Plant-derived lignans, consumed daily by most individuals, are thought to protect against cancer and other diseases1; however, their bioactivity requires gut bacterial conversion to enterolignans2. Here, we dissect a four-species bacterial consortium sufficient for all five reactions in this pathway. A single enzyme (benzyl ether reductase, encoded by the gene ber) was sufficient for the first two biotransformations, variable between strains of Eggerthella lenta, critical for enterolignan production in gnotobiotic mice and unique to Coriobacteriia. Transcriptional profiling (RNA sequencing) independently identified ber and genomic loci upregulated by each of the remaining substrates. Despite their low abundance in gut microbiomes and restricted phylogenetic range, all of the identified genes were detectable in the distal gut microbiomes of most individuals living in northern California. Together, these results emphasize the importance of considering strain-level variations and bacterial co-occurrence to gain a mechanistic understanding of the bioactivation of plant secondary metabolites by the human gut microbiome.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
npj Biofilms and Microbiomes Open Access 29 August 2022
Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome
BMC Microbiology Open Access 29 March 2022
Microbiome Open Access 27 October 2021
Subscribe to Nature+
Get immediate online access to the entire Nature family of 50+ journals
Subscribe to Journal
Get full journal access for 1 year
only $9.92 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Get time limited or full article access on ReadCube.
All prices are NET prices.
Adlercreutz, H. Lignans and human health. Crit. Rev. Clin. Lab. Sci. 44, 483–525 (2007).
Clavel, T., Doré, J. & Blaut, M. Bioavailability of lignans in human subjects. Nutr. Res. Rev. 19, 187–196 (2006).
Spanogiannopoulos, P., Bess, E. N., Carmody, R. N. & Turnbaugh, P. J. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat. Rev. Microbiol. 14, 273–287 (2016).
Carmody, R. N. & Turnbaugh, P. J. Host–microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics. J. Clin. Invest. 124, 4173–4181 (2014).
Koppel, N., Maini Rekdal, V. & Balskus, E. P. Chemical transformation of xenobiotics by the human gut microbiota. Science 356, eaag2770 (2017).
Valsta, L. M. et al. Phyto-oestrogen database of foods and average intake in Finland. Br. J. Nutr. 89, S31–S38 (2011).
Woting, A., Clavel, T., Loh, G. & Blaut, M. Bacterial transformation of dietary lignans in gnotobiotic rats. FEMS Microbiol. Ecol. 72, 507–514 (2010).
Clavel, T. & Mapesa, J. O. in Natural Products: Phytochemistry, Botany and Metabolism of Alkaloids, Phenolics and Terpenes (eds Ramawat, K. G. & Mérillon, J.-M.) 2433–2463 (Springer, 2013).
Olsen, A. et al. Plasma enterolactone and breast cancer incidence by estrogen receptor status. Cancer Epidemiol. Biomarkers Prev. 13, 2084–2089 (2004).
Sonestedt, E. et al. Enterolactone is differently associated with estrogen receptor β-negative and -positive breast cancer in a Swedish nested case-control study. Cancer Epidemiol. Biomarkers Prev. 17, 3241–3251 (2008).
Seibold, P. et al. Enterolactone concentrations and prognosis after postmenopausal breast cancer: assessment of effect modification and meta-analysis. Int. J. Cancer 135, 923–933 (2014).
Mabrok, H. B. et al. Lignan transformation by gut bacteria lowers tumor burden in a gnotobiotic rat model of breast cancer. Carcinogenesis 33, 203–208 (2012).
Saarinen, N. M. et al. Enterolactone inhibits the growth of 7,12-dimethylbenz(a) anthracene-induced mammary carcinomas in the rat. Mol. Cancer Ther. 1, 869–876 (2002).
Zaineddin, A. K. et al. Serum enterolactone and postmenopausal breast cancer risk by estrogen, progesterone and herceptin 2 receptor status. Int. J. Cancer 130, 1401–1410 (2012).
Stitch, S. R. et al. Excretion, isolation and structure of a new phenolic constituent of female urine. Nature 287, 738–740 (1980).
Setchell, K. D. R. et al. Lignans in man and in animal species. Nature 287, 740–742 (1980).
Clavel, T. et al. Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans. Appl. Environ. Microbiol. 71, 6077–6085 (2005).
