The Effects of Antibiotics on Gut Bacteria May be Permanent

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According to new research completed at the Stanford University School of Medicine, the array of microflora present in the human colon is far more vast than once thought. While previous estimates ran to around five hundred species, this new research indicates that as many as 5,600 different bacterial species may be present in the average human gut.

This makes the human colon one of the most diverse ecosystems on the planet, not to mention the most densely-populated microbial community known to science. Estimates of the number of cells in the human body range between ten and one hundred trillion – but it has also been estimated that living in the gut alone, there are ten bacterial cells for every cell in the entire human body.

Clearly, the gut is densely populated. But what happens when antibiotics enter the mix? It has long been known that taking antibiotics disturbs the composition of the microflora which is normally present in the gut, but the extent of this disturbance has never been accurately measured.

Pyrosequencing – the DNA sequencing technique which allowed the Stanford researchers to quantify gut bacteria – has also allowed the same team to determine how the composition of gut microflora changes after exposure to an antibiotic.

To gain their results, the researchers used three healthy human test subjects, each of whom were given a five day course of Ciprofloxacin. Using pyrosequencing, they examined the composition of the gut microflora before, during, and after the antibiotic treatment.

Initially, the researchers found that the abundance of around one third of the species present in the gut was affected by the antibiotic treatment. Some bacteria which were low in number prior to antibiotic treatment became more numerous, while for others, the opposite situation occurred.

Some of these shifts in population persisted for some time – while the bacterial community was overall quick to recover, with most species returning to pre-treatment numbers within four weeks after cessation of antibiotic treatment, some species of bacteria failed to recover even after six months.

What are the Long-term Consequences?

These results raise some important questions about the long-term effects of not only antibiotics, but also other drugs and medical conditions as well – in fact anything which might change the composition of gut microflora.

Certain microbial populations present in the gut are known to mediate chemical reactions – and some of these reactions have been linked to obesity and cancer. Any permanent changes in gut microflora, as a result of antibiotics or any other cause, could therefore have potentially serious – but as yet unknown – health consequences.


Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing. PLoS Biol 6(11): e280 doi:10.1371/journal.pbio.0060280

O’Day K (2008) Gut Reaction: Pyrosequencing Provides the Poop on Distal Gut Bacteria. PLoS Biol 6(11): e295 doi:10.1371/journal.pbio.0060295