Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Commensal bacteria make GPCR ligands that mimic human signalling molecules

A Corrigendum to this article was published on 05 April 2018

This article has been updated


Commensal bacteria are believed to have important roles in human health. The mechanisms by which they affect mammalian physiology remain poorly understood, but bacterial metabolites are likely to be key components of host interactions. Here we use bioinformatics and synthetic biology to mine the human microbiota for N-acyl amides that interact with G-protein-coupled receptors (GPCRs). We found that N-acyl amide synthase genes are enriched in gastrointestinal bacteria and the lipids that they encode interact with GPCRs that regulate gastrointestinal tract physiology. Mouse and cell-based models demonstrate that commensal GPR119 agonists regulate metabolic hormones and glucose homeostasis as efficiently as human ligands, although future studies are needed to define their potential physiological role in humans. Our results suggest that chemical mimicry of eukaryotic signalling molecules may be common among commensal bacteria and that manipulation of microbiota genes encoding metabolites that elicit host cellular responses represents a possible small-molecule therapeutic modality (microbiome-biosynthetic gene therapy).

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: hm-NAS genes in gastrointestinal microbiota.
Figure 2: N-acyl synthase gene expression in vivo.
Figure 3: GPCR activity screen of human N-acyl amides.
Figure 4: Structural mimicry of GPCR ligands.
Figure 5: N-acyl serinols affect GLP-1 secretion in vitro and glucose homeostasis in vivo.

Change history

  • 04 April 2018

    Please see accompanying Corrigendum ( description in the Methods of the human stool samples used for the analysis presented in Extended Data Figure 9 has been corrected, with patient age, gender and transplant indication provided in the table now added to Extended Data Fig. 9. The Reporting Summary has been updated. The original Article has been corrected online.


  1. Koppel, N. & Balskus, E. P. Exploring and understanding the biochemical diversity of the human microbiota. Cell Chem. Biol. 23, 18–30 (2016)

    CAS  PubMed  Google Scholar 

  2. Meinwald, J. & Eisner, T. Chemical ecology in retrospect and prospect. Proc. Natl Acad. Sci. USA 105, 4539–4540 (2008)

    ADS  CAS  PubMed  Google Scholar 

  3. Cohen, L. J. et al. Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist. Proc. Natl Acad. Sci. USA 112, E4825–E4834 (2015)

    CAS  PubMed  Google Scholar 

  4. Cani, P. D. et al. Endocannabinoids — at the crossroads between the gut microbiota and host metabolism. Nat. Rev. Endocrinol. 12, 133–143 (2016)

    CAS  PubMed  Google Scholar 

  5. Pacher, P. & Kunos, G. Modulating the endocannabinoid system in human health and disease—successes and failures. FEBS J. 280, 1918–1943 (2013)

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Moore, E. K. et al. Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans. Front. Microbiol. 6, 637 (2015)

    PubMed  PubMed Central  Google Scholar 

  7. Geiger, O., González-Silva, N., López-Lara, I. M. & Sohlenkamp, C. Amino acid-containing membrane lipids in bacteria. Prog. Lipid Res. 49, 46–60 (2010)

    CAS  PubMed  Google Scholar 

  8. Zhang, X., Ferguson-Miller, S. M. & Reid, G. E. Characterization of ornithine and glutamine lipids extracted from cell membranes of Rhodobacter sphaeroides. J. Am. Soc. Mass Spectrom. 20, 198–212 (2009)

    CAS  PubMed  Google Scholar 

  9. Flock, G., Holland, D., Seino, Y. & Drucker, D. J. GPR119 regulates murine glucose homeostasis through incretin receptor-dependent and independent mechanisms. Endocrinology 152, 374–383 (2011)

    CAS  PubMed  Google Scholar 

  10. Schulze, T. et al. Sphingosine-1-phospate receptor 4 (S1P4) deficiency profoundly affects dendritic cell function and TH17-cell differentiation in a murine model. FASEB J. 25, 4024–4036 (2011)

    CAS  PubMed  Google Scholar 

  11. Le, L. Q. et al. Mice lacking the orphan G protein-coupled receptor G2A develop a late-onset autoimmune syndrome. Immunity 14, 561–571 (2001)

