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Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria

Nature Microbiology volume 5, pages 56–66 (2020)Cite this article

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Abstract

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.

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Fig. 1: Lignan metabolism varies between Coriobacteriia strains and enables the identification of a single enzyme sufficient to catalyse the first two reactions in the lignan metabolism pathway.
Fig. 2: Genomic loci are upregulated in response to each substrate in the lignan metabolism pathway.
Fig. 3: Ber significantly alters enterolignan production in gnotobiotic mice.
Fig. 4: Genes linked to lignan metabolism are significantly correlated with bacterial host genera and prevalent in human gut microbiomes.

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Data availability

16S ribosomal DNA and RNA sequencing data have been deposited in the NCBI Sequence Read Archive under BioProject accession numbers PRJNA450120 and PRJNA412637. Figure source data and additional study data are available on request from the corresponding author.

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Acknowledgements

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.).

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Authors and Affiliations

  1. Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA

    Elizabeth N. Bess, Jordan E. Bisanz, Fauna Yarza, Annamarie Bustion, Emily Waligurski, Qi Yan Ang, Peter Spanogiannopoulos & Peter J. Turnbaugh

  2. Department of Chemistry, University of California, Irvine, Irvine, CA, USA

    Elizabeth N. Bess & Barry E. Rich

  3. Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA

    Elizabeth N. Bess

  4. University of Hawaii Cancer Center, Honolulu, HI, USA

    Xingnan Li & Adrian A. Franke

  5. Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA

    Seiya Kitamura & Dennis W. Wolan

  6. Diabetes Center, University of California San Francisco, San Francisco, CA, USA

    Diana L. Alba & Suneil K. Koliwad

  7. United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA

    Stephen Nayfach

  8. Chan Zuckerberg Biohub, San Francisco, CA, USA

    Peter J. Turnbaugh

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Contributions

E.N.B. performed or supervised all of the experimental work. J.E.B. performed the bioinformatics analyses and a subset of the experimental work. S.N. developed the metagenome database. P.S. assisted with bacterial culturing and heterologous expression. F.Y. and A.B. designed and implemented the culture-independent assays for gene prevalence. F.Y. performed the ex vivo incubations. E.W. generated the bacterial mutants. B.E.R. performed mass spectrometry on the bacterial cultures. X.L. and A.A.F. performed mass spectrometry on the mouse samples. Q.Y.A. extracted DNA from the human samples collected by D.L.A. and S.K.K. S.K. and D.W.W. synthesized dmSECO. P.J.T. supervised the study.

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Correspondence to Peter J. Turnbaugh.

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Competing interests

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.

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Extended data

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.

Extended Data Fig. 4 Colonization and PINO levels for gnotobiotic mice dosed with PINO-diGlc.

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.

Extended Data Fig. 5 The putative enzymes mediating bacterial metabolism of dietary lignans.

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.

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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

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