DNA pushes back the microbiome frontier

 

 

Over the past 15 years, researchers have come to appreciate how profoundly the diverse zoo of microbes in the human gut, skin, and mouth affects our health. But their identities and exactly how they exert their effects have remained mysterious. Now, two research groups have made this microbial dark matter more visible, by starting with its best-known aspect: its DNA.

One team harnessed DNA sequence information to isolate specific microbes they wanted to grow in lab dishes. The other used it to discover chemicals that microbes make to communicate with each other and influence their human host. By opening the way to a more detailed understanding of the trillions of microbes we contain, the techniques could ultimately lead to new treatments, says Eric Schmidt, a chemist at the University of Utah in Salt Lake City. “Microbes make many of our best drugs, such as life-saving antibiotics,” he notes. More such molecules could be waiting in our own microbiomes, he says. “It is amazing to think that the human microbiome has genes to make countless complex chemicals, but we don’t know what those chemicals are.”

Mircea Podar, who studies evolutionary microbial genomics at Oak Ridge National Laboratory in Tennessee, and his co-workers used DNA to isolate and then culture bacteria that, until now, have never been grown in the lab. The team targeted Saccharibacteria, inhabitants of the human mouth. The dozen species living there make up less than 1% of the mouth’s microbiome and are difficult to isolate and grow.

Podar’s team first searched for genes in previously sequenced Saccharibacteria DNA that likely code for proteins capable of jutting through the surfaces of cells, where antibodies can “see” them. The researchers then identified specific regions of those surface proteins that would likely trigger strong antibody responses and injected these protein fragments into rabbits. Antibodies made by the animals gave the researchers a molecular tool for plucking out Saccharibacteria from the mix of microbes in human mouth fluids. To grow the few cells they snagged, the researchers tried a wide variety of culture broths—variously made from body organs, sugars, soy, vitamins, and gastric juices—until they found a congenial growth medium, they report this week in Nature Biotechnology.

“This is a wonderful study,” says Norman Pace, a microbiologist at the University of Colorado in Boulder who did groundbreaking work to discover new microbes in hot springs and other extreme environments. The new work, he says, “uses thoroughly modern technology” to obtain uncultured species. “I find the study inspiring, something we couldn’t even imagine in the early 1980s.”

 

 

 

Culturing previously obscure microbes should allow researchers to determine how they function. It could also explain why many strains won’t grow in mixed cultures. “Once you separate your target organisms, then you can explore conditions under which your microbe can flourish,” Podar says. You might find, he says, that an apparently “uncultivable” organism is actually inhibited by another species.

Mohamed Donia didn’t want to wait for a microbe to grow to find out how it worked. So the pharmacist at Princeton University and his colleagues came up with a way to comb through metagenomic data—thousands of short DNA sequences from the whole panoply of microbes in, say, the mouth, gut, or an ecosystem—for clues to the molecules produced by the microbes. Then, they made the mystery molecules in well-studied microbes and tested their function. The work, reported online in Science this week, “will greatly expand our understanding of the chemical capabilities of microbiomes,” says Lora Hooper, an immunologist at the University of Texas Southwestern Medical Center in Dallas, who was not part of the project.

Donia’s team started by picking an enzyme critical to making a particular type of molecule, then searching the metagenome for the gene encoding that enzyme. In the past, finding such genes in metagenomic data was daunting because those databases contain only short, fragmentary DNA sequences. But the team developed what Schmidt calls “an efficient approach to comb the microbiome for new chemicals.” Its computer algorithm divides a molecule-producing gene into small segments. Then it tests those segments and selects the best for searching for the gene sequences. The sequences pulled out by the probe tend to come with sequences of other enzymes needed to make the molecule.

The researchers tested the program by looking for aromatic polyketides, a class of molecules that includes the antibiotic tetracycline and the anticancer drug doxorubicin. Although soil microbes produce these compounds, no one had found them among the human microbiome’s products. The effort yielded 13 clusters of polyketide-producing genes—all new to science—in the mouth, skin, and gut, the team reports. “These are not rare, yet no one had seen these before,” Donia says.

His group then put these sets of genes into lab bacteria and tested the products. None inhibited cancer cell growth, but two proved to be potent antibiotics. In the human body, they may destroy microbial competitors or help protect the host from certain pathogens, Donia says—a possibility that suggests bright prospects in medicine for the microbial dark matter.

 

 

 

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