CoChat
Sign Up
Cited by 88

The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.

Host immunity modulates the efficacy of microbiota transplantation for treatment of Clostridioides difficile infection

Littmann, Eric R., Lee, Jung-Jin, Denny, Joshua E., Alam, Zahidul, Maslanka, Jeffrey R., Zarin, Isma, Matsuda, Rina, Carter, Rebecca A., Susac, Bože, Saffern, Miriam S., Fett, Bryton, Mattei, Lisa M., Bittinger, Kyle, Abt, Michael C.·2021·Nature Communications
DOI 10.1038/s41467-020-20793-xPMC PMC7854624
Open this paper in CoChat — free account

Abstract

Fecal microbiota transplantation (FMT) is a successful therapeutic strategy for treating recurrent Clostridioides difficile infection. Despite remarkable efficacy, implementation of FMT therapy is limited and the mechanism of action remains poorly understood. Here, we demonstrate a critical role for the immune system in supporting FMT using a murine C. difficile infection system. Following FMT, Rag1 heterozygote mice resolve C. difficile while littermate Rag1 −/− mice fail to clear the infection. Targeted ablation of adaptive immune cell subsets reveal a necessary role for CD4 + Foxp3 + T-regulatory cells, but not B cells or CD8 + T cells, in FMT-mediated resolution of C. difficile infection. FMT non-responsive mice exhibit exacerbated inflammation, impaired engraftment of the FMT bacterial community and failed restoration of commensal bacteria-derived secondary bile acid metabolites in the large intestine. These data demonstrate that the host’s inflammatory immune status can limit the efficacy of microbiota-based therapeutics to treat C. difficile infection.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-020-20793-x

