Research ArticleMICROBIOLOGY

Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies

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Science Advances  27 Jun 2018:
Vol. 4, no. 6, eaat0062
DOI: 10.1126/sciadv.aat0062
  • Fig. 1 Induction of putrescine production by mixed microbial cultures.

    (A) Extracellular putrescine concentrations in cocultures and individual cultures of 14 bacterial strains in GAM medium supplemented with 2 mM arginine. (B) Extracellular putrescine concentrations in cocultures of each pair of 14 bacterial strains (total 91 combinations). N.D. means not detected; that is, the levels fell below the minimum detectable amount. (C) Extracellular concentration of l-arginine, putrescine, and agmatine in the medium after culture of E. coli for 24 hours (0 to 24 hours), followed by culture of En. faecalis for another 24 hours (24 to 48 hours) in the same medium; E. coli was removed by filtration after 24 hours. (D) Extracellular concentrations of l-arginine, putrescine, and agmatine in the medium after culture of En. faecalis for 24 hours (0 to 24 hours), followed by culture of E. coli for another 24 hours (24 to 48 hours) in the same medium. En. faecalis was removed by filtration after 24 hours.

  • Fig. 2 Hypothetical putrescine production pathway consisting of the acid resistance system of E. coli and an ATP synthesis system of En. faecalis.

    A putrescine biosynthesis pathway consisting of sequential reactions accomplished by E. coli and En. faecalis. Details are shown in the text.

  • Fig. 3 Validation of the hypothesis of sequential reactions in E. coli and En. faecalis using bacteria whose genes encoding transporters and enzymes were deleted or complemented.

    (A and B) Extracellular putrescine concentration in cocultures of wild-type (WT) En. faecalis (Enf; SK947) and E. coli (Ec) including gene knockout mutants or complementary transformants of arginine decarboxylase (adiA) of E. coli (A) or arginine-agmatine antiporter (adiC   ) of E. coli (B). (C) Extracellular putrescine concentrations in cocultures of wild-type E. coli (LKM10096) and En. faecalis including the wild type, gene knockout mutants, or complementary transformants of agmatine-putrescine antiporter (aguD). (D) Extracellular putrescine concentration in cocultures of putrescine-deficient E. coli (SK930) and wild-type En. faecalis (SK947). Coculture of these bacteria was conducted under anaerobic conditions at 37°C for 24 hours in LB-RGC medium. (E and F) Putrescine concentrations in the content of cecal lumen (E) and colonic lumen (F) of gnotobiotic mice colonized with putrescine-deficient E. coli (SK930) and wild-type En. faecalis (SK947). Error bars represent SEs. *P < 0.05 and **P < 0.01, one-way analysis of variance (ANOVA) with Tukey’s test.

  • Fig. 4 Effects of acidification by bifidobacteria on putrescine production by E. coli and En. faecalis.

    (A) Extracellular putrescine concentration in cocultures of putrescine-deficient E. coli (SK930), wild-type En. faecalis (V583), and each Bifidobacterium sp. (B and C) Extracellular pH (B) and putrescine concentration (C) in cocultures of putrescine-deficient E. coli (SK930), wild-type En. faecalis (V583), and B. animalis subsp. lactis LKM512 (Bal). Coculture of these bacteria was conducted under anaerobic conditions at 37°C for 24 hours in LB medium containing 2 mM l-arginine, d-glucose (1.5 g/liter), galacto-oligosaccharide (5 g/liter), 2 mM MgSO4, 60 mM NH4Cl, and LB-RGC (0.5 g/liter) (pH 6.5). (D and E) Fecal pH (D) and putrescine concentration (E) in gnotobiotic mice colonized with putrescine-deficient E. coli (SK930), wild-type En. faecalis (V583), and B. animalis subsp. lactis LKM512. (F and G) Fecal pH (F) and putrescine (G) concentration in gnotobiotic mice inoculated with putrescine-deficient E. coli (SK930), wild-type En. faecalis (V583), and B. adolescentis JCM1275T. (H) Extracellular putrescine concentration in human feces incubated at different pHs. Error bars represent SEs. *P < 0.05 and **P < 0.01, one-way ANOVA with Tukey’s test, Student’s t tests, and Steel-Dwass test.

  • Fig. 5 General putrescine production pathway from arginine via agmatine in the human intestinal microbiome.