Clavel, T., Borrmann, D., Braune, A., Doré, J. & Blaut, M. Occurrence and activity of human intestinal bacteria involved in the conversion of dietary lignans. Anaerobe 12, 140–147 (2006).
Wang, L.-Q., Meselhy, M. R., Li, Y., Qin, G.-W. & Hattori, M. Human intestinal bacteria capable of transforming secoisolariciresinol diglucoside to mammalian lignans, enterodiol and enterolactone. Chem. Pharm. Bull. 48, 1606–1610 (2000).
Clavel, T., Henderson, G., Engst, W., Doré, J. & Blaut, M. Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside. FEMS Microbiol. Ecol. 55, 471–478 (2006).
Bisanz, J. E. et al. Illuminating the microbiome’s dark matter: a functional genomic toolkit for the study of human gut Actinobacteria. Preprint at https://www.biorxiv.org/content/10.1101/304840v1 (2018).
Haiser, H. J. et al. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 341, 295–298 (2013).
Koppel, N., Bisanz, J. E., Pandelia, M.-E., Turnbaugh, P. J. & Balskus, E. P. Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins. eLife 7, e33953 (2018).
Maini Rekdal, V., Bess, E. N., Bisanz, J. E., Turnbaugh, P. J. & Balskus, E. P. Discovery and inhibition of an interspecies gut bacterial pathway for levodopa metabolism. Science 364, eaau6323 (2019).
Davis, R. M., Muller, R. Y. & Haynes, K. A. Can the natural diversity of quorum-sensing advance synthetic biology? Front. Bioeng. Biotechnol. 3, 30 (2015).
Rohman, A., van Oosterwijk, N., Thunnissen, A.-M. W. H. & Dijkstra, B. W. Crystal structure and site-directed mutagenesis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 explain its catalytic mechanism. J. Biol. Chem. 288, 35559–35568 (2013).
Fukuhara, Y. et al. Discovery of pinoresinol reductase genes in sphingomonads. Enzyme Microb. Technol. 52, 38–43 (2013).
Maier, L. et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018).
Milder, I. E. J. et al. Intake of the plant lignans secoisolariciresinol, matairesinol, lariciresinol, and pinoresinol in Dutch men and women. J. Nutr. 135, 1202–1207 (2005).
Matthews, R. G. Cobalamin- and corrinoid-dependent enzymes. Met. Ions Life Sci. 6, 53–114 (2009).
Hille, R. The molybdenum oxotransferases and related enzymes. Dalton Trans. J. Inorg. Chem. 42, 3029–3042 (2013).
Nayfach, S., Fischbach, M. A. & Pollard, K. S. MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics 31, 3368–3370 (2015).
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).
Alba, D. L. et al. Subcutaneous fat fibrosis links obesity to insulin resistance in Chinese-Americans. J. Clin. Endocrinol. Metab. 103, 3194–3204 (2018).
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Tang, H. & Mayersohn, M. Porcine prediction of pharmacokinetic parameters in people: a pig in a poke? Drug Metab. Dispos. 46, 1712–1724 (2018).
Bolvig, A. K., Adlercreutz, H., Theil, P. K., Jørgensen, H. & Bach Knudsen, K. E. Absorption of plant lignans from cereals in an experimental pig model. Br. J. Nutr. 115, 1711–1720 (2016).
Gohl, D. M. et al. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nat. Biotechnol. 34, 942–949 (2016).
Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).
Franke, A. A. et al. Liquid chromatographic–photodiode array mass spectrometric analysis of dietary phytoestrogens from human urine and blood. J. Chromatogr. B 777, 45–59 (2002).
Franke, A. A., Halm, B. M., Kakazu, K., Li, X. & Custer, L. J. Phytoestrogenic isoflavonoids in epidemiologic and clinical research. Drug Test. Anal. 1, 14–21 (2009).
Begum, A. N. et al. Dietary lignins are precursors of mammalian lignans in rats. J. Nutr. 134, 120–127 (2004).
Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T.-Y. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).
