Are there environments where there are abundant bacteria and no phages? Sounds like one of our Talmudic Questions, but this one has a specific answer, and that answer is Yes. That environment was found within a cystic fibrosis (CF) lung.
This story comes from a pair of papers recently published by a group of microbial ecologists reporting their survey of the microbes and DNA viruses present in the lungs of two late-stage CF patients. Previous studies had all relied on sampled sputum or bronchial alveolar lavage fluid. These researchers instead took advantage of the opportunity to investigate the explant lungs from a CF patient who received a lung transplant. They dissected the lungs, isolated the microbes and viruses separately from each lobe, and then extracted the DNA. This approach enabled them to determine not only the diversity within each lobe, but also to ask whether each lobe housed its own distinctive community.
Their analyses yielded several interesting findings, but the one that caught my attention most concerned the upper lobes. For most environments, it is common to find five to ten viruses (mostly phages) for every microbial cell (mostly bacteria), and high viral diversity, but these lobes with their rampant microbial community had no detectable phages. To the best of my knowledge, this is the first report of such a circumstance.
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