Cites

23 of 23 references verified0 citation errors · 0 not checkable

Statistics

Figures

Fig. 1 Immunodeficient Rag1−/− mice exhibit impaired resolution of C. difficile infection following FMT. a Schematic of antibiotic (ABX) treatment, C. difficile infection, and FMT. b Weight loss following infection in littermate, antibiotic-treated RagHET (n = 6) and Rag1−/− (n = 5) mice. Data is representative of three independent experiments. Data are presented as mean values ± SEM. c C. difficile burden and d toxin B levels in the fecal pellets of Rag1−/− (n = 10) and Rag1HET (n = 14) mice following FMT. Data is a combination of three independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. ***p < 0.0001. Data are presented as mean values ± SEM. e H&E stained cecal tissue sections and f mean crypt length from naïve, C. difficile-infected PBS treated, or C. difficile-infected FMT-treated Rag1HET and Rag1−/− mice. n = 3 naïve Rag1HET and Rag1−/− mice; n = 3 C. difficile-infected PBS treated Rag1HET mice; n = 4 C. difficile-infected PBS treated Rag1−/− mice; n = 6 C. difficile-infected FMT-treated Rag1HET mice; n = 4 C. difficile-infected FMT-treated Rag1−/− mice. Scale bar = 100 μm. Data is representative of two independent experiments. Statistical significance was calculated by a two-sided unpaired Mann–Whitney test; *p = 0.01 Data are presented as mean values ± SEM. b.d. below detection.
Fig. 1 Immunodeficient Rag1−/− mice exhibit impaired resolution of C. difficile infection following FMT. a Schematic of antibiotic (ABX) treatment, C. difficile infection, and FMT. b Weight loss following infection in littermate, antibiotic-treated RagHET (n = 6) and Rag1−/− (n = 5) mice. Data is representative of three independent experiments. Data are presented as mean values ± SEM. c C. difficile burden and d toxin B levels in the fecal pellets of Rag1−/− (n = 10) and Rag1HET (n = 14) mice following FMT. Data is a combination of three independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. ***p < 0.0001. Data are presented as mean values ± SEM. e H&E stained cecal tissue sections and f mean crypt length from naïve, C. difficile-infected PBS treated, or C. difficile-infected FMT-treated Rag1HET and Rag1−/− mice. n = 3 naïve Rag1HET and Rag1−/− mice; n = 3 C. difficile-infected PBS treated Rag1HET mice; n = 4 C. difficile-infected PBS treated Rag1−/− mice; n = 6 C. difficile-infected FMT-treated Rag1HET mice; n = 4 C. difficile-infected FMT-treated Rag1−/− mice. Scale bar = 100 μm. Data is representative of two independent experiments. Statistical significance was calculated by a two-sided unpaired Mann–Whitney test; *p = 0.01 Data are presented as mean values ± SEM. b.d. below detection.CC BY · PubMed Central
Fig. 2 C. difficile-infected Rag1−/− and Rag1HET mice exhibit enhanced induction of proinflammatory immune response genes. a Unweighted UniFrac principal coordinate analysis plot of 16S bacterial rRNA ASVs from fecal pellets of Rag1−/− and Rag1HET mice prior to ABX treatment, at day 0 of infection, and at day 36 post-C. difficile infection or ABX-treatment alone. Ellipses signify different experimental groups. b Relative abundance of top 15 bacterial ASVs from C. difficile-infected of Rag1−/− and Rag1HET mice at day 36 p.i. Bar plot is displayed at the genus level except for orange bars that represent an ASV aligning to C. difficile. c Unweighted UniFrac distance comparing the microbiota beta diversity dissimilarity within and between C. difficile-infected Rag1−/− and Rag1HET groups at day 36 p.i. One-way ANOVA conducted for statistical comparison. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. d Dendrogram representation of intestinal microbial communities of C. difficile-infected of Rag1−/− and Rag1HET mice at day 36 p.i. using unsupervised hierarchical clustering of unweighted UniFrac distances to identify similarities between samples. e mRNA expression of proinflammatory immune response genes in whole colon tissue as assessed by qRT-PCR. Gene expression relative to ABX-treated Rag1HET mice and normalized to Hprt. Statistical significance was calculated by a two-sided unpaired t-test. *p < 0.05, **p < 0.01. Data are presented as mean values ± SEM. f Proinflammatory cytokine and chemokine protein levels in cecal tissue homogenates. Statistical significance was calculated by a two-sided unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Data are presented as mean values ± SEM. g Relative abundance of Proteobacteria and gamma-Proteobacteria ASVs in fecal pellets of Rag1−/− and Rag1HET mice at day 36 p.i. Statistical significance was calculated by a two-sided unpaired t test. Data are presented as mean values ± SEM. Data presented in figure are representative of three independent experiments. Prior to ABX treatment (n = 10 Rag1−/−; n = 12 Rag1HET mice), day 0 of infection (n = 6 Rag1−/−; n = 5 Rag1HET mice), day 36 post-C. difficile (n = 5 Rag1−/− and Rag1HET mice) or ABX-treatment alone (n = 2 Rag1−/− and Rag1HET mice).
