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Microbiology: The new germ theory

Jillian Banfield trades in hell holes. In September, she could be found wading through the dark, hot, sulphurous innards of Richmond Mine at Iron Mountain, California, where blue stalactites ooze the most acidic water ever discovered, with a pH of −3.6. A year before that, she was pumping up a toxic soup of uranium, arsenic, molybdenum and other metals from underneath a decommissioned nuclear-processing site in Rifle, Colorado. From both sites she took samples back to her lab at the University of California, Berkeley, where she sequenced and analysed the DNA they contain in an attempt to work out which bacteria, archaea, viruses and fungi have decided to make that particular hell their home — and what it takes to survive there.

About a year ago, Banfield added a new location to her repertoire of foul study sites: the pencil-thin intestines coiled inside premature infants weighing less than 1.5 kilograms, in the neonatal intensive care unit of the University of Chicago, Illinois. Banfield had never dealt with microbes that live in humans. But her well-regarded work on the microbial communities of Richmond Mine had attracted the attention of two medical researchers.

One was Michael Morowitz, a neonatal surgeon then at the University of Chicago, and now at the University of Pittsburgh, Pennsylvania. Morowitz was studying necrotizing enterocolitis (NEC), a potentially fatal disease that destroys the bowels of premature babies. The other was David Relman of Stanford University in California, a leader in the burgeoning field exploring the human microbiota — the vast populations of microorganisms that live in and on the human body. Morowitz and Relman asked Banfield if she could help them understand the microbial mass in this unexplored landscape.

Banfield said yes — and the three struck up a collaboration. They are now bringing Banfield's techniques to bear on humans, and are sequencing and analysing microbial genes in fine detail to resolve whether hard-to-distinguish species or strains correlate with NEC and might promote it. Elsewhere, similar collaborations are linking those exploring the human microbiota in the intestine, skin, mouth and other surfaces with microbial ecologists, such as Banfield, who have already made a career out of studying microbial universes in environments such as soil, ocean water and toxic waste sites.

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