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Personalized Bug Genomics

Megan Scudellari

Like fingerprints, the DNA of the microbes in your gut has a unique profile and can be used to identify you.

Just three point mutations in two genes make Escherichia coli resistant to a major class of antibiotics. So, which of those mutations does the E. coli in your stomach harbor? A new technique to identify and characterize the DNA of all the microbes in the gut could provide the answer.

Researchers identified a remarkable amount of variation in the genomes of gut microbes—more than in the human genome. Source: NIH

In the first-ever study to catalog the genetic variation of microbes in the human gut, researchers at the Washington University School of Medicine in St. Louis, MO, and the European Molecular Biology Laboratory (EMBL) in Germany identified a remarkable amount of variation in the genomes of gut microbes—more than in the human genome, in fact. Also, the group showed for the first time that those differences vary from person to person and remain stable over time (1).

Each of us, the authors said, has a personalized gut microbial fingerprint, and knowledge about that unique profile could improve human health and medicine.

The researchers analyzed the DNA sequences of 252 stool samples obtained from the National Institutes of Health Human Microbiome Project and the Metagenomics of the Human Intestinal Tract (MetaHIT) project in Europe. Then, they compared those sequences with reference genomes from 101 microbes, including E. coli and species of Streptococcus and Clostridium.

It turns out that microbes in an individual’s gut have, on average, one genetic variant or single nucleotide polymorphism (SNP), per 150 nucleotides. The human genome, on the other hand, has about one variant for every 1000 nucleotides. “There seems to be more variation in bacteria” than in humans, said George Weinstock, senior author on the paper and associate director of The Genome Institute at Washington University, “which makes sense—they divide faster than we do and are more versatile when responding to selective pressures in their environment.”

Most of that genetic variation was found in genes that require versatility, such as antibiotic resistance genes. Areas of least variation occurred in genes coding for proteins that interact with the host and are necessary to survive in a hostile gut environment.

A subset of the samples in the study included 43 individuals sampled twice, at different times. From these samples, the team concluded that an individual’s collection of microbial strains is maintained over time, though the abundance of individual microbes may increase or decrease. “Your unique individualized microbiome is stable, and distinguishable from other people,” said Weinstock. “It’s just like your human genome. Slight differences in yours and mine distinguish us from each other.”

The genetic profile of the microbes in the gut can provide useful information for health, said Weinstock. An individual may harbor strains of bacteria that are particularly susceptible or resistant to certain drugs, for example, and a doctor could make medical decisions based on that information. And one day, perhaps, our own collection of gut bugs could be manipulated to improve the effectiveness of certain medications.


1. Schloissnig, S., M. Arumugam, S. Sunagawa, M. Mitreva, J. Tap, A. Zhu, et al. 2012. Genomic variation landscape of the human gut microbiome. Nature. (Epub ahead of print, December 5, 2012, doi:10.1038/nature11711)