Colorized scanning electron micrograph of Escherichia coli, grown in culture and adhered to a cover slip.
NAIAD/Attribution 2.0 Generic (CC BY 2.0)

The FDA has halted trials of fecal transplants after one recipient has died and another is ill. Both were being treated for an intestinal infection called C. difficile and received transplants from an ostensibly healthy donor who turned out to be carrying an antibiotic resistant strain of E. coli. The incident highlights the risks inherent in a procedure that has rapidly gained favor for treating a host of health problems.

Researchers have found that we get good microbes in our system when we play in the dirt.
Jelleke Vanooteghem

Microbiologist Jack Gilbert says, as parents, we’ve been making a mistake in over-sterilizing our environment. For one thing, we shouldn’t keep our children from getting dirty outside or sterilize them as soon as they come inside. We should let the dog lick them. Sure, wash their hands a lot when it’s cold season, but don’t be afraid of a little dirt.

Courtesy of Lora Hooper

There are at least as many bacterial cells in your body as their human cells. And there’s a growing recognition that they’re critical for everything from digestion to mental health. They also play a big role in immunity – our ability to fight off diseases. But the relationship isn’t always easy or friendly. For all the good they do, if gut bacteria get into the wrong places, it can be problematic.

Heat and minerals from hydrothermal vents fuel abundant microbial and animal life, as well as intense scientific research.
NOAA PMEL EOI Program / www.pmel.noaa.gov

It’s known as the deep biosphere, or the dark energy biosphere. What is it? Microbes - bacteria, archaea, even fungi - living not at the bottom of the ocean, but in the bottom of the ocean. We aren't just talking about the ocean version of soil bacteria, living in the seafloor mud (although that is part of the story). No, we're talking about microbes living in cracks in the rocks deep below that mud, in the most extreme case to date, a mile and a half below the seafloor.

Mike Baird / flickr

We like to think we’re in charge of our health, but it increasingly looks like the ones really running the show are the microbes in, on, and around us -  and not just the ones that cause diseases. Bacteria and other microbes on our skin and in our intestines far outnumber our actual human cells, and are responsible for a large fraction of what our bodies do - from digestion to mental health.