Scientists zero in on antibiotic-induced disruptions of gut microbes, amplified by intestinal activity

An antibiotic commonly found at low concentrations in the environment can have major impacts on gut bacteria, according to a new study by researchers at the University of Oregon and published in the Proceedings of the National Academy of Sciences of the United States of America.

The study applied three-dimensional microscopy to nearly transparent zebrafish to show how weak levels of antibiotics induce structural changes in gut bacterial communities that cause severe drops in the bacterial populations. Zebrafish larvae are a good model because they share many anatomical similarities with humans and other vertebrates, and their intestinal microbes can be directly observed, according to Raghuveer Parthasarathy, PhD, co-author of the study and a professor of physics.

For the study, larvae were observed with 3D microscopy as they were exposed to concentrations of the antibiotic ciprofloxacin at levels comparable to that often found in environmental samples. The researchers looked separately at zebrafish carrying one of two different bacterial species that are each frequently found in the zebrafish gut. Bacteria of one of the species are motile and fast-swimming. Bacteria of the other species are almost completely aggregated in dense colonies.

In the presence of the antibiotic, both types of bacteria showed dramatic changes in their behavior. The normally motile species became much slower and formed aggregates. The normally aggregated species shifted in structure to form even larger colonies, with less fragmentation.

In both cases, the enhanced aggregation made the bacteria more sensitive to the mechanical contractions of the intestines, leading to increased expulsion from the gut and more than hundred-fold drops in the intestinal populations.

Based on their observations, the researchers developed a mathematical model of bacterial dynamics in the gut, with predictions for colony sizes that matched experimental data. The model is similar to those of polymer and microparticle growth, showing, the co-authors write, that methods developed in physics can be fruitfully applied to studies of the gut microbiome. Parthasarathy said he expects the team's findings to apply to more than zebrafish.

"A wide range of bacteria respond to weak antibiotics by changing their shape and aggregation behaviors," he said. "All vertebrate intestines, humans' included, transport food and microbes, and their mechanics drive the motion of bacterial groups. We suspect, therefore, that the things we've discovered are quite general across species, including humans and other animals."