NIH Launches Human Microbiome Project

NIH Roadmap Effort to Use Genomic Technologies To Explore Role of Microbes in Human Health and Disease.

The human body contains trillions of microorganisms, living together with human cells, usually in harmony. Because of their small size, however, microorganisms make up only about one to two percent of the body’s mass. Many microbes maintain our health, while others cause illness. Yet, surprisingly little is known about the role this astounding assortment of bacteria, fungi and other microbes play in human health and disease. To better understand these interactions, the National Institutes of Health (NIH) today announced the official launch of the Human Microbiome Project. The human microbiome is the collective genomes of all microorganisms present in or on the human body.

“The human microbiome is largely unexplored,” said NIH Director Elias A. Zerhouni, M.D. “It is essential that we understand how microorganisms interact with the human body to affect health and disease. This project has the potential to transform the ways we understand human health and prevent, diagnose and treat a wide range of conditions.”

Part of the NIH’s Roadmap for Medical Research, the Human Microbiome Project will award a total of $115 million to researchers over the next five years. Initially, researchers will sequence 600 microbial genomes, completing a collection that will total some 1,000 microbial genomes and providing a resource for investigators interested in exploring the human microbiome. Other microbial genomes are being contributed to the collection by individual NIH institutes and internationally funded projects. A meeting between international partners was recently convened to discuss forming an international consortium.

Researchers will then use new, comprehensive laboratory technologies to characterize the microbial communities present in samples taken from healthy human volunteers, even for microbes that cannot be grown in the laboratory. The samples will be collected from five body regions known to be inhabited by microbial communities: the digestive tract, the mouth, the skin, the nose, and the female urogenital tract. Demonstration projects will subsequently be funded to sample the microbiomes from volunteers with specific diseases. This will allow researchers to correlate the relationship between changes in a microbiome present at a particular body site to a specific illness.

“We now understand that there are more microbial cells than human cells in the human body. The Human Microbiome Project offers an opportunity to transform our understanding of the relationships between microbes and humans in health and disease,” said Dr. Alan Krensky, the director of the Office of Portfolio Analysis and Strategic Initiatives (OPASI), which oversees the NIH Roadmap for Medical Research.

While the term “microbiome” may be relatively new in biomedical research, most people are familiar with some of the effects — both good and bad — that microbes can have on our health. Consider the example of the biggest reservoir of microbes in humans: the digestive tract. The human gut harbors many beneficial microorganisms, including certain bacteria called probiotics. There is evidence these probiotics, found in dietary supplements, yogurt and other dairy products as well as various soy products, can stimulate the immune system and improve digestive functions. In contrast, previous research suggests that variations in the composition of microbial communities may contribute to chronic health conditions, including diabetes, asthma, obesity and digestive disorders. […]

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Propionibacterium acnes strain populations in the human skin microbiome associated with acne

Kate

The human skin microbiome plays important roles in skin health and disease. However, bacterial population structure and diversity at the strain level is poorly understood. We compared the skin microbiome at the strain level and genome level of Propionibacterium acnes, a dominant skin commensal, between 49 acne patients and 52 healthy individuals by sampling the pilosebaceous units on their noses. Metagenomic analysis demonstrated that while the relative abundances of P. acnes were similar, the strain population structures were significantly different in the two cohorts. Certain strains were highly associated with acne and other strains were enriched in healthy skin. By sequencing 66 previously unreported P. acnes strains and comparing 71 P. acnes genomes, we identified potential genetic determinants of various P. acnes strains in association with acne or health. Our analysis suggests that acquired DNA sequences and bacterial immune elements may play roles in determining virulence properties of P. acnes strains and some could be future targets for therapeutic interventions. This study demonstrates a previously unreported paradigm of commensal strain populations that could explain the pathogenesis of human diseases. It underscores the importance of strain level analysis of the human microbiome to define the role of commensals in health and disease.

The diversity of the human microbiota at the strain level and its association with human health and disease is largely unknown. However, many studies have shown that microbe-related human diseases are often caused by certain strains of a species, rather than the entire species being pathogenic. Examples include methicillin-resistant Staphylococcus aureus (MRSA) (Chambers and Deleo, 2009; Chen et al., 2010; Hansra and Shinkai) and Escherichia coli O157 (Chase-Topping et al., 2008; Tarr et al., 2005). Acne vulgaris (commonly called acne) is one of the most common skin diseases with a prevalence of up to 85% of teenagers and 11% of adults (White, 1998). Although the etiology and pathogenesis of acne are still unclear, microbial involvement is considered one of the main mechanisms contributing to the development of acne (Bojar and Holland, 2004; Cunliffe, 2002). In particular, Propionibacterium acnes has been hypothesized to be an important pathogenic factor (Webster, 1995). Antibiotic therapy targeting P. acnes has been a mainstay treatment for more than 30 years (Leyden, 2001). However, despite decades of study, it is still not clear how P. acnes contributes to acne pathogenesis while being a major commensal of the normal skin flora (Bek-Thomsen et al., 2008; Cogen et al., 2008; Costello et al., 2009; Dominguez-Bello et al., 2010; Fierer et al., 2008; Gao et al., 2007; Grice et al., 2009). Whether P. acnes protects the human skin as a commensal bacterium or functions as a pathogenic factor in acne, or both, remains to be elucidated. […]

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Probiotics: Cure for Acne?

Kate

Your odds of having acne may depend on whether the “good” strain of a particular type of bacteria lives on your skin, a new study suggests.

“People never think of wanting to have good bacteria on their skin,” said lead author Huiying Li, an assistant professor of molecular and medical pharmacology at the University of California, Los Angeles. “But some of them you should love.” It’s the presence of acne-defeating bacteria that allows people without acne to live relatively pimple-free, she explained.

Li and her team studied the bacterial strains on people’s faces using genomic analysis of microbial DNA. They discovered that the bacteria responsible for acne — called Propionibacterium acnes or P. acnes — are more complex than previously understood.

When studied at the genomic level, bacteria with the same name were actually representative of three different strains. People with acne tend to have one or two of the strains associated with the condition, while those with healthy skin have a good strain that seems to destroy offending bacteria.

So whether or not you develop acne may be tied to what strain of P. acnes your skin carries.

The strain of P. acnes that is associated with healthy skin works much like the way live bacteria in yogurt help defend the intestines from harmful bacteria, Li said.

“Our next step will be to explore whether a probiotic cream might block bad bacteria from invading the skin, preventing pimples before they start,” Li said. She hopes to find a way to transplant the good strain of bacteria that is plentiful on the faces of people with healthy skin to those with acne.

Acne is the most common skin condition in the United States, affecting 40 to 50 million people — primarily teens and young adults — but it can strike at any age, according to the American Academy of Dermatology. Li said archeological records show the disease goes back to ancient Egypt, where Pharaohs used magic and spells to try to treat the problem. Acne is typically treated with oral medications such as antibiotics, and topical creams that can help reduce oil on the skin and kill bacteria.

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