Healthy lungs are sterile and contain no microbial community.

For much of modern medicine, the healthy lower respiratory tract was described as sterile. If bacteria were recovered from a lung sample, they could be treated as contamination from the mouth or as evidence of infection.

That conclusion fit the available methods. Standard clinical cultures are good at finding many disease-causing bacteria that grow readily in the laboratory. They are much less suited to describing a sparse community containing organisms that may grow poorly under routine culture conditions.

DNA-based methods changed the picture. Researchers began detecting microbial genetic material in carefully collected samples from the lower airways of people without pneumonia or other obvious infection. Better sampling and contamination controls showed that at least some of these signals represented genuine lung communities.

The lung microbiome is very different from the dense microbial ecosystem of the gut. The lower airways contain far fewer microbes. Their composition is continually influenced by organisms inhaled from the environment, tiny amounts of material entering from the mouth and throat, immune removal, and whether local conditions allow particular microbes to grow.

Finding microbial DNA also does not automatically mean that an organism is actively growing or causing disease. The important correction is to the old sterile-versus-infected binary: healthy lungs can contain microbes without being infected.