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Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra

Nature Microbiology volume 8, pages 2420–2434 (2023)Cite this article

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Abstract

Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.

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Fig. 1: Genome mining and reconstruction of lanthipeptide gene clusters.
Fig. 2: RiPP modifications deduced by mass spectroscopy.
Fig. 3: Activity of RiPPs against human-derived bacterial species, including commensal and pathogenic strains.
Fig. 4: Structural and functional analyses of LANII-687 (left) and LANII-287 (right).

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Data availability

The RiPPs biosynthetic pathways found in this study are available in NCBI (https://www.ncbi.nlm.nih.gov/), with identifiers listed in Supplementary Table 5 and Source data. All DNA sequences are listed in Supplementary Table 5. Data supporting the findings of this study are available within the paper and supplementary materials. Additional data, strains and plasmids are available from the corresponding author upon reasonable request. Source data are provided with this paper.

Code availability

Python scripts used for LC–MS processing have been released as open source software under the MIT license (GitHub repository: https://github.com/dantheand/msms_structure_annot).

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Acknowledgements

We thank C. A. Sheahan (Harvard Medical School) for help with nuclear magnetic resonance. This research was funded by a research award from Novartis Institute for BioMedical Research (Cambridge, USA), US Defense Advanced Research Projects Agency’s Living Foundries programme award HR0011-15-C-0084, and the Banting Fellowships Program (A.M.K).

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  1. These authors contributed equally: Andrew M. King, Zhengan Zhang.

Authors and Affiliations

  1. Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Andrew M. King, Zhengan Zhang, Emerson Glassey & Christopher A. Voigt

  2. Synthetic Biology Group, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA

    Piro Siuti

  3. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA

    Jon Clardy

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  1. Andrew M. King
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Contributions

Z.Z., A.M.K., P.S., J.C. and C.A.V. conceived the study and designed the experiments. Z.Z. and A.M.K. performed experiments. E.G. performed the bioinformatics. Z.Z., A.M.K. and C.A.V. wrote the manuscript.

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Correspondence to Christopher A. Voigt.

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Extended data

Extended Data Fig. 1 Network map of sequence similarities between RiPP gene clusters from human microbiome genomes.

antiSMASH 4.0 was used to identify BGCs from 2,229 HMP genome sequences. 2,248 RiPP BGCs were then clustered using BiG-SCAPE with default cutoff parameters (0.30) and visualized with Cytoscape. Nodes represent individual clusters colored by biosynthetic class. BGC nodes with similar cluster architecture are attached by edges using cutoff values as described in Methods.

Extended Data Fig. 2 Network map of sequence similarities between RiPP gene clusters selected for expression.

The networks for (a) lasso peptides and (b) lanthipeptides are shown. BGC nodes from the same network generated in Extended Data Fig. 1 were extracted to create the simplified visualization shown here. BGCs selected for gene synthesis and heterologous expression are colored with green circles.

Extended Data Fig. 3 Genome mining and reconstruction of lasso peptide gene clusters.

(a) An example of a native gene cluster. The precursor peptide is expressed, the leader cleaved (LasB), and the resulting free amine cyclized to the side chain of an Asp/Glu residue (LasC). The grey gene encodes a transporter. To build the synthetic gene cluster, each gene is codon optimized (dashed lines) and placed under the control of a synthetic ribozyme insulator, RBS, and terminator. The precursor peptide is fused to RSTC. (b) An example synthetic gene cluster is shown along with synthetic genetic parts (Supplementary Table 4). The components of the RSTN tag are shown (black, His6-tag; dark blue, SUMO; orange, thrombin protease site; white, linkers). A thrombin protease site (orange) is added before SUMO (dark blue) in the precursor peptide, and this leaves a C-terminal RVLP on the core (black circle). Dashed lines in the genome indicate the presence of other inducible systems in the E. coli Marionette X strain.

Extended Data Fig. 4 Mass spectrometry data for LANII-286.

(a) Peptide and biosynthetic gene cluster details. The genes synthesized are shown in blue and sequences are provided in Supplementary Table 3. (b) Proposed annotated structure. (c) High-res mass spectrometry traces of peptides selected for tandem MS/MS. An arrow indicates the monoisotopic mass chosen for fragmentation (m/z 1793.7391). (d) N-ethylmaleimide (NEM) labeling of peptides. Top trace, TCEP-treated peptide without the addition of NEM (black). Bottom trace, TCEP-treated peptides with the addition of NEM (purple). Each NEM adduct would lead to an increase in mass of 125.05 Da. For each peptide, the predicted masses for up to the maximum number of NEM adducts were used to generate extracted ion chromatograms. An extraction window of the mass +/- 0.25 Da was used. The grey bars correspond to the predicted masses for 1, 2,… n non-cyclized residues (no grey bars means that no adduct is detected, meaning the product is completely cyclized). (e) MS/MS spectrum of the modified peptide. The amino acid sequence of the peptide is shown with observed b and y ions mapped. The blue lines capped with a blue dot mark the labeled experimental peaks.

Extended Data Fig. 5 Mass spectrometry data for LANII-287.

