There is a growing appreciation for the importance of the gut microbiota as a therapeutic target in various diseases. However, there are only a handful of known commensal strains that can potentially be used to manipulate host physiological functions. Here we isolate a consortium of 11 bacterial strains from healthy human donor faeces that is capable of robustly inducing interferon-γ-producing CD8 T cells in the intestine. These 11 strains act together to mediate the induction without causing inflammation in a manner that is dependent on CD103+ dendritic cells and major histocompatibility (MHC) class Ia molecules. Colonization of mice with the 11-strain mixture enhances both host resistance against Listeria monocytogenes infection and the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumour models. The 11 strains primarily represent rare, low-abundance components of the human microbiome, and thus have great potential as broadly effective biotherapeutics.
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Genomic sequences of the 21 strains are deposited in the European Nucleotide Archive with accession number PRJEB29940. Microbiome data are deposited in the DNA Data Bank of Japan with accession number DRA007611. Accession numbers for metagenomics datasets: NCBI BioProjects PRJNA275349 (HMP1-2)38, PRJNA48479 (HMP1-2), PRJNA398089 (HMP2)39, PRJNA319574 (500FG)40, PRJDB3601 (healthy Japanese adults)34 and PRJNA399742 (Gajewski)31. EBI study accession EGAS00001001704 (LLDeep)41, PRJEB22894 (Wargo)30, PRJEB22863 (Zitvogel)29. EBI ENA ERP002061 (MetaHIT), ERP003612 (MetaHIT) and ERP004605 (MetaHIT)42,43.
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K.H. was funded through AMED LEAP under grant number JP18gm0010003, the Takeda Science Foundation, and the Mitsubishi Foundation. T.T. was funded through AMED PRIME under grant number JP18gm6010013 and the Nakajima Foundation. R.J.X. was funded through NIH DK43351, AT009708, and the Center for Microbiome Informatics and Therapeutics, MIT. The LC–MS platform used in this study was provided by the JST ERATO Gas Biology Project, which was led by M.S. until March 2015. We thank N. Palm, J. Faith and J. S. Weber for discussion, J. Baginska and O. Ohara for their technical support, P. Burrows for comments, and RIKEN BRC and the International Mouse Phenotyping Consortium for generating and providing the H2-M3 knockout mice.
Nature thanks S. Mazmanian and the anonymous reviewer(s) for their contribution to the peer review of this work.
B.O., B.R. and J.M.N. are employees of Vedanta Biosciences Inc. A.S. is an employee of JSR Corporation. K.H. is co-founder and scientific advisor to Vedanta Biosciences since 11 August 2011.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data figures and tables
a, b, Representative flow cytometry histograms and plots showing the expression of CD8β, CD44, T-bet, ICOS, CD103, KLRG1 and GrB by colonic lamina propria IFNγ+ CD8 T cells isolated from SPF mice from two independent experiments. c, Number of IFNγ+ CD8 T cells in the colonic or small intestinal lamina propria of germ-free and SPF mice. d, Percentage of IFNγ+ cells among CD8 T cells in the colon of SPF mice (between 8 and 12 weeks old) treated with or without AVMN (ampicillin, vancomycin, metronidazole and neomycin) via the drinking water for 4 weeks. e, Faeces from SPF mice (SPFfae) were orally inoculated into germ-free mice (7 weeks old), and 4 weeks later the percentage of IFNγ+ cells among CD8 T cells was analysed. f, Left, percentage of IFNγ+ cells among CD8 T cells in the colonic lamina propria of SPF C57BL/6 mice (10 weeks old), reared at the indicated institute or vendor. Right, SPF C57BL/6 mice (8 weeks old) obtained from Charles River were cohoused with C57BL/6 mice from CLEA for 0, 2 or 6 weeks, and the percentage of IFNγ+ cells among colonic lamina propria CD8 T cells was analysed. Each circle represents an individual animal, and the number of mice in each group is shown. Data are mean and s.d. ***P < 0.001; *P < 0.05; one-way ANOVA with Tukey’s test (c, f) or two-tailed unpaired t-test (d, e). See Source Data for exact P values. Source Data
Extended Data Fig. 2 Bacteria from the healthy human gut microbiota associated with IFNγ+ CD8 T cell induction.
