts of your nose, the damp patch of your armpit, the dry patch on your elbow—are also home to different communities tailored to the specific environment.

The scientists who study these communities are microbial ecologists, and like ecologists of the macro world, they like to think about the interactions between different organisms. But this research is still new, and this way of thinking is only just starting to make it into the world of clinical microbiology, which is still focused on defeating the bad microbes. “We noticed there is kind of a division between the clinical human skin microbiology research and this more recent emergence of microbial ecology,” says Roo Vandegrift, an ecologist who co-authored the recent paper, “There wasn’t very much crosstalk between those segments of the scientific literature.”

Even the language the two groups use is different. Microbial ecologists tend to divide microbes into how they behave in communities: are commensal or pathogenic? Clinical microbiologist divide them up based on whether they’re usually found on human skin: resident or transient?* You could say the two sets of vocabulary roughly map onto one another. Resident microbes tend to be commensal (the bacteria are harmless to you but they’re benefitting from living on you) and the transients are the pathogens that make you sick when they appear.

The central insight of the ecological view is that getting rid of harmless or beneficial microbes can have consequences, too. Once they’re gone, pathogenic microbes have little competition. Complicating the idea of “good” versus “bad” bacteria is that some bacteria are perfectly harmless until for some reason they’re not. Staphylococcus aureus, for example, can cause dreaded staph infections. But it also lives in the nose of many people with no ill effects.

It’s actually analogous to what happens in the gut, says Elaine Larson, an epidemiologist at Columbia and editor of the American Journal of Infection Control. Clostridium difficile infections, for example, can take hold when a patient is given antibiotics that have wiped out the rest of their gut flora, allowing this bacteria that normally lives harmlessly in their guts to take over. The gut microbiota is better known—to the point where supermarkets sell probiotic pills and doctors exercise more caution about prescribing indiscriminate antibiotics willy nilly. The more poorly understood world of skin microbiota, on the other hand, still has to deal with alcohol-based hand sanitizers that advertise their ability to kill 99.99 percent of germs.

The world is changing, if slowly. There’s a lot more sequencing of the skin rather than just culturing on petri dishes now. The problem is “it’s much more expensive to be sequencing,” says Val Curtis, a hygiene expert at the London School of Hygiene and Tropical Medicine. Curtis has also done hygiene studies that specifically zero on fecal bacteria, which are more likely to have pathogens among them. “The important question is, ‘What is the health impact of different way of washing hands?’” she reiterates. “It doesn’t matter if you get rid of a load of bacteria that’s not harmful.”

But what would hand hygiene that nurtures the skin microbiota look like? Could we have skin probiotics? Well the skincare company AOBiome actually does sell a microbial mist to use in place of soap. Though that spray is less about reducing infection than about keeping your skin balanced without chemical products. In the clinical context, it could mean products like Nozin, an alcohol spray for the nose, that specific targets nasal bacteria that often include Staphylococcus aureus. Or it could be something we can’t imagine yet.  “I don’t think we know the answer right now, but I think it’ll be a very interesting,” says Larson.

Goodbye paper towels versus hand dryers. Hello to the unknown, bacteria-filled future.

* This article originally misstated the language used by microbial ecologists and clinical microbiologists. We regret the error.