Bacterial production of drug-like molecules in the human gut

The human gut microbiota offers a new venue for unexplored natural compounds that can be used for drug development.

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Article highlights

  • Heterologous expression of biosynthetic gene clusters from the human gut microbiome enables exploitation of organisms that are refractory to culturing or genetic manipulation
  • The human gut microbiota produce secondary metabolites that are structurally similar to existing clinical drugs and can inhibit human targets (e.g. proteases)
  • Transcription of biosynthetic gene clusters is linked to host-colonization

The majority of studies attempting to study the human gut microbiome seek to identify the members composing this community. However, the ultimate goal is to find functional linkages between the different perturbations to which the microbial communities in the human gastrointestinal (GI) tract are being exposed in both healthy and diseased states. Towards this end, Fischback et al. identified a set of biosynthetic gene clusters (BGCs) in the GI microbiome that encode nonribosomal peptide synthetases (NRPSs) which are well-established factories of complex and effective natural products. This is particularly interesting since most of the human gut microbiota are refractory for culturing and genetic manipulation. To overcome this hurdle, the authors heterologously expressed BCGs in routinely cultured lab bacterial species; E. coli and B. subtilis. The authors also confirmed that these gene cluster families are widely distributed in healthy human subjects by screening against a large gene catalog of > 9 million gut microbiome genes and ~ 150 metagenomic stool samples. In addition, since the mere presence of a gene cluster doesn’t necessarily indicate its activity, the authors analysed metatranscriptomics data from stool samples where at least one cluster was actively transcribed in > 90% of the samples. Several of the newly characterised gut NRPSs produced peptide aldehydes which were shown to inhibit proteases, particularly cathepsin, as their principal target.

Overall, the identification of new BCGs from the human gut microbiome expands the pool of natural products that can be potential drug candidates.

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases


The gut microbiota modulate host biology in numerous ways, but little is known about the molecular mediators of these interactions. Previously, we found a widely distributed family of nonribosomal peptide synthetase gene clusters in gut bacteria. Here, by expressing a subset of these clusters in Escherichia coli or Bacillus subtilis, we show that they encode pyrazinones and dihydropyrazinones. At least one of the 47 clusters is present in 88% of the National Institutes of Health Human Microbiome Project (NIH HMP) stool samples, and they are transcribed under conditions of host colonization. We present evidence that the active form of these molecules is the initially released peptide aldehyde, which bears potent protease inhibitory activity and selectively targets a subset of cathepsins in human cell proteomes. Our findings show that an approach combining bioinformatics, synthetic biology, and heterologous gene cluster expression can rapidly expand our knowledge of the metabolic potential of the microbiota while avoiding the challenges of cultivating fastidious commensals.


Chun-Jun Guo, Fang-Yuan Chang, Thomas P. Wyche, Keriann M. Backus, Timothy M. Acker, Masanori Funabashi, Mao Taketani, Mohamed S. Donia, Stephen Nayfach, Katherine S. Pollard, Charles S. Craik, Benjamin F. Cravatt, Jon Clardy, Christopher A. Voigt, Michael A. Fischbach. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017 Jan 26;168(3):517-526.e18. doi: 10.1016/j.cell.2016.12.021.

Image credit: National Human Genome Research Institute (NHGRI) on Flickr used under Creative Commons (CC BY 2.0)

Alyaa Mohamed

PhD student, King Abdullah University of Science and Technology

I am a PhD student at the Computational Bioscience Research Centre (CBRC) at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia. I am interested in using open source data to understand human infectious diseases. My research interests is mainly in systems biology of infectious agents and how they interact with the infected hosts.