Fig. 2 C. difficile-infected Rag1−/− and Rag1HET mice exhibit enhanced induction of proinflammatory immune response genes. a Unweighted UniFrac principal coordinate analysis plot of 16S bacterial rRNA ASVs from fecal pellets of Rag1−/− and Rag1HET mice prior to ABX treatment, at day 0 of infection, and at day 36 post-C. difficile infection or ABX-treatment alone. Ellipses signify different experimental groups. b Relative abundance of top 15 bacterial ASVs from C. difficile-infected of Rag1−/− and Rag1HET mice at day 36 p.i. Bar plot is displayed at the genus level except for orange bars that represent an ASV aligning to C. difficile. c Unweighted UniFrac distance comparing the microbiota beta diversity dissimilarity within and between C. difficile-infected Rag1−/− and Rag1HET groups at day 36 p.i. One-way ANOVA conducted for statistical comparison. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. d Dendrogram representation of intestinal microbial communities of C. difficile-infected of Rag1−/− and Rag1HET mice at day 36 p.i. using unsupervised hierarchical clustering of unweighted UniFrac distances to identify similarities between samples. e mRNA expression of proinflammatory immune response genes in whole colon tissue as assessed by qRT-PCR. Gene expression relative to ABX-treated Rag1HET mice and normalized to Hprt. Statistical significance was calculated by a two-sided unpaired t-test. *p < 0.05, **p < 0.01. Data are presented as mean values ± SEM. f Proinflammatory cytokine and chemokine protein levels in cecal tissue homogenates. Statistical significance was calculated by a two-sided unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Data are presented as mean values ± SEM. g Relative abundance of Proteobacteria and gamma-Proteobacteria ASVs in fecal pellets of Rag1−/− and Rag1HET mice at day 36 p.i. Statistical significance was calculated by a two-sided unpaired t test. Data are presented as mean values ± SEM. Data presented in figure are representative of three independent experiments. Prior to ABX treatment (n = 10 Rag1−/−; n = 12 Rag1HET mice), day 0 of infection (n = 6 Rag1−/−; n = 5 Rag1HET mice), day 36 post-C. difficile (n = 5 Rag1−/− and Rag1HET mice) or ABX-treatment alone (n = 2 Rag1−/− and Rag1HET mice).CC BY · PubMed Central
Fig. 3 CD4+ T cells support FMT-mediated resolution of C. difficile infection. a Cohoused C57BL/6, μMT−/−, β2M−/− mice were infected with C. difficile and bacterial burden was assessed in the fecal pellets following FMT. n = 5 C57BL/6; n = 4 β2M−/−; n = 5 μMT−/− mice. Data is representative of two independent experiments. b C. difficile burden in fecal pellets of cohoused C57BL/6 (n = 11) and C-II−/− (n = 14) mice following FMT. Data is a combination of three independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. ***p < 0.0001. Data are presented as mean values ± SEM. c Toxin titers in the cecal content at day 15 post-FMT. n = 4 mice per group. Statistical significance was calculated by two-sided Mann–Whitney test. *p = 0.029. Data are presented as mean values ± SEM. d–f Single cell suspensions isolated from the large intestine lamina propria of naïve, C. difficile infected, or C. difficile-infected FMT-treated C57BL/6 mice were stimulated ex vivo with PMA/Ionomycin in the presence of BFA and assessed for cytokine production. d Frequency and total number of e IL-17a or f IL-22 competent CD4+ T cells. FACS plots gated on live, CD45+, CD3ε+, CD4+ cells. Gating strategy shown in Supplemental Fig. 13. g–i Intranuclear transcription factor staining of cells isolated from the large intestine lamina propria of naïve, C. difficile infected, or C. difficile-infected FMT-treated C57BL6 mice. g Frequency and total number of h Foxp3+ or i Foxp3+ RoRγt+ CD4+ T cells. FACS plots gated on live, CD45+, CD3ε+, CD4+ cells. Data in d–i are representative of two independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. n = 5 mice per group. e (N vs. C. diff *p = 0.014; N vs FMT *p = 0.011. f, N vs FMT *p = 0.007. h, N vs. C. diff *p = 0.003; N vs FMT *p = 0.021. i N vs. C. diff *p = 0.004; N vs FMT *p = 0.028) Data are presented as mean values ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001. b.d. below detection.
Fig. 3 CD4+ T cells support FMT-mediated resolution of C. difficile infection. a Cohoused C57BL/6, μMT−/−, β2M−/− mice were infected with C. difficile and bacterial burden was assessed in the fecal pellets following FMT. n = 5 C57BL/6; n = 4 β2M−/−; n = 5 μMT−/− mice. Data is representative of two independent experiments. b C. difficile burden in fecal pellets of cohoused C57BL/6 (n = 11) and C-II−/− (n = 14) mice following FMT. Data is a combination of three independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. ***p < 0.0001. Data are presented as mean values ± SEM. c Toxin titers in the cecal content at day 15 post-FMT. n = 4 mice per group. Statistical significance was calculated by two-sided Mann–Whitney test. *p = 0.029. Data are presented as mean values ± SEM. d–f Single cell suspensions isolated from the large intestine lamina propria of naïve, C. difficile infected, or C. difficile-infected FMT-treated C57BL/6 mice were stimulated ex vivo with PMA/Ionomycin in the presence of BFA and assessed for cytokine production. d Frequency and