    CAS  PubMed  Google Scholar 

  12. Konya, V., Marsche, G., Schuligoi, R. & Heinemann, A. E-type prostanoid receptor 4 (EP4) in disease and therapy. Pharmacol. Ther. 138, 485–502 (2013)

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Kabashima, K. et al. The prostaglandin receptor EP4 suppresses colitis, mucosal damage and CD4 cell activation in the gut. J. Clin. Invest. 109, 883–893 (2002)

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Manieri, N. A. et al. Mucosally transplanted mesenchymal stem cells stimulate intestinal healing by promoting angiogenesis. J. Clin. Invest. 125, 3606–3618 (2015)

    PubMed  PubMed Central  Google Scholar 

  15. Hansen, K. B. et al. 2-Oleoyl glycerol is a GPR119 agonist and signals GLP-1 release in humans. J. Clin. Endocrinol. Metab. 96, E1409–E1417 (2011)

    CAS  PubMed  Google Scholar 

  16. Overton, H. A. et al. Deorphanization of a G protein-coupled receptor for oleoylethanolamide and its use in the discovery of small-molecule hypophagic agents. Cell Metab. 3, 167–175 (2006)

    CAS  PubMed  Google Scholar 

  17. Khan, S. Y. et al. Lysophosphatidylcholines activate G2A inducing Gαi−1-/Gαq/11- Ca2+ flux, Gβγ-Hck activation and clathrin/β-arrestin-1/GRK6 recruitment in PMNs. Biochem. J. 432, 35–45 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Kabarowski, J. H. G2A and LPC: regulatory functions in immunity. Prostaglandins Other Lipid Mediat. 89, 73–81 (2009)

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Rimmerman, N. et al. N-palmitoyl glycine, a novel endogenous lipid that acts as a modulator of calcium influx and nitric oxide production in sensory neurons. Mol. Pharmacol. 74, 213–224 (2008)

    CAS  PubMed  Google Scholar 

  20. Ritter, K., Buning, C., Halland, N., Pöverlein, C. & Schwink, L. G protein-coupled receptor 119 (GPR119) agonists for the treatment of diabetes: recent progress and prevailing challenges. J. Med. Chem. 59, 3579–3592 (2016)

    CAS  PubMed  Google Scholar 

  21. Nunez, D. J. et al. Gut hormone pharmacology of a novel GPR119 agonist (GSK1292263), metformin, and sitagliptin in type 2 diabetes mellitus: results from two randomized studies. PLoS ONE 9, e92494 (2014)

    ADS  PubMed  PubMed Central  Google Scholar 

  22. Ha, T. Y. et al. Novel GPR119 agonist HD0471042 attenuated type 2 diabetes mellitus. Arch. Pharm. Res. 37, 671–678 (2014)

    CAS  PubMed  Google Scholar 

  23. Katz, L. B. et al. Effects of JNJ-38431055, a novel GPR119 receptor agonist, in randomized, double-blind, placebo-controlled studies in subjects with type 2 diabetes. Diabetes Obes. Metab. 14, 709–716 (2012)

    CAS  PubMed  Google Scholar 

  24. Chu, Z. L. et al. A role for β-cell-expressed G protein-coupled receptor 119 in glycemic control by enhancing glucose-dependent insulin release. Endocrinology 148, 2601–2609 (2007)

    CAS  PubMed  Google Scholar 

  25. Chu, Z. L. et al. A role for intestinal endocrine cell-expressed G protein-coupled receptor 119 in glycemic control by enhancing glucagon-like peptide-1 and glucose-dependent insulinotropic peptide release. Endocrinology 149, 2038–2047 (2008)

    CAS  PubMed  Google Scholar 

  26. Lauffer, L. M., Iakoubov, R. & Brubaker, P. L. GPR119 is essential for oleoylethanolamide-induced glucagon-like peptide-1 secretion from the intestinal enteroendocrine L-cell. Diabetes 58, 1058–1066 (2009)

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Serrano, A. et al. Oleoylethanolamide: effects on hypothalamic transmitters and gut peptides regulating food intake. Neuropharmacology 60, 593–601 (2011)

