These days, most doctor’s are acutely aware of the problems of overprescribing antibiotics. Historically given as more of a placatory gesture – ‘I have to prescribe something, else this patient will think I’m an incompetent buffoon’ – their overuse almost single-handedly drove the rapid development of antibiotic-resistant bacteria, like MRSA. Yet we’re becoming more and more aware that antibiotics don’t only drive huge reactive changes in the bugs that we’re trying to kill, but also in our own bodies. Because the problem with antibiotics is their broad approach to killing – they don’t only target the ‘bad’ bugs, but also the trillions of happy, healthy bugs that live in our gut and work with us to digest food that we couldn’t process alone. The collective term for this huge community of microorganisms inhabiting our digestive tract is the, ‘microbiota‘, and it’s vital for maintaining a healthy gut.

We don’t really know much about the reactions of gut bacteria to antibiotic therapy, but since around 60% of faecal matter is made up of these microbes, your poop gives a good indication of what’s going on in the digestive tract. Researcher’s at the University of València in Spain analysed microbial changes in the faeces of one individual undergoing a 14 day course of beta-lactam therapy, a common class of antibiotics that control bacteria by interfering with their ability to build cell walls. The first bugs to be affected by the antibiotics were the gram-negative ones, whose numbers dropped off rapidly. The overall diversity of the gut microbiota plummeted, as only bugs that were naturally resistant to beta-lactams were able to survive: they began thriving after the death of antibiotic-susceptible bugs freed up large pools of nutrients. Then, gram-positive bugs began to overpopulate the gut. This bacterial imbalance hampered the metabolism of vitamins D and B12, cholesterol, hormones and iron, leading to potential dietary deficiencies. Four weeks after antibiotic treatment had finished, gut digestive function improved as surviving gut microbes began to re-establish normal service, but certain ‘good’ bugs that had been present before antibiotic therapy began did not reappear and likely had been permanently wiped out.

This research builds up an intriguing picture of how the gut microbiota changes during antibiotic therapy. It also suggests that antibiotics should continue to be reserved for only the most compelling bacterial diseases, since such disturbances in the gut microbiota are likely to drive the acquisition of antibiotic-resistance, the overgrowth of dangerous bacteria and the unhealthy loss of ancient ‘good’ gut bacteria.

Pérez-Cobas AE, Gosalbes MJ, Friedrichs A, Knecht H, Artacho A, Eismann K, Otto W, Rojo D, Bargiela R, von Bergen M, Neulinger SC, Däumer C, Heinsen FA, Latorre A, Barbas C, Seifert J, Dos Santos VM, Ott SJ, Ferrer M, & Moya A (2012). Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut PMID: 23236009