a, Schematic representation of the strategy for isolating IFNγ+ CD8 T cell-inducing bacteria from the healthy human gut microbiota. b, Representative flow cytometry plots showing the expression of IFNγ and CD8α by colonic or small intestinal lamina propria CD3+TCRβ+ T cells from germ-free mice orally inoculated with healthy human faecal samples (from donors A to F). c, Spearman’s correlation coefficient and P values for the relationship between the number of individual bacterial 228 OTUs (among 3,000 reads) detected in mice shown in Fig. 1e and the percentage of colonic IFNγ+ CD8 T cell population shown in Fig. 1d was calculated using GraphPad Prism. OTUs positively and negatively correlated with the frequency of colonic IFNγ+ CD8 T cells with statistical significance (P < 0.05) are highlighted in red and dark blue, respectively. OTUs detected in GF+CHL B5 mice are marked in light and dark blue. OTUs showing no significant correlation (P > 0.05) are marked in grey. The closest species/strain and individual Rho (ρ) value for each OTU are shown. Source Data
Extended Data Fig. 3 Induction of IFNγ+CD8 T cells by the 11-mix via non-inflammatory immunomodulation.
a, Percentage of IFNγ+ cells among colonic CD8 T cells from mice of the indicated genetic background, colonized with or without the 11-mix. b, c, Representative flow cytometry histograms and plots showing the expression of CD103, PD-1, CD44, T-bet, ICOS, KLRG1 and GrB by colonic IFNγ+ CD8 T cells from germ-free mice colonized with or without the 11-mix for 4 weeks, from two independent experiments. d, Expression of the indicated pro-inflammatory genes in colonic epithelial cells from germ-free, GF+11-mix (4 weeks after colonization), and SPF mice, as determined by qPCR. e, Representative photographs of caecums and colons from germ-free, GF+11-mix (4 weeks after colonization) and SPF mice from several independent experiments. f–h, Haematoxylin and eosin-stained colon photomicrographs (f), histology score (g), and percentage of IFNγ+ cells among CD8 T cells in the colonic lamina propria (h) of germ-free and GF+11-mix mice (4 weeks or 6 months after colonization). Scale bar, 50 μm. i, Percentages of IL-17A+ (TH17) and IFNγ+ (TH1) cells among CD3+TCRβ+CD4 T cells and IFNγ+ cells among CD3+TCRβ+CD4− T cells (representing primarily CD8 T cells) in the colons of gnotobiotic mice colonized with the 11 strains, a reported TH1 cell-inducing Klebsiella pneumoniae strain (Kp2H7), or 20 reported TH17 cell-inducing strains (TH17 20-mix). Each circle represents an individual animal. The number of mice in each group is shown. Data are mean and s.d. ***P < 0.001; **P < 0.01; *P < 0.05; two-tailed unpaired t-test (a) or one-way ANOVA with Tukey’s test (d, g, h, i) was used. See Source Data for exact P values. Source Data
a, DNA was extracted from each of the 26 strains and 16S rRNA gene sequences were determined by PCR and Sanger sequencing. Genome sequencing was conducted for 21 strains using the Illumina MiSeq or the MinION nanopore sequencer. To identify the closest reference species or strain, 16S rRNA gene and genes encoding 42 ribosomal proteins predicted from the assembled draft genome of each strain were blasted to the RDP and NCBI genome databases (RefSeq genome representative), respectively. Top-hit strains were defined as those with the highest 16S rRNA sequence similarity or those with the highest ribosomal gene sequence similarity for the maximum percentage of the 42 queried genes (strains for which this is less than 37 out of 42 are listed in parentheses). Percentage similarity refers to average sequence similarity between ribosomal genes of the isolated strain and those of the top-hit reference strain. b, A phylogenetic tree was constructed by comparing 42 concatenated ribosomal gene sequences of each isolate using the MEGAv7.0 package and the neighbour-joining method with a bootstrap of 1,000 replicates. c, Relative expression of the indicated genes in colonic epithelial cells (ECs) of germ-free mice colonized with or without the 11-mix for 1 week, as determined by qPCR. d, Frequencies of TCR Vβ gene usage among IFNγ+ CD8 T cells (left) and IFNγ− CD8 T cells (right) from the colons of GF (grey) or GF+11-mix (red) mice, as determined by flow cytometry. 