    CAS  PubMed  Google Scholar 

  28. Fu, J. et al. Oleylethanolamide regulates feeding and body weight through activation of the nuclear receptor PPAR-α. Nature 425, 90–93 (2003)

    ADS  CAS  PubMed  Google Scholar 

  29. Lan, H. et al. GPR119 is required for physiological regulation of glucagon-like peptide-1 secretion but not for metabolic homeostasis. J. Endocrinol. 201, 219–230 (2009)

    CAS  PubMed  Google Scholar 

  30. Lauffer, L., Iakoubov, R. & Brubaker, P. L. GPR119: “double-dipping” for better glycemic control. Endocrinology 149, 2035–2037 (2008)

    CAS  PubMed  Google Scholar 

  31. Chen, Z. et al. Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity. J. Clin. Invest. 124, 3391–3406 (2014)

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Mimee, M. Tucker, A. C., Voigt, C. A. & Lu, T. K. Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Syst. 1, 62–71 (2015)

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Vaudry, H. Molecular evolution of GPCRs: What we know and what the future holds. J. Mol. Endocrinol. 52, E1–E2 (2014)

    CAS  PubMed  Google Scholar 

  34. Lovejoy, D. A., Chang, B. S., Lovejoy, N. R. & del Castillo, J. Molecular evolution of GPCRs: CRH/CRH receptors. J. Mol. Endocrinol. 52, T43–T60 (2014)

    CAS  PubMed  Google Scholar 

  35. Hla, T. Genomic insights into mediator lipidomics. Prostaglandins Other Lipid Mediat. 77, 197–209 (2005)

    CAS  PubMed  Google Scholar 

  36. Wieland Brown, L. C. et al. Production of α-galactosylceramide by a prominent member of the human gut microbiota. PLoS Biol. 11, e1001610 (2013)

    PubMed  PubMed Central  Google Scholar 

  37. Ou, G. et al. Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease. Am. J. Gastroenterol. 104, 3058–3067 (2009)

    ADS  PubMed  Google Scholar 

  38. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012)

  39. Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl Acad. Sci. USA 111, E2329–2338 (2014)

    CAS  PubMed  Google Scholar 

  40. Peterson, S. N. et al. Functional expression of dental plaque microbiota. Front. Cell. Infect. Microbiol. 4, 108 (2014)

    PubMed  PubMed Central  Google Scholar 

  41. Tang, Y., Li, X., Han, X., Lu, J. & Diwu, Z. Functional analysis of endogenous β-adrenergic receptor through fluorimetric monitoring of cyclic nucleotide-gated ion channel. Anal. Biochem. 360, 303–305 (2007)

    CAS  PubMed  Google Scholar 

  42. Van Wagoner, R. M. & Clardy, J. FeeM, an N-acyl amino acid synthase from an uncultured soil microbe: structure, mechanism, and acyl carrier protein binding. Structure 14, 1425–1435 (2006)

    CAS  PubMed  Google Scholar 

  43. Chen, Y. et al. Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology. Sci. Rep. 6, 34055 (2016)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  44. Cheng, J. et al. Duodenal microbiota composition and mucosal homeostasis in pediatric celiac disease. BMC Gastroenterol. 13, 113 (2013)

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

Download references


We thank the High-Throughput and Spectroscopy Resource Center, Center for Clinical and Translational Science and the Comparative Bioscience Center at Rockefeller University for the use of their facilities; members of the Mangelsdorf laboratory at UT Southwestern and D. Drucker at Mount Sinai Hospital, Toronto for the use of the GLUTag cell line; A. Milshteyn, A. Estrela and J. Craig for their critical review of the manuscript. This work was supported in part by a grant from the Robertson Foundation, the Center for Basic and Translational Research on Disorders of the Digestive System, the Leona M. and Harry B. Helmsley Charitable Trust, Rainin Foundation, U01 GM110714-1A1 (S.F.B.), GM122559-01 (S.F.B.), the Crohn’s and Colitis Foundation Career Development Award (L.J.C.) and NIDDK K08 DK109287-01 (L.J.C.).

