Our Microbes, Ourselves

In the womb, a fetus enjoys the protection of a sterile environment. Only when the mother’s amniotic sac ruptures before delivery does her baby face microbes for the first time. As he’s squeezed through the birth canal, he picks up millions of bacteria from his mother. Most of the microbes are friendly and quickly take up residence on the baby’s skin and in his gastrointestinal tract.

The bacteria not only persist but also form complex communities throughout the newborn’s body that will aid in his general well-being throughout life. The body’s microbes play a critical role in digesting food, metabolizing drugs, and maintaining overall health.

In fact, in every person’s body, there are 10 times as many microbial cells as there are human cells. “The microbial part of ourselves is highly evolved,” says Jeffrey Gordon, a microbiologist at Washington University in St. Louis. “These organisms have learned to adapt to life with us.”

It’s no wonder then that this vast microbiota has captured the attention of researchers working to understand not just health, but also diseases, particularly those lacking clear diagnoses or effective treatments. With new laboratory techniques, these researchers have begun to survey the microbial communities in the body. Several groups already report that disruptions in these communities are related to conditions including obesity, inflammatory bowel disease, vaginal infections, and gum disease.

Scientists have long recognized that the body’s microbiota matters. In the 19th century, Louis Pasteur declared that normal microbes are important in human health and that their disruption can lead to disease. Until recently, however, scientists studying human-microbial populations had been hampered because the majority of such microbes can’t be cultured in the lab. Now, researchers can extract DNA from a sample and rapidly identify thousands of bacterial species at once without having to grow each bug in a dish.

New studies are also showing that microbes within a community work together to influence health, a finding that may have a large impact on conventional views of disease. Instead of an illness being caused by the presence or absence of a single pathogen, “the real pathogenic agent is the collective,” says David Relman, an infectious-disease investigator at Stanford University.

Gutting it out

Washington University’s Gordon regards the gut as a bioreactor—something like a living septic tank that breaks down organic matter. The human gut is filled with microbes that interact with one another and their host in mutually beneficial ways (SN: 5/31/03, p. 344: Gut Check).

Several years ago, Gordon and his group conducted a series of experiments in which they transplanted microbial communities from the guts of normal mice into mice reared in a sterile environment. The formerly germ-free mice began to accumulate fat in their tissues. The transplanted microbes not only permitted the mice to metabolize nutrients that would otherwise have been lost but also appeared to manipulate mouse genes in a way that increased the animals’ capacity to store fat, the team reported in 2004.

The researchers homed in on the gene for a protein called fasting-induced adipocyte factor, which is known to regulate energy storage. Normally, the protein is secreted from the cells lining the gut. The protein blocks lipoprotein lipase, an enzyme that controls the transfer of fat molecules from the blood into fat cells.

In mice that had received the transplanted gut microbes, fasting-induced adipocyte factor was suppressed. This increased the lipase’s activity, resulting in more fat being stored.

The results prompted Gordon and his colleagues to hypothesize that differences in gut-microbial communities might explain differences in how well people harvest energy from food and store it as fat. So, the group decided to compare the gut microbiota of lean and obese mice.

“We saw this amazing, mind-boggling shift in the relative representation of the two principal groups of bacteria that normally inhabit mammalian guts,” says Gordon. Those bacterial types are called Firmicutes and Bacteroidetes.

The researchers identified the members of the animals’ gut microbial communities by sequencing a specific gene whose sequence varies from one species to the next. Researchers frequently use this gene, called the 16S ribosomal gene, as a mini–bar code for identifying bacteria.

Mice bred to be obese had a larger proportion of Firmicutes and a smaller proportion of Bacteroidetes than their lean counterparts did. The change wasn’t the result of one bacterial species taking over a group or of another species being suppressed. “Everything moved up or down,” Gordon says.

To determine how changes in the bacterial communities relate to the animals’ body weights, Gordon and his team transferred gut microbes from the obese and lean mice to germfree mice. The mice receiving gut bacteria from obese animals gained significantly more fat than did mice receiving gut microbes from lean animals, the team reported in the Dec. 21/28, 2006 Nature.