2-way ANOVA interaction p-values: 0.0001 (IFNγ+ subset), 0.31 (IFNγ− subset). e, Luminal contents from the indicated anatomical positions of the gut as well as faecal samples were collected from three GF+11-mix mice 3-4 weeks post-colonization. The relative abundance of each of the 11 strains’ DNA was determined by qPCR. f, MLNs were collected from GF+11-mix mice 1 week after colonization and bacterial DNA was extracted. The relative abundance of each of the 11 strains’ DNA was determined by qPCR. Each circle represents an individual animal (c, e) or a pool of mice (d), and the height of each bar indicates the mean, and the number of mice in each group is shown. n.d., not detected. Error bars, s.d. ***P < 0.001; **P < 0.01; *P < 0.05; two-tailed unpaired t-test. See Source Data for exact P values. Source Data
a, Representative flow cytometry histograms showing the expression of CD103, PD-1, CD44, ICOS and KLRG1 by inguinal lymph node (iLN) or colonic IFNγ+ CD8 T cells from the indicated mice from two independent experiments. b, Frequencies of TCR Vβ gene usage among IFNγ+ CD8 T cells (left) and IFNγ− CD8 T cells (right) from the inguinal lymph nodes of germ-free (grey) or GF+11-mix (red) mice, and those from the colons of GF+11-mix mice (blue). c, Principal component analysis plots of the water-soluble caecal metabolome from gnotobiotic mice colonized with the indicated bacterial mixtures. d–f, Heat maps depicting differentially elevated metabolites in the caecum (d, e) or serum (f) of gnotobiotic mice colonized with the indicated bacterial mixtures. Raw metabolomic data was screened for metabolites specifically increased in GF+11-mix mice only (d, e) or in GF+11-mix and GF+4-mix mice only (d) with at least fourfold enrichment as compared to GF controls and at least twofold enrichment compared to the other gnotobiotic groups, with a cut-off P value of 0.05. Overlapping metabolites between the two datasets were selected (highlighted in green), and their levels in the serum were queried (f). The most promising candidate effector molecules for the local and systemic effects observed in GF+11-mix mice were identified by considering the metabolomic data in light of the phenotypic immunomodulatory data, and are highlighted in red font (d–f). For a more detailed discussion of how these metabolites were chosen, see Supplementary Discussion. The area under each individual metabolite peak was normalized by dividing by the area under the peak of the corresponding internal standard. Heat map colours represent the z-score (red and blue indicate high and low abundance, respectively). Caecal contents were isolated 4 weeks after gavage unless otherwise noted (1w, 1 week; 4w, 4 weeks). 2PG, 2-phospho-d-glycerate; 3PG, 3-phospho-d-glycerate; GlcNAc 6P, N-acetyl-d-glucosamine 6-phosphate; GlcNAc 1P, N-acetyl-d-glucosamine 1-phosphate; Rib5P, ribose-5-phosphate; Ru5P, ribulose-5-phosphate; Xu5P, xylulose-5-phosphate. Each circle represents an individual mouse (b, iLN, c), a pool of mice (b, colon). The number of mice in each group is shown. Data are mean and s.d. *P < 0.05; two-tailed unpaired t-test. See Source Data for exact P values. Source Data
Extended Data Fig. 6 11-mix-mediated enhancement of host protection against Listeria monocytogenes infection.
