The Culture of Antibiotic Discovery

Illustration by Anna Deen

Illustration by Anna Deen

Imagine transplanting every species on Earth onto the moon. Most species would not be able to survive the conditions of outer space, while a few might find ways to adapt to the new environment. This can be likened to the process of culturing bacterial samples in standard laboratory media: only a small fraction of the bacterial species in the sample grow in these conditions. Therefore, studying the microbial composition of an environmental sample through culturing techniques is inherently biased. In fact, 99 percent of this planet’s microorganisms remain unable to be cultivated in the laboratory and have been termed “microbial dark matter.”

This has dire consequences on the field of natural products research. Bacteria produce secondary metabolites, which are exploited for therapeutic use by humans. Given that up to 70 percent of drugs on the market were inspired by the chemical structures of natural products found in nature, the molecules that are produced by these uncultivable bacteria may represent a huge reservoir of potential medicines. This gives rise to the multi-million dollar question: how can we grow “microbial dark matter” in a laboratory setting and isolate the therapeutically useful molecules that they produce?

“The key is to maximize biodiversity,” states Michael Kinch, Director of the Centers for Research Innovation in Biotechnology & Drug Discovery at Washington University in St. Louis (WUSTL). This philosophy has manifested itself in the formulation of novel culturing strategies, which take environmental stimuli into account. Scientists are moving away from studying the secondary metabolite production of individual bacterial species, and towards examining populations of bacteria that coexist in various environments.

One microbiome of significant value to natural products research is the associated microbiota of marine invertebrates. Since these organisms are sessile (i.e., immobile), they rely on chemical, rather than physical, defense mechanisms to ward off predators. By engaging in a symbiotic relationship with microorganisms, these invertebrates can further capitalize on the chemical cornucopia biosynthesized by the microbes. In turn, the microbes thrive on the nutrients from the filter-feeding activity of the invertebrates and the stable supply of the scarce element nitrogen. Moreover, the microenvironment of the marine invertebrate surface presents a special set of conditions, even beyond pH, temperature, and pressure: chemical cues exchanged by microorganismal populations may be involved in the regulation of bacterial secondary metabolite production. This process, termed “quorum sensing,” cannot yet be recapitulated in the laboratory, due to the complexity of, and our lack of knowledge about, these kinds of interactions. As a consequence, the individual strains of bacteria present on the surface of marine invertebrates are difficult to culture in laboratory petri dishes that lack such biodiversity.    

The soil has also been regarded as a rich source of new natural products. Plant-associated bacteria engage in warfare and quorum sensing here in the rhizosphere using small molecules that can be exploited for therapeutic use. These secondary metabolites are produced in small quantities that often go undetected in chemical analyses of soil extracts. Here, too, the phenomenon of culturing bias limits the variety of strains that can be cultivated and investigated for natural product production. As such, the scientific media erupted in a frenzy in January 2015 when researchers at Northeastern University developed an instrument to accommodate the effects of environmental stimuli on bacterial growth. This device, called the iChip, enables scientists to incubate the bacterial sample in the soil itself, sandwiched between two semipermeable membranes that allow for diffusion of small molecules. By modeling the bacteria’s natural conditions, Dr. Lewis’s and Dr. Epstein’s labs were able to discover the production of a novel antibiotic by the soil bacteria.

The Human Microbiome Project, established by the National Institute of Health, studied the genetic information of the intestinal microbial community in the context of human health. Metagenomic techniques allowed researchers to harvest genetic material directly from the environment  without the need for cultivation–thus precluding culturing bias when determining which bacterial species populate our gut. While analyzing the metagenome of the gut microbiota in the context of human health, the genetic potential of these bacteria to biosynthesize antibiotics became apparent. In January 2016, Dr. Kim, et. al. of Harvard University probed the human microbiome with an innovative gut-on-a-chip microfluidic device that enables the gut microbiome to be co-cultured with commensal bacteria and epithelial cells. Moreover, the device mimics the mechanics of peristalsis and mucus production by microengineered intestinal villi to make the bacteria really feel at home.

Overall, in order to maximize the efforts of drug discovery from bacteria, scientists are modelling naturally existing microbiomes in the laboratory. Just as we are a product of our environment, bacteria, too, are influenced by many external interactions. Thus, the culture of antibiotic discovery is shifting towards inclusivity of the elements that define unique microenvironments while simulating biodiversity.  

For further reference:

  1. Hentschel, Ute, Jörn Piel, Sandie M. Degnan, and Michael W. Taylor. “Genomic insights into the marine sponge microbiome.” Nature Reviews Microbiology 10 (2012): 641-654. doi:10.1038/nrmicro2839
  2. Ling, Losee L., et al. “A new antibiotic kills pathogens without detectable resistance.” Nature 517 (2014): 455-459. doi:10.1038/nature14098
  3. Kim, Hyun Jung, Hu Li, James J. Collins, and Donald E. Ingber. “Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip.” PNAS 113.1 (2015): E7-E15. doi: 10.1073/pnas.1522193112

Neha Prasad is a junior from New Jersey. She can be reached at

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