total number of e IL-17a or f IL-22 competent CD4+ T cells. FACS plots gated on live, CD45+, CD3ε+, CD4+ cells. Gating strategy shown in Supplemental Fig. 13. g–i Intranuclear transcription factor staining of cells isolated from the large intestine lamina propria of naïve, C. difficile infected, or C. difficile-infected FMT-treated C57BL6 mice. g Frequency and total number of h Foxp3+ or i Foxp3+ RoRγt+ CD4+ T cells. FACS plots gated on live, CD45+, CD3ε+, CD4+ cells. Data in d–i are representative of two independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. n = 5 mice per group. e (N vs. C. diff *p = 0.014; N vs FMT *p = 0.011. f, N vs FMT *p = 0.007. h, N vs. C. diff *p = 0.003; N vs FMT *p = 0.021. i N vs. C. diff *p = 0.004; N vs FMT *p = 0.028) Data are presented as mean values ± SEM. *p < 0.05, **p < 0.01, ***p < 0.001. b.d. below detection.CC BY · PubMed Central
Fig. 4 Treg cell depletion impairs FMT-mediated resolution of C. difficile infection. a Schematic of C. difficile infection, Treg cell depletion and FMT in Foxp3DTR mice. b Weight loss of C. difficile infected Foxp3DTR mice following DT (n = 7) or PBS (n = 7) administration. Data are presented as mean values ± SEM. c C. difficile burden in the feces of Foxp3DTR mice following DT or PBS administration and FMT. n = 9 mice per group. Data is a combination of three independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. *p = 0.015, **p = 0.001, ***p < 0.0001. d Frequency of Foxp3+ CD4+ T cells in the large intestine lamina propria of Foxp3DTR mice at day 12 p.i. (day 4 post-DT treatment) or day 21 p.i. (day of FMT). n = 4–6 mice per group. FACS plots gated on live, CD45+, CD3ε+, CD4+ cells. Gating strategy shown in Supplemental Fig. 13. e Total number of Foxp3+ CD4+ T cells and f relative proportion of CD4+ T cell subsets in the large intestine lamina propria at day 12 p.i. (day 4 post-DT treatment). n = 4 PBS- treated Foxp3DTR mice; n = 5 DT-treated Foxp3DTR mice. Statistical significance was calculated by a two-sided Mann–Whitney test. ***p < 0.0001. Data are presented as mean values ± SEM. g Total number of Foxp3+ CD4+ T cells and h relative proportion of CD4+ T cell subsets in the large intestine lamina propria at day 21 p.i. (day of FMT). n = 6 PBS & DT-treated Foxp3DTR mice. Statistical significance was calculated by a two-sided unpaired Mann-Whitney test. Data are presented as mean values ± SEM. i Total number of TH17 cells, TH1 cells, inflammatory monocytes, and neutrophils in the large intestine lamina propria at day 21 p.i. (day of FMT). n = 10 uninfected PBS-treated Foxp3DTR mice; n = 8 uninfected DT-treated Foxp3DTR mice; n = 10 C. difficile infected PBS-treated Foxp3DTR mice; n = 10 C. difficile infected DT-treated Foxp3DTR mice examined over three independent experiments. Statistical significance was calculated by two-sided unpaired t-test. *p = 0.013, **p = 0.002 Data are presented as mean values ± SEM. j mRNA expression of proinflammatory immune response genes in whole colon tissue as assessed by qRT-PCR. Gene expression relative to ABX-treated, uninfected Foxp3DTR mice and normalized to Hprt. n = 10 uninfected PBS-treated Foxp3DTR mice; n = 8 uninfected DT-treated Foxp3DTR mice; n = 10 C. difficile infected PBS-treated Foxp3DTR mice; n = 9 C. difficile infected DT-treated Foxp3DTR mice examined over three independent experiments. Statistical significance was calculated by two-sided unpaired t-test. *p < 0.05, **p < 0.01. Data are presented as mean values ± SEM.
Fig. 4 Treg cell depletion impairs FMT-mediated resolution of C. difficile infection. a Schematic of C. difficile infection, Treg cell depletion and FMT in Foxp3DTR mice. b Weight loss of C. difficile infected Foxp3DTR mice following DT (n = 7) or PBS (n = 7) administration. Data are presented as mean values ± SEM. c C. difficile burden in the feces of Foxp3DTR mice following DT or PBS administration and FMT. n = 9 mice per group. Data is a combination of three independent experiments. Statistical significance was calculated by a two-sided unpaired t-test. *p = 0.015, **p = 0.001, ***p < 0.0001. d Frequency of Foxp3+ CD4+ T cells in the large intestine lamina propria of Foxp3DTR mice at day 12 p.i. (day 4 post-DT treatment) or day 21 p.i. (day of FMT). n = 4–6 mice per group. FACS plots gated on live, CD45+, CD3ε+, CD4+ cells. Gating strategy shown in Supplemental Fig. 13. e Total number of Foxp3+ CD4+ T cells and f relative proportion of CD4+ T cell subsets in the large intestine lamina propria at day 12 p.i. (day 4 post-DT treatment). n = 4 PBS- treated Foxp3DTR mice; n = 5 DT-treated Foxp3DTR mice. Statistical significance was calculated by a two-sided Mann–Whitney test. ***p < 0.0001. Data are presented as mean values ± SEM. g Total number of Foxp3+ CD4+ T cells and h relative proportion of CD4+ T cell subsets in the large intestine lamina propria at day 21 p.i. (day of FMT). n = 6 PBS & DT-treated Foxp3DTR mice. Statistical significance was calculated by a two-sided unpaired Mann-Whitney test. Data are presented as mean values ± SEM. i Total number of TH17 cells, TH1 cells, inflammatory monocytes, and neutrophils