Author information

Authors and Affiliations



L.J.C. and S.F.B. designed research; L.J.C. assisted with all experiments; S.-H.K. assisted with molecule characterization; E.A.G., P.Y.C., J.K.B. and R.R.A. assisted with gene cloning; D.E., A.B.E., S.M.H., C.H. and A.R. assisted with mouse experiments; J.C., X.V.-F., J.K. assisted with molecule synthesis; A.J.P. and J.R.C. assisted with metabolite analysis in human and mouse samples; L.J.C. and C.L. analysed data; L.J.C. and S.F.B. wrote the paper.

Corresponding author

Correspondence to Sean F. Brady.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Reviewer Information Nature thanks D. J. Drucker and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Figure 1 Analysis of hm-NAS clone families.

a, LC–MS analysis of crude extracts prepared from E. coli transformed with each hm-NAS gene expression construct (number 1–58, see Supplementary Table 1 for details about each clone number) compared to negative control extracts derived from E. coli containing an empty vector (Con). On the basis of metabolite retention time and observed mass hm-NAS genes could be grouped into 6 N-acyl amide families (1–6). The mass of the major metabolite (pictured) from each N-acyl amide family is shown in either the ESI+ or ESI mass spectrometry detection mode for each hm-NAS extract, including the control extract. Functional differences in NAS enzymes follow the pattern of the NAS phylogenetic tree, with hm-NAS genes from the same clade or sub-clade mostly encoding the same metabolite family. Commendamide (Comm.) was previously isolated and is part of family 1 (ref. 3). b, Phylogenetic tree of PFAM13444, showing the location of each hm-NAS gene that we synthesized and examined by heterologous expression. c, Crude ethyl acetate extracts were prepared from cultures of bacterial species that contain the same or a highly related (>80% nucleotide identity) hm-NAS gene that was expressed by heterologous expression. The only exception was for the N-acyl alanine family, for which a representative cultured commensal bacterial species was not available. N-acyl glycines were previously analysed in the same manner3. The extracted-ion chromatogram for the hm-NAS gene family is shown for the E. coli clone compared to the crude extract from the commensal species. For family 6, hm-NAS clone 58 is pictured in c and not in a owing to formatting constraints.

Extended Data Figure 2 Proposed biosynthesis of N-acyl serinol.

Proposed two-step biosynthesis of N-acyl serinol using the two domains encoded by the hm-NAS N-acyl serinol synthase gene.

Extended Data Figure 3 Validation of hits from the high-throughput GPCR screen.

When structural analogues were independently screened in the GPCR panel (for example, N-oleoyl and palmitoyl serinol or N-3-hydroxypalmitoyl lysine and ornithine), they yielded the same GPCR profile and when N-acyl serinol was re-assayed across all GPCRs in the panel, it also yielded the same GPCR activity profile. a, b, N-3-hydroxypalmitoyl lysine and ornithine both interact with S1PR4. *Did not repeat. b, inset technical repeat of N-3-hydroxypalmitoyl ornithine dose–response curve. c, d, Technical repeats of N-palmitoyl serinol. ce, N-palmitoyl and oleoyl serinol both interact with GPR119. Screening data were performed once, dose–response curves were performed in duplicate. Data are mean ± s.e.m.

Extended Data Figure 4 Combined analysis of protein and transcript expression of GPCRs in the gastrointestinal tract.

Links between GPCR, N-acyl amide, bacterial genus and the site where these co-occur in the gastrointestinal tract (coloured) are shown. On the basis of protein expression data (Human Protein Atlas) GPR119 is most highly expressed in the pancreas and duodenum, S1PR4 in the spleen and lymph node, G2A in the lymph node and appendix, PTGIR in the lung and appendix and PTGER4 in the bone marrow and small intestine. From gene expression data in the colon (GTEx dataset, n = 88 patient samples from small intestine, 345 patient samples from colon) GPR132, PTGER4 and PTGIR are all expressed alongside the N-acyl synthase genes that are known to encode metabolites that target these GPCRs (Fig. 1). In the gastrointestinal tract, GPR119 and S1PR4 are most highly expressed in the small intestine where 16S studies have identified bacteria from the genera Gemella and Neisseria. All known reference genomes (NCBI) from these genera contain N-acyl synthase genes that are highly similar (BLASTN, E = 2 ×10 −132) to those we found to encode GPR119 or S1PR4 ligands37,43,44.

