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Antibiotics Can Cause Pervasive, Persistent Changes To Microbiota In
Human Gut

ScienceDaily (Nov. 19, 2008) — 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 three healthy 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 distinct types) of bacteria
in the human distal gut, and antibiotic treatment influenced the
abundance of about a third of those taxa.

“You clearly get shifts in the structure of the microbial community
with antibiotic treatment,” says Sogin. “Some bacteria that were in
low abundance prior 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
quickly, and others won’t recover for many months.”

In all the individuals tested in this study, the bacterial community
recovered and closely resembled its pre-treatment state within four
weeks after the antibiotic course ended, 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, such as may occur with
antibiotic treatment. Because specific microbial populations mediate
many chemical transformations in the gut—and previous studies have
related these processes to cancer and obesity, among other conditions—
changes in the composition of the gut microbiota could have important,
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 normally cause
problems may begin to grow more rapidly, and cause disease.

The study is part of a large, international effort to fully
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 essential
roles in nutrition, development, metabolism, pathogen resistance, and
regulation of immune responses.

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

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Story Source:

The above story is reprinted (with editorial adaptations by
ScienceDaily staff) from materials provided by Marine Biological


Journal Reference:

1.Dethlefsen et al. The Pervasive Effects of an Antibiotic on the
Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing. PLoS
Biology, 2008; 6 (11): e280 DOI: 10.1371/journal.pbio.0060280