in the large intestine lamina propria at day 21 p.i. (day of FMT). n = 10 uninfected PBS-treated Foxp3DTR mice; n = 8 uninfected DT-treated Foxp3DTR mice; n = 10 C. difficile infected PBS-treated Foxp3DTR mice; n = 10 C. difficile infected DT-treated Foxp3DTR mice examined over three independent experiments. Statistical significance was calculated by two-sided unpaired t-test. *p = 0.013, **p = 0.002 Data are presented as mean values ± SEM. j mRNA expression of proinflammatory immune response genes in whole colon tissue as assessed by qRT-PCR. Gene expression relative to ABX-treated, uninfected Foxp3DTR mice and normalized to Hprt. n = 10 uninfected PBS-treated Foxp3DTR mice; n = 8 uninfected DT-treated Foxp3DTR mice; n = 10 C. difficile infected PBS-treated Foxp3DTR mice; n = 9 C. difficile infected DT-treated Foxp3DTR mice examined over three independent experiments. Statistical significance was calculated by two-sided unpaired t-test. *p < 0.05, **p < 0.01. Data are presented as mean values ± SEM.CC BY · PubMed Central
Fig. 5 C. difficile-infected Rag1−/− and C-II−/− mice exhibit impaired FMT engraftment. C. difficile-infected (a–d) Rag1−/− and Rag1HET mice or (e–h) C57BL/6 and C-II−/− mice were administered a FMT and microbial composition was analyzed. a Unweighted UniFrac principal coordinate analysis plot of 16S bacterial rRNA ASVs from the FMT inoculum, fecal pellets of C. difficile infected Rag1−/− and Rag1HET mice at the time of FMT, and cecal content of Rag1−/− and Rag1HET mice at day 21 post-FMT. b Relative abundance of top 15 bacterial ASVs in the microbiota of C. difficile-infected FMT-treated Rag1−/− and Rag1HET mice (day 21 post-FMT) Bar plot is displayed at the genus level except for orange bars that represent an ASV aligning to C. difficile. c Unweighted UniFrac distance comparing the microbiota beta diversity dissimilarity of Rag1−/− and Rag1HET groups to FMT inoculum. n = 9 C. diff. Rag1HET; n = 8 C. diff. Rag1−/−; n = 6 FMT Rag1HET; n = 4 FMT Rag1−/− mice. Statistical significance was calculated by one-way ANOVA test using Dunnett method for multiple comparison adjustments. ***p < 0.0001. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. d Dendrogram representation of intestinal microbial communities of FMT inoculum, Rag1−/− and Rag1HET groups using unsupervised hierarchical clustering of unweighted UniFrac distances to identify similarities between samples. e Unweighted UniFrac principal coordinate analysis plot of 16S bacterial rRNA ASVs from the FMT inoculum and fecal pellets from C. difficile infected C57BL/6 and C-II−/− mice at time of FMT and day 15 post-FMT. f Relative abundance of top 15 bacterial ASVs in the microbiota of C. difficile-infected FMT-treated C57BL/6 and C-II−/− mice (day 15 post-FMT). Bar plot is displayed at the genus level except for orange bars that represent an ASV aligning to C. difficile. g Unweighted UniFrac distance comparing the microbiota beta diversity dissimilarity of C57BL/6 and C-II−/− groups to FMT inoculum. n = 4 mice per group . Statistical significance was calculated by a one-way ANOVA test using Dunnett method for multiple comparison adjustments. ***p < 0.0001. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. h Dendrogram representation of intestinal microbial communities of FMT inoculum, C57BL/6 and C-II−/− groups using unsupervised hierarchical clustering of unweighted UniFrac distances to identify similarities between samples. Data are presented as mean values ± SEM. ***p < 0.001.
Fig. 5 C. difficile-infected Rag1−/− and C-II−/− mice exhibit impaired FMT engraftment. C. difficile-infected (a–d) Rag1−/− and Rag1HET mice or (e–h) C57BL/6 and C-II−/− mice were administered a FMT and microbial composition was analyzed. a Unweighted UniFrac principal coordinate analysis plot of 16S bacterial rRNA ASVs from the FMT inoculum, fecal pellets of C. difficile infected Rag1−/− and Rag1HET mice at the time of FMT, and cecal content of Rag1−/− and Rag1HET mice at day 21 post-FMT. b Relative abundance of top 15 bacterial ASVs in the microbiota of C. difficile-infected FMT-treated Rag1−/− and Rag1HET mice (day 21 post-FMT) Bar plot is displayed at the genus level except for orange bars that represent an ASV aligning to C. difficile. c Unweighted UniFrac distance comparing the microbiota beta diversity dissimilarity of Rag1−/− and Rag1HET groups to FMT inoculum. n = 9 C. diff. Rag1HET; n = 8 C. diff. Rag1−/−; n = 6 FMT Rag1HET; n = 4 FMT Rag1−/− mice. Statistical significance was calculated by one-way ANOVA test using Dunnett method for multiple comparison adjustments. ***p < 0.0001. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. d Dendrogram representation of intestinal microbial communities of FMT inoculum, Rag1−/− and Rag1HET groups using unsupervised hierarchical clustering of unweighted UniFrac distances to identify similarities between samples. e Unweighted UniFrac principal coordinate analysis plot of 16S bacterial rRNA ASVs from the FMT inoculum and fecal pellets from C. difficile infected C57BL/6 and C-II−/− mice at time of FMT and day 15 post-FMT. f Relative abundance of top 15 bacterial ASVs in the microbiota of C. difficile-infected FMT-treated C57BL/6 and C-II−/− mice (day 15 post-FMT). Bar plot is displayed at the genus level except for orange bars that represent an ASV aligning to C. difficile. g Unweighted UniFrac distance comparing the microbiota beta diversity dissimilarity of C57BL/6 and C-II−/− groups to FMT inoculum. n = 4 mice per group . Statistical significance was calculated by a one-way ANOVA test using Dunnett method for multiple comparison adjustments. ***p < 0.0001. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. h Dendrogram representation of intestinal microbial communities of FMT inoculum, C57BL/6 and C-II−/− groups using unsupervised hierarchical clustering of unweighted UniFrac distances to identify similarities between samples. Data are presented as mean values ± SEM. ***p < 0.001.CC BY · PubMed Central
Fig. 6 FMT non-responsive Rag1−/− mice fail to restore their intestinal metabolite profile to pre-infection conditions. C. difficile-infected Rag1−/− and Rag1HET mice were administered FMT or PBS, sacrificed 21 days later along with naïve mice and amino acid, short chain fatty acid (SCFA), 1° and 2° bile acid pools were analyzed in cecal content. a Heatmap of relative concentration of amino acids, SCFA, 1° and 2° bile acids in cecal content of naïve (n = 5), C. difficile-infected (n = 6) or C. difficile-infected FMT-treated (n = 4 Rag1−/−; n = 6 Rag1HET mice). b Principal coordinate analysis plot comparing metabolite profile in the cecum of naïve, C. difficile-infected, and C. difficile-infected FMT-treated Rag1−/− and Rag1HET mice. Ellipses represent 95% confidence intervals. c Volcano plot of metabolites in the cecum of C. difficile-infected FMT-treated Rag1−/− and Rag1HET mice. Blue circles indicate metabolites enriched in Rag1HET mice. Red circles indicate metabolites enriched in Rag1−/− mice. Significance threshold criteria set at a two-fold change in concentration and an adjusted p-value of 0.05 using an unpaired t-test and adjusted for false discovery rate. d Concentration of individual 2° bile acids. n = 5 naïve Rag1−/− and Rag1HET mice; n = 6 C. difficile-infected Rag1−/− and Rag1HET mice; n = 4 C. difficile-infected FMT-treated Rag1−/−; n = 6 C. difficile-infected FMT-treated Rag1HET mice examined over two independent experiments. Statistical significance was calculated by a one-way ANOVA using Dunnett method for multiple comparison adjustments. DCA ***p < 0.0001, LCA *p = 0.043, TDCA *p = 0.014, ωMCA **p = 0.002. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. *p < 0.05, **p < 0.01, ***p < 0.001. TCDCA taurochenodeoxycholic acid, αMCA alphamuricholic acid, βMCA betamuricholic acid, γMCA gammamuricholic acid, CDCA chenodeoxycholic acid, TCA taurocholic acid, CA cholic acid, TLCA taurolithocholic acid, TDCA taurodeoxycholic acid, GDCA glycodeoxycholic acid, LCA lithocholic acid, ωMCA omegamuricholic acid, DCA deoxycholic acid. b.d. below detection.
Fig. 6 FMT non-responsive Rag1−/− mice fail to restore their intestinal metabolite profile to pre-infection conditions. C. difficile-infected Rag1−/− and Rag1HET mice were administered FMT or PBS, sacrificed 21 days later along with naïve mice and amino acid, short chain fatty acid (SCFA), 1° and 2° bile acid pools were analyzed in cecal content. a Heatmap of relative concentration of amino acids, SCFA, 1° and 2° bile acids in cecal content of naïve (n = 5), C. difficile-infected (n = 6) or C. difficile-infected FMT-treated (n = 4 Rag1−/−; n = 6 Rag1HET mice). b Principal coordinate analysis plot comparing metabolite profile in the cecum of naïve, C. difficile-infected, and C. difficile-infected FMT-treated Rag1−/− and Rag1HET mice. Ellipses represent 95% confidence intervals. c Volcano plot of metabolites in the cecum of C. difficile-infected FMT-treated Rag1−/− and Rag1HET mice. Blue circles indicate metabolites enriched in Rag1HET mice. Red circles indicate metabolites enriched in Rag1−/− mice. Significance threshold criteria set at a two-fold change in concentration and an adjusted p-value of 0.05 using an unpaired t-test and adjusted for false discovery rate. d Concentration of individual 2° bile acids. n = 5 naïve Rag1−/− and Rag1HET mice; n = 6 C. difficile-infected Rag1−/− and Rag1HET mice; n = 4 C. difficile-infected FMT-treated Rag1−/−; n = 6 C. difficile-infected FMT-treated Rag1HET mice examined over two independent experiments. Statistical significance was calculated by a one-way ANOVA using Dunnett method for multiple comparison adjustments. DCA ***p < 0.0001, LCA *p = 0.043, TDCA *p = 0.014, ωMCA **p = 0.002. Boxes represent median, first and third quartile. Whiskers extend to the highest and lowest data point. *p < 0.05, **p < 0.01, ***p < 0.001. TCDCA taurochenodeoxycholic acid, αMCA alphamuricholic acid, βMCA betamuricholic acid, γMCA gammamuricholic acid, CDCA chenodeoxycholic acid, TCA taurocholic acid, CA cholic acid, TLCA taurolithocholic acid, TDCA taurodeoxycholic acid, GDCA glycodeoxycholic acid, LCA lithocholic acid, ωMCA omegamuricholic acid, DCA deoxycholic acid. b.d. below detection.CC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 75

