Medical Research News

Using a novel technique developed by Mitchell Sogin of the Marine Biological Laboratory (MBL) to identify different types of bacteria, scientists have completed the most precise survey to date of how microbial communities in the human gut respond to antibiotic treatment.

Sogin, director of the MBL's Josephine Bay Paul Center, and Susan Huse of the MBL, along with David Relman and Les Dethlefsen of Stanford University, identified pervasive changes in the gut microbial communities of 3 healthful humans after a five-day course of the antibiotic Ciprofloxacin. Their results are reported in the Nov. 18 issue of PloS Biology .

Using very conservative criteria, the scientists identified at least 3,300 to 5,700 different taxa (genetically different types) of bacteria in the human distal gut, and antibiotic treatment influenced the abundance of about a third of those taxa.

"You evidently get shifts in the structure of the microbial community with antibiotic treatment," says Sogin. "Some bacteria that were in low abundance previous to treatment may become more abundant, and bacteria that were dominant may decrease in abundance. When you get these shifts, they may be persistent. Some individuals may recover rapidly, and others won't recover for many months."

In all the individuals tested in this study, the bacterial community recovered and nearly resembled its pre-treatment state within four weeks after the antibiotic course finished, but several bacterial taxa failed to recover within six months.

This raises questions about the health effects of perturbations to the human-microbial symbiosis in the gut, like may happen with antibiotic treatment. Because particular microbial populations mediate many chemical transformations in the gut-and preceding studies have related these processes to cancer and fatness, among other conditions-changes in the composition of the gut microbiota could have meaningful, but as yet undiscovered, health effects.

"When you change the microbial population structure in the gut, you may affect how that population is keeping indigenous pathogens at manageable levels," says Sogin. Bacteria that do not typically cause problems, for instance, may start to grow more speedily, and cause disease.

The study is part of a large, international effort to completely characterize the microbiota in the human gut, which is the highest-density natural bacterial ecosystem known. Up to 100 trillion microbial cells reside in the gut, and this community plays important roles in nutrition, development, metabolism, pathogen resistance, and regulation of immune responses.

Until lately, descriptions of human-associated microbiota were constrained by techniques of cultivating (and therefore identifying) bacteria. Less than 20-40% of the microbes in the human distal gut, for instance, have been cultured in the laboratory. Since the late 1980s, on the other hand, cultivation-independent microbial surveys have been developed that identify community members by genetic sequencing. Sogin's technique, for instance, which was used in this study, characterizes microbial populations by sequencing short, hypervariable regions of one gene usual to all microbes, the 16S rRNA gene. This pyrosequencing technique reveals greater taxonomic richness in microbial samples at a fraction of the cost of traditional sequencing technologies.

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