Human Microbiome-Sequenced Data Yields an Antibiotic Candidate

by Jalwa Afroz ’17

Figure 1: Rapidly developing sequencing methods and analytical techniques are improving the way we understand the human microbiome.


Dr. John Chu and a team of researchers at Rockefeller University created a new bioinformatics approach in drug discovery to circumvent the need for bacterial culture and gene expression. Bacterial physiology is limited by the inability to culture most bacteria and also from the gene clusters silenced under lab fermentation conditions. The researchers set out to functionally characterize the data from the sequencing and bioinformatics analysis of the human microbiome and explore their synthetic bioinformatics natural products, syn-BNPs, for potential antibacterial activity.

The systematic bioinformatics analysis of sequenced bacterial genomes demonstrated that non-ribosomal peptides, NRPs, are common secondary metabolites produced by bacteria. The genomic sequence data of the human-microbiome for gene clusters predicted to encode NRPs of less than or equal to five residues. This analysis led to the discovery of 57 unique gene clusters that encoded for NRPs. Using these genes, 30 syn-BNPs targets on gene clusters were found in human bacterial sequence data. Then these syn-BNPs were assayed for antibacterial activity against a panel of common human pathogenic bacteria. This led to the discovery of two antibiotics that the researchers named humimycin A and humimycin B for ‘human microbiome mycin’.

Testing broth culture extracts from Rhodococcus through liquid chromatography (LC) and LC-mass spectrometry did not reveal any metabolites that resembled humimycins. However, the humimycins were active against Stapholococcus and Streptococcus species, which interestingly dominate the human microbiome of the gut. The researchers selected 23 S.aureus USA300 mutants that could survive 2.5 times the minimum inhibitory concentration (MIC) of 20 μg/mL, and sequenced their genomes. Compared to the parent strain, the mutants contained one non-synonymous mutation of a critical gene SAV1754. In addition, over expression of SAV1754 made S. aureus resistant to humimycins A. By inhibiting SAV1754, it is likely for humimycins to kill bacteria.

In some patients diagnosed with ulcerative colitis (UC), the Rhodococcus species in their guts is 30% higher than usual. Thus, the production of antibiotics, such as humimycin A, with activity against the R.erythropolis overpopulation in the UC gut could be a potential treatment. Also, the discovery of humimycins provides a testable lead for how disintegration of the gut microbiome in humans might lead to UC. This new bioinformatics approach to identifying bioactive metabolites has the potential to enable rapid and broader access to diverse bioactive compounds inspired by gene clusters found in the increasingly sequenced data of the microbiome.  


  1. J. Chu et al., Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nature Chemical Biology (2016). doi:10.1038/nchembio.2207.
  1. Image acquired from:

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