Gut Reaction: Environmental Effects on the Human Microbiota

By Phillips, Melissa Lee | Environmental Health Perspectives, May 2009 | Go to article overview

Gut Reaction: Environmental Effects on the Human Microbiota


Phillips, Melissa Lee, Environmental Health Perspectives


Living with each of us--on our skin, in our mucosa, and in our gastrointestinal (GI) tract--are microorganisms whose numbers dwarf the number of our own cells and genes. Although some of these microbes are pathogens, most are harmless or even beneficial. The body's assortment of microorganisms, collectively called the microbiota, is similar to an organ in that it performs functions essential for our survival. Some microbes produce vitamins and other essential nutrients. Many metabolize food that we can't digest on our own. They also break down drugs and toxins, and regulate many aspects of innate and acquired immunity, protecting the host from infections and chronic inflammation, as well as possibly many immune-based disorders. And just as with the heart or the lungs, when an environmental agent alters the function of the microbiota, the result can be disease.

Most environment-microbiota research has focused on the gut, home to some 100 trillion microorganisms--the vast majority of our complement of microbes. Shifts in the microbial species that reside in our intestines have been associated with a long list of pathologies, from allergies and autoimmune diseases to obesity and cancer. Some researchers even suspect that the microbiota may play a role in autism spectrum disorders (ASDs).

Each of us carries thousands of bacterial species in our gut along with a few species of other types of organisms. Although all humans have grossly similar microbiota, no two people have exactly the same composition of bacterial species in their guts--in fact, each individual's microbial consortium may turn out to be as unique as a fingerprint. Yet a study published 22 January 2009 in Nature reported that, although individual bacterial species can differ widely between people, the species tend to encode the same metabolic pathways, says coauthor Ruth Ley, an assistant professor of microbiology at Cornell University. "You see the same gene functions regardless of the suite of bacteria present," Ley says.

Outside influences such as antibiotic use, diet, and psychological stress have shown strong correlations with what lives inside our bodies, and researchers are just beginning to understand how these environmental factors may affect our health. Recent advances in genomic sequencing technologies have pushed the field forward. Whereas scientists once could study only those microorganisms that are easily cultured in a lab--which precludes most of the anaerobic gut microbes--they can now sequence the entire collection of DNA in a microbial sample and identify the component species. This approach, called metagenomics, has been key to many recent advances in understanding the relationship between our microbiota and our health.

Our Microbial Partners

The infant GI tract is colonized with microorganisms in a complex process that begins during birth and is thought to depend partly on host genetics and partly on the microbes that happen to be in the child's environment. Babies delivered via cesarean section show different microbial profiles than those born vaginally--whereas vaginally delivered infants are colonized at first by fecal and vaginal bacteria from the mother, infants born through cesarean section are exposed initially to bacteria originating from the hospital environment and health care workers. Research by Giacomo Biasucci et al. in the September 2008 issue of the Journal of Nutrition showed that the gut microbiota after cesarean delivery was characterized by an absence of Bifidobacteria species, which are thought to be important to the postnatal development of the immune system, whereas vaginally delivered neonates showed a predominance of these species. In general, cesarean-born children also tend to have delayed access to mother's milk, which has a potent influence on gut microbiota. [For more information, see "Contaminants in Human Milk: Weighing the Risks against the Benefits of Breast-feeding," EHP 116:A426-A434 (2008). …

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