    (A) Extracellular putrescine concentration in monoculture of Ci. youngae ATCC 29220 or F. varium ATCC 27725 and in coculture of Ci. youngae ATCC 29220 or F. varium ATCC 27725 with wild-type En. faecalis (V583). (B) Fecal putrescine concentration in gnotobiotic mice inoculated with F. varium ATCC 27725 and wild-type En. faecalis (V583). Mono- and cocultures of these bacteria were conducted under anaerobic conditions at 37°C for 24 hours in LB-RGC medium. (C) Symbiont-symbiont co-occurrence networks of key genes in the putrescine production pathway using previously described human microbiome data from U.S. metropolitan areas (26). Blue and red lines between bacterial species indicate statistically significant aggregation and segregation, respectively. Names of Bifidobacterium spp. and E. coli are shown in red. The size of the circles represents the number of reads identified. Circle colors: red, bacterial species that have AdiC and AdiA; deep pink, bacterial species that have AdiC; gold, bacterial species that have AdiA; blue, bacterial species that have AguD and AguA; chartreuse, bacterial species that have AguD; cyan, bacterial species that have AguA; gray, other bacterial species. Error bars represent SE. *P < 0.05 and **P < 0.01, one-way ANOVA with Tukey’s test and Student’s t tests.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/6/eaat0062/DC1

    fig. S1. Induction of putrescine production by coculture of E. coli and En. faecalis.

    fig. S2. Effects of extracellular pH and glucose concentration on bacterial metabolism in monocultures of En. faecalis and E. coli.

    fig. S3. Viable bacterial counts and change of extracellular pH in cocultures of putrescine-deficient E. coli (SK930), wild-type En. faecalis (V583), and each Bifidobacterium sp.

    fig. S4. Viable bacterial counts in feces of gnotobiotic mice.

    fig. S5. Extracellular putrescine concentration and total viable bacterial counts in human feces incubated at different pH values (n = 5).

    fig. S6. Effect of pH on extracellular agmatine concentration in monocultures of E. coli, Ci. youngae, and F. varium.

    fig. S7. Symbiont-symbiont co-occurrence networks of key genes in the putrescine production pathway using previously described human microbiome data from U.S. metropolitan areas.

    fig. S8. Symbiont-symbiont co-occurrence network patterns of key genes in the putrescine production pathway using previously described human microbiome data from Venezuela.

    fig. S9. Symbiont-symbiont co-occurrence network patterns of key genes in the putrescine production pathway using previously described human microbiome data from Malawi.

    fig. S10. Mechanistic model of a novel pathway for putrescine production from arginine through agmatine via the collaboration of three different bacterial species.

    fig. S11. Outline of gnotobiotic mouse experiments.

    table S1. List of species expressing homologs of the enzymes AdiA and AdiC, as determined by in silico analyses of 126 bacterial strains present in the human gut.

    table S2. Detection of RNA sequences of AdiA, AdiC, AguA, and AguD by metatranscriptomic analysis of human feces.

    table S3. List of bacteria used for screening of polyamine producing bacteria.

    table S4. Strains, plasmids, and oligonucleotides used in this study.

  • Supplementary Materials

    This PDF file includes:

    • fig. S1. Induction of putrescine production by coculture of E. coli and En. faecalis.
    • fig. S2. Effects of extracellular pH and glucose concentration on bacterial metabolism in monocultures of En. faecalis and E. coli.
    • fig. S3. Viable bacterial counts and change of extracellular pH in cocultures of putrescine-deficient E. coli (SK930), wild-type En. faecalis (V583), and each Bifidobacterium sp.
    • fig. S4. Viable bacterial counts in feces of gnotobiotic mice.
    • fig. S5. Extracellular putrescine concentration and total viable bacterial counts in human feces incubated at different pH values (n = 5).
    • fig. S6. Effect of pH on extracellular agmatine concentration in monocultures of E. coli, Ci. youngae, and F. varium.
    • fig. S7. Symbiont-symbiont co-occurrence networks of key genes in the putrescine production pathway using previously described human microbiome data from U.S. metropolitan areas.
    • fig. S8. Symbiont-symbiont co-occurrence network patterns of key genes in the putrescine production pathway using previously described human microbiome data from Venezuela.
    • fig. S9. Symbiont-symbiont co-occurrence network patterns of key genes in the putrescine production pathway using previously described human microbiome data from Malawi.
    • fig. S10. Mechanistic model of a novel pathway for putrescine production from arginine through agmatine via the collaboration of three different bacterial species.
    • fig. S11. Outline of gnotobiotic mouse experiments.
    • table S1. List of species expressing homologs of the enzymes AdiA and AdiC, as determined by in silico analyses of 126 bacterial strains present in the human gut.
    • table S2. Detection of RNA sequences of AdiA, AdiC, AguA, and AguD by metatranscriptomic analysis of human feces.
    • table S3. List of bacteria used for screening of polyamine producing bacteria.
    • table S4. Strains, plasmids, and oligonucleotides used in this study.

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