  1. Hartstra, A. V., Bouter, K. E., Backhed, F. & Nieuwdorp, M. Insights into the role of the microbiome in obesity and type 2 diabetes. Diabetes Care 38, 159–165 (2015). · DOI · Paper page
  2. Bashiardes, S., Tuganbaev, T., Federici, S. & Elinav, E. The microbiome in anti-cancer therapy. Semin. Immunol. 32, 74–81 (2017). · DOI
  3. Cammarota, G. et al. The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy. Pharm. Ther. 149, 191–212 (2015). · DOI
  4. Hsiao, E. Y. et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155, 1451–1463 (2013). · DOI · Paper page
  5. Buffington, S. A. et al. Microbial reconstitution reverses maternal diet-induced social and synaptic deficits in offspring. Cell 165, 1762–1775 (2016). · DOI · Paper page
  6. Ridaura, V. K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013). · DOI · Paper page
  7. Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205–208 (2015). · DOI · Paper page
  8. Steidler, L. et al. Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science 289, 1352–1355 (2000). · DOI · Paper page
  9. Sgritta, M. et al. Mechanisms underlying microbial-mediated changes in social behavior in mouse models of autism spectrum disorder. Neuron 101, 246–259 e246 (2019). · DOI · Paper page
  10. Mimee, M., Citorik, R. J. & Lu, T. K. Microbiome therapeutics - advances and challenges. Adv. Drug Deliv. Rev. 105, 44–54 (2016). · DOI
  11. Gupta, S., Allen-Vercoe, E. & Petrof, E. O. Fecal microbiota transplantation: in perspective. Ther. Adv. Gastroenterol. 9, 229–239 (2016). · DOI
  12. Guh, A. Y. et al. Trends in U.S. burden of clostridioides difficile infection and outcomes. N. Engl. J. Med. 382, 1320–1330 (2020). · DOI
  13. Drekonja, D. M. et al. Comparative effectiveness of Clostridium difficile treatments: a systematic review. Ann. Intern. Med 155, 839–847 (2011). · DOI
  14. Dudukgian, H., Sie, E., Gonzalez-Ruiz, C., Etzioni, D. A. & Kaiser, A. M. C. difficile colitis–predictors of fatal outcome. J. Gastrointest. Surg. 14, 315–322 (2010). · DOI
  15. Viswanathan, V. K., Mallozzi, M. J. & Vedantam, G. Clostridium difficile infection: an overview of the disease and its pathogenesis, epidemiology and interventions. Gut Microbes 1, 234–242 (2010). · DOI
  16. Debast, S. B., Bauer, M. P. & Kuijper, E. J. European Society of Clinical Microbiology and Infectious Diseases European Society of Clinical Microbiology and Infectious Diseases: update of the treatment guidance document for Clostridium difficile infection. Clin. Microbiol Infect. 20, 1–26 (2014). · DOI
  17. Jernberg, C., Lofmark, S., Edlund, C. & Jansson, J. K. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J. 1, 56–66 (2007). · DOI · Paper page
  18. Schubert, A. M. et al. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. MBio 5, e01021–01014 (2014). · DOI
  19. Seekatz, A. M. et al. Recovery of the gut microbiome following fecal microbiota transplantation. MBio 5, e00893–00814 (2014). · DOI
  20. Seekatz, A. M. et al. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection. Anaerobe 53, 64–73 (2018). · DOI
  21. Weingarden, A. R. et al. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am. J. Physiol. Gastrointest. Liver Physiol. 306, G310–G319 (2014). · DOI · Paper page
  22. Weingarden, A. R. et al. Changes in colonic bile acid composition following fecal microbiota transplantation are sufficient to control Clostridium difficile germination and growth. PLoS ONE 11, e0147210 (2016). · DOI
  23. Khan, M. Y., Dirweesh, A., Khurshid, T. & Siddiqui, W. J. Comparing fecal microbiota transplantation to standard-of-care treatment for recurrent Clostridium difficile infection: a systematic review and meta-analysis. Eur. J. Gastroenterol. Hepatol. 30, 1309–1317 (2018). · DOI
  24. Seekatz, A. M. et al. Fecal microbiota transplantation eliminates clostridium difficile in a murine model of relapsing disease. Infect. Immun. 83, 3838–3846 (2015). · DOI
  25. Abt, M. C. et al. Innate immune defenses mediated by two ilc subsets are critical for protection against acute Clostridium difficile infection. Cell Host Microbe 18, 27–37 (2015). · DOI
  26. Hasegawa, M. et al. Interleukin-22 regulates the complement system to promote resistance against pathobionts after pathogen-induced intestinal damage. Immunity 41, 620–632 (2014). · DOI
  27. Leslie, J. L., Vendrov, K. C., Jenior, M. L. & Young, V. B. The gut microbiota is associated with clearance of Clostridium difficile infection independent of adaptive immunity. mSphere 4, e00698-18 (2019). · DOI
  28. Chen, X. et al. A mouse model of Clostridium difficile-associated disease. Gastroenterology 135, 1984–1992 (2008). · DOI · Paper page
  29. Korn, L. L. et al. Conventional CD4+ T cells regulate IL-22-producing intestinal innate lymphoid cells. Mucosal. Immunol. 7, 1045–1057 (2014). · DOI
  30. Janda, J. M. & Abbott, S. L. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J. Clin. Microbiol 45, 2761–2764 (2007). · DOI
  31. Lupp, C. et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2, 119–129 (2007). · DOI
  32. Johnston, P. F., Gerding, D. N. & Knight, K. L. Protection from Clostridium difficile infection in CD4 T Cell- and polymeric immunoglobulin receptor-deficient mice. Infect. Immun. 82, 522–531 (2014). · DOI
  33. Sakaguchi, S., Yamaguchi, T., Nomura, T. & Ono, M. Regulatory T cells and immune tolerance. Cell 133, 775–787 (2008). · DOI
  34. Kim, J. M., Rasmussen, J. P. & Rudensky, A. Y. Regulatory T cells prevent catastrophic autoimmunity throughout the lifespan of mice. Nat. Immunol. 8, 191–197 (2007). · DOI
  35. Bos, P. D., Plitas, G., Rudra, D., Lee, S. Y. & Rudensky, A. Y. Transient regulatory T cell ablation deters oncogene-driven breast cancer and enhances radiotherapy. J. Exp. Med. 210, 2435–2466 (2013). · DOI
  36. Battaglioli, E. J. et al. Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea. Sci. Transl. Med. 10 (2018). · DOI
  37. Fletcher, J. R., Erwin, S., Lanzas, C. & Theriot, C. M. Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model. mSphere 3, eaam7019 (2018). · DOI
  38. Ferreyra, J. A. et al. Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance. Cell Host Microbe 16, 770–777 (2014). · DOI