The authors thank E. Balskus, A. Patterson and K. Pollard for comments on the manuscript. We are indebted to M. Blaut for providing E. lenta SECO-Mt75m2, L. Ortiz de Ora for assistance with generating the control construct for Edl expression, F. Grun, K. Torii and L. Custer for technical assistance with the mass spectrometry assays, and Separation Research (Turku, Finland) for donating chemicals. This work was supported by the National Institutes of Health (R01HL122593 and R21CA227232), Searle Scholars Program (SSP-2016-1352) and University of California, Irvine, Department of Chemistry. P.J.T. is a Chan Zuckerberg Biohub investigator and Nadia’s Gift Foundation Innovator, supported in part by the Damon Runyon Cancer Research Foundation (DRR-42-16). Fellowship support was provided by the Natural Sciences and Engineering Research Council of Canada (to J.E.B.), Canadian Institutes of Health and Research (to P.S.), Agency for Technology, Science and Research (to Q.Y.A.), and Life Sciences Research Foundation and Howard Hughes Medical Institute (to E.N.B.).
P.J.T. is on scientific advisory boards for Kaleido, Pendulum, Seres and SNIPR Biome. There is no direct overlap between the current study and these consulting duties. All of the other authors declare no competing interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended Data Fig. 1 A four-member gut bacterial consortium is capable of converting dietary lignans to phytoestrogenic enterolignans.
a, Time-course experiments exhibiting the conversion of PINO to ENL and the growth profile of each bacterium with the lignan it metabolizes. Due to the chemical instability of dmSECO, this compound could not be accurately measured. Red arrows indicate time at which culture was exposed to lignan. Lignan concentrations were measured by HPLC. Culture turbidity, measured as optical density at 600 nm (OD600), is plotted. Values are mean±SEM (n=3 biological replicates). b, Growth profiles of each bacterium cultured with and without lignan. Culture turbidity, measured as optical density at 600 nm (OD600), is plotted. Values are mean±SEM (n=3 biological replicates).
Extended Data Fig. 2 PINO-metabolizing Coriobacteriia strains cannot be predicted based on phylogeny.
Phylophlan-based phylogenetic tree produced using ElenMatchR: Comparative Genomics Tool v0.321. This tree demonstrates the non-monophyletic nature of PINO metabolism across the strain collection and suggests that this phenotypic trait is decoupled from bacterial evolutionary history, suggesting the repeated gain or loss of the genes responsible.
Extended Data Fig. 3 Domain maps for gut bacterial genes implicated in the lignan metabolism pathway.
Annotations, assigned by homology, of the domains that constitute the putative lignan-metabolizing enzymes are presented and provide support for the inferred biochemical functions. All proteins are predicted to be cytoplasmic with the exception of Ber, which has an N-terminal TAT signal sequence, targeting Ber for secretion.
a, Relative abundance of bacterial genera for each of the strains used to colonize mice, as measured by 16S rRNA gene sequencing. b-c, Lignan levels in mice dosed with PINO-diglucoside (20 mg/kg) measured by Orbitrap mass spectrometry. Bars are mean±SEM (n = 5 biologically independent samples/colonization group, except in the ileum samples where ber+ n=4 biologically independent samples). Kruskal-Wallis with Dunn’s multiple comparisons test: *p<0.05. ns: not significant. ber+ and ber−: germ-free mice colonized with E. lenta DSM2243T (ber+ group) or E. lenta 1-3-56 (ber− group) and B. producta DSM3507, G. pamelaeae 3C, and L. longoviformis DSM17459T; mice dosed with PINO-diglucoside were also colonized with C. saccharogumia DSM17460T. GF: germ-free mice.
A working model of the bacterial lignan metabolism pathway is presented. Several transporters, which traffic small molecules (ABC transporters) or ions (MFS transporters) across bacterial membranes, were significantly up-regulated in response to lignan doses and may be responsible for funneling substrates or products across cell membranes. Ber: benzyl ether reductase; Glm: guaiacol lignan methyltransferase; Cldh: catechol lignan dehydroxylase; Edl: enterodiol lactonizing enzyme; ABC: ATP-binding cassette; MFS: major facilitator superfamily.
About this article
Cite this article
Bess, E.N., Bisanz, J.E., Yarza, F. et al. Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria. Nat Microbiol 5, 56–66 (2020). https://doi.org/10.1038/s41564-019-0596-1
Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome
BMC Microbiology (2022)
npj Biofilms and Microbiomes (2022)
Nature Communications (2021)
Genome Medicine (2020)