‘We are 90 percent bacteria,’ says researcher for Hospital Microbiome Project

Biologist Daniel Smith swabs the floor in a new hospital room to collect microbial samples at the new University of Chicago Hospital in Chicago. The hospital is not open to the public yet.
Biologist Daniel Smith swabs the floor in a new hospital room to collect microbial samples at the new University of Chicago Hospital in Chicago. The hospital is not open to the public yet.

CHICAGO — Biologist Daniel Smith crouched in an empty patient room at the new University of Chicago hospital and dragged a white cotton swab across the gleaming tile.

Mr. Smith studied the dust-smudged tip before breaking it off into a plastic tube labeled “floor.”

“A good sample for us,” said Mr. Smith, securing the tiny vial in a box chilled by dry ice. “Although you can’t see them, there are literally billions of [bacteria] cells on these surfaces.”

Like scientists who began classifying the world’s plants and animals centuries ago, Mr. Smith and his colleagues at Argonne National Laboratory are embarking on a similar exploration, only in the micro realm.

Over the next year, they plan to trace the ebb and flow of the hospital’s microbiome — a vast wilderness of viruses, fungi and, perhaps most importantly, bacteria — to better understand how it may affect human health in an environment where about 100,000 people die nationally every year from acquired infections.

The effort, known as the Hospital Microbiome Project, follows similar surveys of bacterial communities in the human body, where the single-cell organisms outnumber human cells by 10 to 1. It is also part of a growing area of microbial research, bolstered by recent advances in molecular biology and computer science, that has led some scientists to wonder whether the strongest forces shaping human life may not, in fact, be human.

Or, as California Institute of Technology microbiologist Sarkis Mazmanian likes to tell people, “We are 90 percent bacteria.”

“If you think about the way we function on a cellular level, all the activities that confer health and disease are not just encoded in our own DNA. Some of those are encoded in our bacterial DNA,” Mazmanian said.

“So how much of the way we function, even maybe the way we think, is from our own doing? How much of us is really human?”

Since at least the late 17th century, when Dutch scientist Anton van Leeuwenhoek scraped scum from his teeth and observed tiny “animalcules” in the plaque samples beneath his microscope, humans have had an inkling of the microbial world in and around them.

But that understanding has been overly simplistic, according to Jack Gilbert, a microbial ecologist at Argonne and head of the laboratory’s microbiome endeavors.

Human beings are blanketed by microbes from the moment they emerge into the world. A vast majority of the human microbiome, comprising 10 trillion to 100 trillion cells, thousands of species and at least 8 million unique genes, is not only harmless, but vital to life. By breaking down food, bacteria produce essential vitamins, anti-inflammatories and compounds that fuel the human metabolism.

Yet the overriding premise has been that microorganisms are the ecological foes of humans, meant only to be destroyed.

“We equate bacteria with small insects,” said Gilbert during a recent interview on Argonne’s sprawling campus near Lemont. The use “of the word ‘bug’ for bacteria, comes from this fear of these little creepy, crawly insects crawling all over everything,” he said.

The arsenal of microbial warfare — antibiotics, vaccines, and simple soap and water — has saved millions of lives, and Gilbert and his ilk do not recommend the retirement of such vital weapons.

Instead, their mission is more nuanced: By sifting through microbe genomes, they hope to sort out the complex interactions that make some landscapes beneficial while turning others more destructive.

The work, in part, builds on the Human Microbiome Project, which began in 2007 to sequence the microbial DNA in healthy humans and those suffering from a variety of medical conditions like gastroesophageal reflux disease and irritable bowel syndrome.

The project, funded by the National Institutes of Health, concluded that certain microbiomes appear to be associated with or even precede specific diseases.

“It isn’t just the human on this side and microbes on the other side,” said NIH project coordinator Lita Proctor. “It helped us think about microbes not as single entities, not as a single germ or pathogen, but as whole communities interacting with each other and their environment.”

Scientists are still defining that relationship, but recent studies have shown that changes in the microbiome may impact health in varied ways.

To underscore that point, Dr. Alexander Khoruts often mentions a patient who contracted a persistent Clostridium difficile infection in 2009. The rod-shaped bacteria typically take up residence in the colon after normal bacteria have been wiped out by antibiotics. Left unchecked, the bacteria can cause diarrhea, inflammation of the colon and, in about 14,000 cases a year, death.

By the time the patient came to him, Khoruts said, she had already lost more than 60 pounds and had to use a wheelchair.

“She was, essentially, slowly dying,” said Khoruts, a gastroenterologist at the University of Minnesota Medical Center, Fairview.