a, Experimental design for germ-free mouse-based studies in b, c (and Fig. 3a–d), C57BL/6 germ-free mice were colonized with 11- or 10-mix, or were left uncolonized as a control. The mice were then orally infected with Lm-WT. b, Listeria CFU in the colon on day 3 after infection. c, Representative H&E staining on day 3 after infection. Scale bar, 50 μm. d, Experimental design for SPF mouse-based studies in e–l (and Fig. 3e–g). C57BL/6 SPF mice were treated with AVMN, then reconstituted with SPFfae by oral gavage. In the 11-mix treatment group (+11mix), initial administration of the 11-mix was done simultaneously with SPFfae, followed by repetitive oral gavage of the 11-mix alone at the indicated time points. Mice were then orally (e–k) or intraperitoneally (l) treated with Lm-InlAm (e, f), Lm-WT (g–j, l) or Lm-OVA (k). e, g, Representative H&E staining on days 5 (e) and 3 (g) after infection. Scale bar, 50 μm. f, l, Listeria CFU in the indicated tissues on day 5 (f) or 3 (l) after infection. h, Colonic histology score at the indicated time points after Lm-WT infection. i, j, Percentage weight change over the course of Lm-WT infection. k, Number of OVA peptide SIINFEKL-specific or general (determined by PMA+ionomycin stimulation) colonic IFNγ+ CD8 T cells induced after Lm-OVA infection, as enumerated by flow cytometry at the indicated time points. The mean of each group is represented by a line. Note that the expansion of general IFNγ+ CD8 T cells occurred as early as 3 days after infection, sooner than that of antigen-specific IFNγ+ CD8 T cells. Therefore, the 11-mix seems to elicit both general and antigen-specific induction. To deplete CD8 T cells, anti-CD8α antibody was administered intraperitoneally 1 day before the administration of 11-mix, and every 3–4 days thereafter. Each circle represents an individual animal. The number of mice in each group is shown. Data are mean and s.d. **P < 0.01; *P < 0.05; Kruskal–Wallis with Dunn’s test (b, f), two-tailed unpaired t-test (h), two-way ANOVA with Bonferroni’s test (j, k), or two-tailed Mann–Whitney test (l). See Source Data for exact P values. Source Data
a, Experimental design for germ-free mouse-based studies in b and c (and Fig. 4a–c). C57BL/6 germ-free mice were colonized with 11- or 10-mix on day −7, or left uncolonized, and were subjected to subcutaneous implantation of MC38 adenocarcinoma cells on day 0. Anti-PD-1 monoclonal antibody was injected intraperitoneally every third day between days 3 and 9. b, Representative flow cytometry histograms showing the expression of CD103, PD-1, ICOS, CD44 and KLRG1 by colonic lamina propria or TIL IFNγ+ CD8 T cells from the indicated mice. c, Left, Frequencies of TCR Vβ gene usage among IFNγ+ CD8 TILs from GF+MC38+anti-PD-1 (grey) or GF+11-mix+MC38+anti-PD-1 (red) mice. Right, Frequencies of TCR Vβ gene usage among IFNγ+ CD8 T cells from the colons of GF+11-mix mice (blue) or the tumours of GF+11-mix+MC38+anti-PD-1 (red). Each circle represents an individual mouse (TIL) or a pool of mice (colon). The number of mice in each group is shown. Data are mean and s.d. **P < 0.01; *P < 0.05; two-tailed unpaired t-test. See Source Data for exact values. Source Data
Extended Data Fig. 8 Efficacy of 11-mix in enhancing treatment of MC38 tumours in the context of a complex microbiota.
a, Experimental design for SPF mouse-based studies in b and c (and in Fig. 4d–k). SPF mice were subjected to treatment with AVMN (from day −7 to day 2) and subcutaneous implantation of MC38 adenocarcinoma or BrafV600E Pten−/− melanoma cells on day 0. The mice were reconstituted with SPFfae on day 3. For the 11- or 10-mix treatment groups, the initial oral administration was done simultaneously with SPFfae on day 3, followed by repetitive dosing of the 11- or 10-mix alone, two or three times per week until the end of the experiment. An anti-PD-1 or anti-CTLA-4 antibody was injected intraperitoneally every third day between days 3 and 9. b, Representative photograph of excised MC38 tumours on day 23. Scale bar, 10 mm. c, H&E staining, along with histology score, of the colon on day 27 (SPF, SPF+anti-PD-1, SPF+11mix, and SPF+11mix+anti-PD-1 groups) and on day 44 (SPF+anti-CTLA-4 and SPF+11mix+anti-CTLA-4 groups). Scale bar, 50 μm. For comparison, the colonic histology score of SPF Il10−/− (colitis-prone) mice is shown. d, Experimental design for GF+donor C human microbiota-based studies in e and f. C57BL/6 germ-free mice were colonized with donor C human faecal microbiota or left uncolonized on day 0. For the 11- or 10-mix treatment groups, the initial oral administration was done simultaneously with the donor C human faecal sample on day 0, followed by repetitive dosing of the 11- or 10-mix alone two or three times per week until the end of the experiment. e, Faeces were collected at the indicated time points. The relative abundance of each of the 11 strains’ DNA was determined by qPCR. Colonization with all 11 strains was confirmed. f, Percentage of IFNγ+ CD8 T cells in the colonic lamina propria and iLNs at day 21 was enumerated by flow cytometry. g, h, C57BL/6 germ-free mice were inoculated with donor C faecal samples with or without 11- or 10-mix, following the same protocol as in d. Mice were then subjected to subcutaneous implantation of MC38 cells on day 0. Anti-PD-1 was injected intraperitoneally every third day between days 3 and 9. Experimental design is shown in g and tumour growth data of MC38 is shown in h. Each circle represents an individual animal, except in h, where each circle represents the mean. The number of mice in each group is shown. Red, grey and brown asterisks show significance versus the C+11-mix+anti-PD-1, C+anti-PD-1, and C+10-mix+anti-PD-1 groups, respectively. Data are mean and s.e.m. (e) or s.d. (all others). ***P < 0.001; **P < 0.01; *P < 0.05; one-way (f) or two-way (h) ANOVA with Tukey’s test. See Source Data for exact P values. Source Data
Extended Data Fig. 9 Strain- and species-level abundance of the 11 isolates in the human gut microbiome.