In a separate report published in the same issue, the researchers addressed whether a similar pattern exists in the human gut. The team studied 12 people who volunteered to be randomly assigned to either a low-calorie, fat-restricted diet or a low-calorie, carbohydrate-restricted diet. The researchers monitored changes in the volunteers’ gut-microbial communities over the course of a year. Sure enough, as individuals of both groups lost weight, the proportion of Bacteroidetes in their guts rose, while the proportion of Firmicutes dropped (See note, below).

Gordon is quick to point out that gut-microbial ecology isn’t the only factor affecting body weight. Genetics and easy access to high-calorie foods play important roles. Still, the research suggests that microbial communities in the gut form alliances with one another as well as with their host, and that scientists will need to understand the entire community to understand obesity and many other complex conditions.

Inflammatory bowel disease, for instance, is a perplexing spectrum of conditions that includes Crohn’s disease and ulcerative colitis. In a preliminary study, Relman and his colleagues identified signs of altered microbial communities in people with Crohn’s disease.

Using tissue samples obtained from the colons of about a dozen individuals, the researchers found that people with Crohn’s disease had more Escherichia coli, Pseudomonas, and other microbes known as proteobacteria than did people with ulcerative colitis or healthy individuals. However, the researchers still don’t know whether these microbes cause the disease and whether other microbes contribute to it.

Microbial signs

Microbial communities are not only critical to maintaining a healthy gut; they also play vital roles in many other parts of the body. David Fredricks, a microbiologist at the Fred Hutchison Cancer Research Center in Seattle, has been investigating a syndrome called bacterial vaginosis, a vaginal infection that affects 10 to 20 percent of women in the United States.

“It’s a curious disease because we still don’t fully understand what causes it,” he says. Although doctors can treat the infection with antibiotics, the rate of relapse is high. About half of affected women will develop another infection within a year after treatment.

In late 2005, Fredricks and his colleagues described experiments in which they sampled vaginal fluid from women with and without bacterial vaginosis. Using the 16S ribosomal gene, the researchers identified 35 bacterial species associated with the syndrome. More than half of these species had never before been identified. Three strains in particular showed up in almost all patients with bacterial vaginosis and were rare in women free of the syndrome.

Fredricks says that the findings support his hypothesis that bacterial vaginosis is “a disease by microbial community.” He believes that these bacteria are always found together because they are metabolically interdependent. “These bacteria can’t exist as single species,” he says.

Fredricks’ lab is currently monitoring a group of 30 women for changes in their vaginal flora over a month. The goal is to determine how women acquire bacterial vaginosis and how the microbial community causing the syndrome responds to antibiotics.

Investigations of the human microbiota could also shed light on complex skin conditions such as psoriasis and eczema. At present, most researchers consider psoriasis to be caused by the immune system gone awry. But because human skin is home to a complex ecosystem of mostly unidentified bacteria, Martin Blaser, a microbiologist at the New York University School of Medicine, suggests that microbes are involved. “The field of investigative dermatology has almost completely ignored the role of microbes,” he says.

To demonstrate the complexity of the skin’s microbiota, Blaser’s group analyzed skin swabs taken from the inner forearms of six healthy people. Reporting in the Feb. 20 Proceedings of the National Academy of Sciences, the researchers identified 182 species of bacteria. Each person showed a unique microbial makeup—only four species of bacteria were found in all six participants, and each participant carried an average of 48 species. The results offer a first glimpse of the diverse array of microbial species inhabiting healthy skin, Blaser says.

The researchers resampled four of the participants 8 to 10 months later and found many of the microbes previously identified along with 65 new bacterial species. All the volunteers had retained some of their previous microbial residents and had acquired new ones. The result suggests that each individual’s skin harbors both a core set of microbes and a group of transient members.

Blaser’s lab is now examining people with psoriasis to see whether there’s a microbial signature for the skin disease.

However, identifying individual species may be irrelevant in some cases of disease caused by microbial communities. “It might not matter who is there but rather what the collective is doing,” says Relman.

