Part of the decline of good bacteria can be attributed to use of antibiotics, especially in children. But a recent study found huge differences in bacteria present on the skin of newborns delivered by C-section vs. those delivered vaginally, possibly explaining why C-section babies are more vulnerable to infections.
The infants were swabbed and tested moments after birth, yet those delivered by C-section were already colonized.
"They're like magnets," said Maria Dominguez-Bello, who led the study. She said she's not sure where the bacteria are coming from or what her finding means. It was a tiny study, examining just 10 infants, but she and her colleagues are now following a larger group of infants over time.
The C-section babies were colonized mostly by staphylococcus, a type of skin bacteria that sometimes causes infections. The other babies were colonized by species similar to those living in their mothers' vaginas, said Dominguez-Bello, a biologist at the University of Puerto Rico.
Previous studies have shown that babies delivered by C-section are more vulnerable to infection with the antibiotic-resistant staph strain known as MRSA, she said, but the reason has been unclear.
The bacterial differences may also be connected to another mystery: why C-section babies are more likely to get asthma later on.
"We believe there is so much we acquire very early and they live with us forever," said Dominguez-Bello.
The C-section study, published in Proceedings of the National Academy of Sciences, is part of a larger effort to study the way modern lifestyles and medicine have altered and perhaps disrupted humans' natural microbial communities. To get the "before" picture, Dominguez-Bello is studying natives of the Venezuelan Amazon.
"In a sense they live in conditions like those of our ancestors," she said.
One of the big differences found so far is that almost everyone in the Amazon has the bacteria Helicobacter pylori, once known mainly for causing stomach ulcers. Before the 20th century, H. pylori was the dominant organism in human stomachs around the world, said New York University biologist Martin Blaser.
About 70 percent of Americans born near the beginning of the 20th century carried H. pylori, Blaser said. Among children born in the 21st century, it's 6 percent.
H. pylori is being eradicated by antibiotics prescribed for childhood ear infections, sore throats, and a host of other conditions, he said. That might mean ulcers and stomach cancers become much less common, but people without H. pylori are more likely to be diagnosed with esophageal reflux and cancer of the esophagus. They also appear to get more asthma in childhood.
"An H. pylori-positive stomach is different from an H. pylori-negative one," Blaser said. "There's a cost to having it . . . but there's also a cost to not having it."
Over the last century, asthma has risen at roughly the same rate that H. pylori has fallen, although a mechanism linking the two has yet to be discovered.
Obesity may also have a bacterial connection. In 2006, biologist Jeffrey Gordon of Washington University in St. Louis and colleagues published a groundbreaking paper showing that obese people had a different mix of gut bacteria than did thin people.
Blaser suspects H. pylori may play an important role. In the stomach, it influences two key appetite hormones: ghrelin, which makes us want to eat, and leptin, which makes us want to stop eating.
"It's well-known that farmers used to give antibiotics to animals to fatten them up," said Blaser, even before antibiotics were used to prevent infections. If it fattened up chickens, geese, turkeys, pigs, and cattle, he thinks it's reasonable to explore the possibility that antibiotic use and the loss of H. pylori are helping fatten up today's humans.
Blaser said he was surprised how long it had taken the medical community to catch on to the importance of beneficial microbes.
One reason is that they were mostly invisible, said Rob Knight, a computational biologist at the University of Colorado and a collaborator on the C-section study. Until a few years ago, the only way to find microorganisms in the body was to place a sample of tissue or fluid in a petri dish and see what grew.
Now scientists can use various types of "DNA fingerprinting" to identify hundreds of species even if they don't grow outside the body. As many as 97 percent of the species inhabiting humans may have been previously undetectable.
Lately, it's become cheap to read out the organisms' whole genetic code through what's called DNA sequencing. That has enabled Knight to begin compiling a sort of atlas of human microbes called the Human "Microbiome" Project - an effort analogous to last decade's Human Genome Project.
So far, it has shown that surprisingly different communities of organisms live on various parts of the body - our forearms are colonized by bugs not usually found in our armpits, which are again different from what's in our navels.
In a paper published in March, Knight demonstrated how people leave unique bacterial fingerprints on objects they touch. These might be used the same way that police use human DNA or actual fingerprints at crime scenes.
A number of other researchers are exploring how good microbes might protect against bad diseases.
Penn biologist Frederic Bushman is studying a possible connection between gut microbes and inflammatory bowel disease (IBD), a group of sometimes debilitating intestinal disorders that include Crohn's disease.
Bushman believes scientists are just beginning to uncover a complicated system of cross talk between immune systems and the communities of microbes that live in them.
"One thing people don't realize is the importance of immune tone," he said. By this, he explained, he means the way your immune system is always on - even when you're not sick with some infectious agent.
Instead of sitting there doing nothing, immune cells are responding to their surrounding community of microbes - "actively sculpting the composition of those communities in your body," he said.
An even newer field of science is beginning to look beyond the human microbiome to the community of human viruses - our viromes. The bacteria that people carry around are themselves carrying viruses, Bushman said - worlds embedded within worlds.
Whether they, too, can be beneficial is not yet known.
Contact staff writer Faye Flam at 215-854-4977 or firstname.lastname@example.org.