A total of 3,327 gut metagenome samples with at least 1 million quality-controlled reads across various data sets (HMP1-2, LLDeep, MetaHIT, 500FG, HMP2 (only the first time point was used), healthy Japanese adults, and three microbiome in cancer immunotherapy studies) were mapped to 1-kb regions in the 11 strains (filtered by 95% mapping identity). The mapped read counts were normalized to RPKM. a, Detection and abundance of the strain-specific marker regions. Median abundance across all marker regions was plotted against marker gene coverage. Points with high abundance at low coverage, for example, less than 75%, indicate limited marker region resolution and likely represent other strains of a species. b, Among the 11 strains, 4 were detected in 16 out of 3,327 microbiome samples evaluated. A strain was deemed detected if at least 95% of 1-kb regions in the marker region were detected. c, Abundance at the species level was calculated as the median abundance across all 1-kb regions in a genome using 3,327 metagenome samples with at least 1 million quality-controlled reads (mapped reads were filtered at 95% mapping identity). The mapped read counts were normalized to reads per RPKM. d, Abundance of the strain-specific marker regions in the faecal microbiome of the six healthy Japanese volunteers (donors A to F) was examined, as shown in a. A strain was deemed detected if at least 95% of the 1-kb regions in the marker region were detected. At our sequencing depth, three strains were detected in the donor B sample, and one in that of donor A. e, Abundance at the species-level was calculated as in c. The mapped read counts were normalized to RPKM.
Extended Data Fig. 10 Antigen-specificity and TCR Vβ usage of IFNγ+CD8 T cells induced by the 11-mix differ by anatomical location.
a, Percentage of IFNγ+ cells among CD8 T cells in either colons from GF+11-mix mice or MC38 tumours from SPF+11mix+anti-PD-1 mice, after ex vivo stimulation with the indicated antigens. b, Principal component analysis plots of TCR Vβ usage by the IFNγ+ and IFNγ- CD8 T cell subsets isolated from the indicated tissues of GF+11-mix (right) or germ-free (left) mice. For TIL data, IFNγ+ and IFNγ− CD8 T cells were isolated from germ-free ± 11mix+MC38+anti-PD-1 mice. Two-way ANOVA interaction P values comparing two populations at a time are as follows. GF group: 0.006 (CLP IFNγ+ versus iLN IFNγ+), 0.50 (CLP IFNγ+ versus TIL IFNγ+), 0.20 (iLN IFNγ+ versus TIL IFNγ+), <0.0001 (CLP IFNγ− versus iLN IFNγ−), <0.0001 (CLP IFNγ− versus TIL IFNγ−), 0.0024 (iLN IFNγ− versus TIL IFNγ−). GF+11-mix group: <0.0001 (CLP IFNγ+ versus iLN IFNγ+), <0.0001 (CLP IFNγ+ versus TIL IFNγ+), 0.0001 (iLN IFNγ+ versus TIL IFNγ+), <0.0001 (CLP IFNγ− versus iLN IFNγ−), <0.0001 (CLP IFNγ− versus TIL IFNγ−), 0.0009 (iLN IFNγ− versus TIL IFNγ−). Each circle represents an individual mouse (iLN and TIL) or a pool of mice (colon). The number of mice in each group is shown. Data are mean and s.d. ***P < 0.001; **P < 0.01; one-way ANOVA with Tukey’s test. See Source Data for exact P values. Source Data
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Tanoue, T., Morita, S., Plichta, D.R. et al. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature 565, 600–605 (2019). https://doi.org/10.1038/s41586-019-0878-z
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