(a) Peptide and biosynthetic gene cluster details. The genes synthesized are shown in blue and sequences are provided in Supplementary Table 3. (b) Proposed annotated structure. (c) High-res mass spectrometry traces of peptides selected for tandem MS/MS. An arrow indicates the monoisotopic mass chosen for fragmentation (m/z 1776.2837). (d) N-ethylmaleimide (NEM) labeling of peptides. Top trace, TCEP-treated peptide without the addition of NEM (black). Bottom trace, TCEP-treated peptides with the addition of NEM (purple). Each NEM adduct would lead to an increase in mass of 125.05 Da. For each peptide, the predicted masses for up to the maximum number of NEM adducts were used to generate extracted ion chromatograms. An extraction window of the mass +/- 0.25 Da was used. (e) MS/MS spectrum of the modified peptide. The amino acid sequence of the peptide is shown with observed b and y ions mapped. The blue lines capped with a blue dot mark the labeled experimental peaks.

Extended Data Fig. 6 Mass spectrometry data for LANII-916.

(a) Peptide and biosynthetic gene cluster details. The genes synthesized are shown in blue and sequences are provided in Supplementary Table 3. (b) Proposed annotated structure. (c) High-res mass spectrometry traces of peptides selected for tandem MS/MS. An arrow indicates the monoisotopic mass chosen for fragmentation (m/z 1163.8450). (d) N-ethylmaleimide (NEM) labeling of peptides. Top trace, TCEP-treated peptide without the addition of NEM (black). Bottom trace, TCEP-treated peptides with the addition of NEM (purple). Each NEM adduct would lead to an increase in mass of 125.05 Da. For each peptide, the predicted masses for up to the maximum number of NEM adducts were used to generate extracted ion chromatograms. An extraction window of the mass +/- 0.25 Da was used. The grey bars correspond to the predicted masses for 1, 2,… n non-cyclized residues (no grey bars means that no adduct is detected, meaning the product is completely cyclized). (e) MS/MS spectrum of the modified peptide. The amino acid sequence of the peptide is shown with observed b and y ions mapped. The blue lines capped with a blue dot mark the labeled experimental peaks.

Extended Data Fig. 7 Mass spectrometry data for LANII-417.

(a) Peptide and biosynthetic gene cluster details. The genes synthesized are shown in blue and sequences are provided in Supplementary Table 3. (b) Proposed annotated structure. (c) High-res mass spectrometry traces of peptides selected for tandem MS/MS. An arrow indicates the monoisotopic mass chosen for fragmentation (m/z 1381.5389). (d) N-ethylmaleimide (NEM) labeling of peptides. Top trace, TCEP-treated peptide without the addition of NEM (black). Bottom trace, TCEP-treated peptides with the addition of NEM (purple). Each NEM adduct would lead to an increase in mass of 125.05 Da. For each peptide, the predicted masses for up to the maximum number of NEM adducts were used to generate extracted ion chromatograms. An extraction window of the mass +/- 0.25 Da was used. (e) MS/MS spectrum of the modified peptide. The amino acid sequence of the peptide is shown with observed b and y ions mapped. The blue lines capped with a blue dot mark the labeled experimental peaks.

Extended Data Fig. 8 Mass spectrometry data for LANII-687.

(a) Peptide and biosynthetic gene cluster details. The genes synthesized are shown in blue and sequences are provided in Supplementary Table 3. (b) Proposed annotated structure. (c) High-res mass spectrometry traces of peptides selected for tandem MS/MS. An arrow indicates the monoisotopic mass chosen for fragmentation (m/z 1619.2318). (d) N-ethylmaleimide (NEM) labeling of peptides. Top trace, TCEP-treated peptide without the addition of NEM (black). Bottom trace, TCEP-treated peptides with the addition of NEM (purple). Each NEM adduct would lead to an increase in mass of 125.05 Da. For each peptide, the predicted masses for up to the maximum number of NEM adducts were used to generate extracted ion chromatograms. An extraction window of the mass +/- 0.25 Da was used. The grey bars correspond to the predicted masses for 1, 2,… n non-cyclized residues (no grey bars means that no adduct is detected, meaning the product is completely cyclized). (e) MS/MS spectrum of the modified peptide. The amino acid sequence of the peptide is shown with observed b and y ions mapped. The blue lines capped with a blue dot mark the labeled experimental peaks.

Extended Data Fig. 9 Mass spectrometry data for LANII-691.

(a) Peptide and biosynthetic gene cluster details. The genes synthesized are shown in blue and sequences are provided in Supplementary Table 3. (b) Proposed annotated structure. (c) High-res mass spectrometry traces of peptides selected for tandem MS/MS. An arrow indicates the monoisotopic mass chosen for fragmentation (m/z 1426.6661). (d) N-ethylmaleimide (NEM) labeling of peptides. Top trace, TCEP-treated peptide without the addition of NEM (black). Bottom trace, TCEP-treated peptides with the addition of NEM (purple). Each NEM adduct would lead to an increase in mass of 125.05 Da. (e) MS/MS spectrum of the modified peptide. The amino acid sequence of the peptide is shown with observed b and y ions mapped. The blue lines capped with a blue dot mark the labeled experimental peaks.

Extended Data Fig. 10 MIC assay for RiPPs against human pathogens and commensals.

The antimicrobial activity of (a) LANII-286, (b) LANII-287, (c) LANII-417, (d) LANII-687, (e) LANII-691 and (f) LANII-916 were tested against human pathogens (Methods). The data points show three replicates performed on different days and the lines show the means of these data. The % Growth was calculated for each day and then these values were averaged.

Supplementary information

Supplementary Information

Supplementary Text, Figs. 1–20, Tables 1–5 and references.

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Source data

Source Data Fig. 2

Antismash files for RiPP gene clusters.

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King, A.M., Zhang, Z., Glassey, E. et al. Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra. Nat Microbiol 8, 2420–2434 (2023). https://doi.org/10.1038/s41564-023-01524-6

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