For instance, he’s found that some people with severe gum disease harbor an abundance of hydrogen-consuming microbes called methanogens. Related to bacteria but properly classified as archaea, methanogens live in the deep gaps between gums and teeth.

But not everyone with severe gum disease hosts methanogens. Other people’s afflicted mouths instead support large populations of hydrogen-consuming bacteria called treponemes.

Hydrogen is a by-product of fermentation in oxygen-deprived environments, such as the tooth-gum gaps, and it also limits growth among hydrogen-producing microbes. Relman says that through a behavior called syntropy, the hydrogen-consuming microbes—whether methanogens or treponemes—work together with the other microbes to stabilize the microbial community and keep it going.

Similarly, Gordon’s group found that two common species of gut microbes work together to boost fat storage in germ-free mice (SN: 6/17/06, p. 373: Available to subscribers at Fat Friends: Gut-microbe partners bring in more calories).

These observations reinforce the notion that to develop new medical therapies, researchers will need to consider all the interacting members of a microbial population.

Human genome II

As they delve deeper into this area, scientists expect to find great variation in the composition of microbial communities that inhabit different parts of the body. The skin microbes on a person’s forearm probably differ from those on his or her back, and the microbial communities in the colon most likely differ from those that inhabit the small intestine, the stomach, and the esophagus. Considering that the gastrointestinal tract is 6.5 meters long and contains up to 100 trillion microbes representing 1,000 different species, “we have our work cut out for us for a while,” says Gordon.

Improvements in DNA-sequencing technology and computational tools are accelerating the pace of research. Last year, a group of scientists led by University of Buffalo (N.Y.) microbiologist Steven Gill and including Gordon and Relman completed the first survey of the microbial genes in the human colon. In samples from two healthy adults, the team tallied more than 60,000 genes. The researchers reported their findings in the June 2, 2006 Science.

Rather than isolating each microbe and sequencing its entire genome, the researchers treated the microbial community as a collective with a single genome. The team analyzed all the microbial genes present without regard to any single gene’s cell of origin.

Called metagenomics, this form of analysis doesn’t produce a list of bacteria but instead describes the metabolic activities going on within a microbial community. These activities include energy conversion and the transport and break down of carbohydrates and amino acids.

Scientists have been using metagenomics for several years to describe microbial communities in soil and in the ocean. Only recently have they started applying the technique to the microbiota in people.

The National Institutes of Health is considering a Human Microbiome Project—an extension of the Human Genome Project—that would create a genetic inventory of the microbial communities inhabiting the body’s major niches, such as the mouth, vagina, skin, and intestinal tract. This spring, NIH is expected to decide whether to proceed with the project.

The Human Genome Project was an international effort that took 13 years to complete. A survey of the entire microbiota of a person would be an even more formidable undertaking. “In any one human, there are a hundred times as many microbial genes as there are human genes,” says Relman.

Furthermore, microbial communities may vary significantly over small distances within any given part of the body. For instance, Relman has found that a community’s membership changes from one part of a person’s mouth to another. There are differences between the front and back sides of teeth, he says, between the gum pockets of two adjacent teeth.

To further complicate matters, different people harbor different collections of microbes. Researchers will have to focus on the microbiota within an individual and within groups of individuals. “I think this is a global project in many senses of the word,” says Gordon. Ideally, researchers would survey microbes from people living in different ecosystems and under different socioeconomic conditions, he says.

The knowledge derived from such investigations could have an enormous impact not only on understanding human health and disease but also on the development of new therapies. Take, for instance, the chemical signals that microbes in the gut might use to manipulate human genes. “These chemicals then become potential components of a 21st-century medicine cabinet,” says Gordon.

Alternatively, pharmaceutical companies could develop drugs that target specific bacterial compounds to restore a microbial community in the body to its normal state.

Ultimately, says Gordon, “we will have a broader view of ourselves as a life form, as a composite of different species.”

Editor’s Note: The text of this online version of the article has been edited to correct an error in the noted passage.

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