  39. Nagao-Kitamoto, H. et al. Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nat. Med. 26, 608–617 (2020). · DOI
  40. Theriot, C. M., Bowman, A. A. & Young, V. B. Antibiotic-induced alterations of the gut microbiota alter secondary bile acid production and allow for Clostridium difficile spore germination and outgrowth in the large intestine. mSphere 1, e00045-15 (2016). · DOI · Paper page
  41. Francis, M. B., Allen, C. A. & Sorg, J. A. Muricholic acids inhibit Clostridium difficile spore germination and growth. PLoS ONE 8, e73653 (2013). · DOI
  42. Sorg, J. A. & Sonenshein, A. L. Inhibiting the initiation of Clostridium difficile spore germination using analogs of chenodeoxycholic acid, a bile acid. J. Bacteriol. 192, 4983–4990 (2010). · DOI · Paper page
  43. Winter, S. E., Lopez, C. A. & Baumler, A. J. The dynamics of gut-associated microbial communities during inflammation. EMBO Rep. 14, 319–327 (2013). · DOI
  44. Winter, S. E. et al. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 467, 426–429 (2010). · DOI
  45. Winter, S. E. et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 339, 708–711 (2013). · DOI · Paper page
  46. Thiennimitr, P. et al. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc. Natl Acad. Sci. USA 108, 17480–17485 (2011). · DOI
  47. Spees, A. M. et al. Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration. MBio 4, e00430-13 (2013). · DOI
  48. Hughes, E. R. & Winter, S. E. Enterococcus faecalis: E. coli’s Siderophore-Inducing Sidekick. Cell Host Microbe 20, 411–412 (2016). · DOI
  49. Gillis, C. C. et al. Dysbiosis-associated change in host metabolism generates lactate to support salmonella growth. Cell Host Microbe 23, 54–64 e56 (2018). · DOI
  50. Byndloss, M. X. et al. Microbiota-activated PPAR-gamma signaling inhibits dysbiotic Enterobacteriaceae expansion. Science 357, 570–575 (2017). · DOI
  51. Staley, C., Weingarden, A. R., Khoruts, A. & Sadowsky, M. J. Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl. Microbiol. Biotechnol. 101, 47–64 (2017). · DOI
  52. Sorg, J. A. & Sonenshein, A. L. Bile salts and glycine as cogerminants for Clostridium difficile spores. J. Bacteriol. 190, 2505–2512 (2008). · DOI · Paper page
  53. Wilson, K. H. Efficiency of various bile salt preparations for stimulation of Clostridium difficile spore germination. J. Clin. Microbiol. 18, 1017–1019 (1983). · DOI
  54. Song, X. et al. Microbial bile acid metabolites modulate gut RORgamma(+) regulatory T cell homeostasis. Nature 577, 410–415 (2020). · DOI · Paper page
  55. Burrello, C. et al. Therapeutic faecal microbiota transplantation controls intestinal inflammation through IL10 secretion by immune cells. Nat. Commun. 9, 5184 (2018). · DOI
  56. Zuo, T. et al. Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome. Gut 67, 634–643 (2018).
  57. Hargreaves, K. R. & Clokie, M. R. Clostridium difficile phages: still difficult? Front. Microbiol. 5, 184 (2014). · DOI
  58. Gogokhia, L. et al. Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis. Cell Host Microbe 25, 285–299 e288 (2019). · DOI
  59. Carlson, P. E. Jr. Regulatory considerations for fecal microbiota transplantation products. Cell Host Microbe 27, 173–175 (2020). · DOI
  60. Di Bella, S., Gouliouris, T. & Petrosillo, N. Fecal microbiota transplantation (FMT) for Clostridium difficile infection: focus on immunocompromised patients. J. Infect. Chemother. 21, 230–237 (2015). · DOI
  61. Kelly, C. R. et al. Fecal microbiota transplant for treatment of Clostridium difficile infection in immunocompromised patients. Am. J. Gastroenterol. 109, 1065–1071 (2014). · DOI · Paper page
  62. Moss, E. L. et al. Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients. PLoS ONE 12, e0182585 (2017). · DOI
  63. Staley, C. et al. Durable long-term bacterial engraftment following encapsulated fecal microbiota transplantation to treat Clostridium difficile infection. MBio 10, e01586-19 (2019). · DOI
  64. Popoff, M. R., Rubin, E. J., Gill, D. M. & Boquet, P. Actin-specific ADP-ribosyltransferase produced by a Clostridium difficile strain. Infect. Immun. 56, 2299–2306 (1988). · DOI
  65. Sorg, J. A. & Dineen, S. S. Laboratory maintenance of Clostridium difficile. Curr. Protoc. Microbio.l Chapter 9, Unit9A 1 (2009). · DOI
  66. Jarchum, I., Liu, M., Lipuma, L. & Pamer, E. G. Toll-like receptor 5 stimulation protects mice from acute Clostridium difficile colitis. Infect. Immun. 79, 1498–1503 (2011). · DOI
  67. Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996–998 (2013). · DOI
  68. Lee, Y. J. et al. Protective factors in the intestinal microbiome against Clostridium difficile infection in recipients of allogeneic hematopoietic stem cell transplantation. J. Infect. Dis. 215, 1117–1123 (2017). · DOI
  69. McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013). · DOI
  70. Wickham, H. ggplot2: Elegant Graphics for Data Analysis. (New York, Springer-Verlag, 2016). · DOI
  71. Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016). · DOI · Paper page
  72. Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013). · DOI · Paper page
  73. Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010). · DOI · Paper page
  74. Ramsteijn, A. S., Jasarevic, E., Houwing, D. J., Bale, T. L. & Olivier, J. D. Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression. Gut Microbes 11, 735–753 (2020). · DOI
  75. Ni, J. et al. A role for bacterial urease in gut dysbiosis and Crohn’s disease. Sci. Transl. Med. 9, eaah6888 (2017). · DOI

Cited by

Sorted by citations

See all 88

Metadata

Authors
Littmann, E. R., Lee, J.-J., Denny, J. E., Alam, Z., Maslanka, J. R., Zarin, I., Matsuda, R., Carter, R. A., Susac, B., Saffern, M. S., Fett, B., Mattei, L. M., Bittinger, K., & Abt, M. C.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2021-02-02
Volume
12
Issue
1
ISSN
2041-1723
DOI
10.1038/s41467-020-20793-x
PMC
PMC7854624
Cited by
88
References
23
Language
en
Licence
Funders
U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (AI125786)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review