Extended Data Figure 5 Secondary assay of GPR119.

ACTOne HEK293 cells (control) and ACTOne HEK293 cells transfected with GPR119 were exposed to equimolar concentrations of the endogenous GPR119 ligand OEA or the bacterial ligand N-oleoyl serinol. Relative fluorescent intensity was recorded for each ligand concentration compared to the background signal. All data points were performed in quadruplicate and data are mean ± s.d. An increase in cAMP concentration was observed in HEK293 cells expressing GPR119, but not in control HEK293 cells. The DCEA (5-(N-ethylcarboxamido)adenosine) control is presented to confirm cAMP response of the parental cell line. The EC50 for N-oleoyl serinol (bacterial) was 1.6 μM and for oleoylethanolamide was 5.1 μM, which are consistent with data from the β-arrestin assay (Fig. 5a).

Extended Data Figure 6 Identification of N-acyl serinol biosynthesis in vivo.

a, LC–MS analysis of crude caecal extracts. Extracted-ion chromatograms for palmitoyl serinol ([M + H]+ m/z: 330.3003) are shown. A peak with the same exact mass and chromatographic retention time as the N-palmitoyl serinol standard was present in treatment mice but not control mice. Treatment mice were colonized with E. coli containing the N-acyl serinol synthase gene. Control mice were colonized with E. coli containing the empty pET28c vector. b, Identification of N-palmitoyl serinol by MS/MS fragmentation of the m/z 330.3003 ion. In the MS2 spectrum the diamond indicates the N-palmitoyl serinol parent ion and the product ion at m/z: 92.0706 shows the presence of the serinol head group.

Extended Data Figure 7 Bacterial colonization of mouse model systems.

One week after inoculation with E. coli, a single faecal pellet from a colonized mouse was collected, resuspended in 400 μl PBS and plated at a 1:100 dilution onto LB agar plates with or without kanamycin 50 μg ml−1. a, The number of colony-forming units per 10−6 g of faeces observed on LB agar plates with kanamycin was similar for the treatment group (E. coli with hm-NAS gene, n = 6 mouse stool samples) and the control group (E. coli with empty vector, n = 8 mouse stool samples). b, In the antibiotic-treated mouse cohort, other colonizing bacteria are present. Stool samples produced threefold more colony-forming units on unselected LB agar plates compared to LB agar plates with kanamycin. Data are mean ± s.e.m. In both cases, when random colonies were picked from the LB with kanamycin plates, all colonies were found to contain the cloning vector. indicating these were in fact E. coli colonizing bacteria.

Extended Data Figure 8 N-acyl serinol synthase point mutant.

LC–MS analysis of crude extracts prepared from cultures of E. coli expressing either the N-acyl serinol synthase gene or the N-acyl serinol synthase gene with an active site point mutation (E91A). N-acyl serinol metabolites (for example, N-palmitoyl serinol and N-oleoyl serinol) are absent from the culture broth with the point mutant (ESI+ mode). This mutant was created to address the possibility that the observed mouse phenotype might be due to overproduction of any protein by E. coli and not specifically from N-acyl serinol production.

Extended Data Figure 9 Detection of N-acyl amides in human faecal samples.

High-resolution reversed-phase LC–MS analysis of human faecal extract pooled from 128 samples representing 21 individuals. Extracted-ion chromatograms for individual N-acyl amides are shown within a 2 p.p.m. tolerance of the exact mass (M + H). Compounds observed to be present in the human faecal extract were confirmed by alignment to authentic standards (top) and by spiked addition of the pure compound (data not shown). No zwitterionic N-acyl amides (N-acyl or N-acyloxyacyl ornithine/lysines) were detected. Patient demographics are provided in the table. Human stool samples were collected with informed consent at MSKCC under institutional review board numbers 09-167, 09-141, and 06-107.

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion, Supplementary Figures and Data, Supplementary Tables 1-3 and an additional reference. (PDF 6066 kb)

Reporting Summary (PDF 67 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Cohen, L., Esterhazy, D., Kim, SH. et al. Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature 549, 48–53 (2017).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing