Fig 2: Ammonia production and bile acid conversion capabilities of 20 mouse-derived strains.a, Carriage of nrfA homologues and their signal sequences [lipoprotein signal peptides (LSPs) or Sec/SPI standard signal peptides (SPs)] was analysed across the genomes of the 20 mouse-derived strains. nrfA genes were annotated using eggNOG-mapper, and signal sequences were predicted with SignalP 6.0. “Percent identity” indicates sequence similarity to the Bilophila NrfA protein, as calculated by BLASTP. “E-value” denotes the expected number of chance alignments with an equal or higher bit score, as computed by BLASTP. “Length” indicates the length of the protein from each isolate that best aligns to NrfA as predicted by eggNOG-mapper. b, The 20 strains were cultured in 10% mGAM (diluted with Milli-Q water) for 1 hour, and ammonia concentrations in the culture supernatants were quantified using an ammonia detection kit (n = 3 biological replicates). c, Each strain was incubated with 50 µM taurocholic acid (tauro-CA) in medium containing varying protein concentrations (100% to 12.5% relative to complete mGAM) for 48 hours, and the resulting bile acids in the culture supernatants were analysed by LC–MS/MS. d, GF mice were colonized with the indicated mouse-derived bacterial consortia (mu20-, mu3-, mu5- or mu7-mix) and fed an LPD for 6 weeks. Hepatic Fgf21 expression and portal vein ammonia concentrations were measured. Each circle represents an individual mouse, and bars show mean ± s.d. Statistical tests: one-way ANOVA with Benjamini–Hochberg correction. Source data

Fig 3: The microbiota mediates remodelling of sympathetic neurons and vasculature.a,d–f, Cox7a1 expression in iWAT was quantified in SPF mice of the indicated genotypes after 6 weeks on a CD or an LPD. Each circle represents an individual mouse, and bars show mean ± s.d. Statistical tests: one-way ANOVA with Benjamini–Hochberg correction. b, GF and SPF B6 male mice were fed either a CD or an LPD for 6 weeks. Whole-mount immunostaining of iWAT with iDISCO tissue clearing was performed using antibodies against tyrosine hydroxylase (sympathetic nerves; red), UCP1 (blue), and CD31 (endothelial cells; green). c, Fgf21+/−, Fgf21−/−, Nr1h4+/−, and Nr1h4−/− mice were fed an LPD for 1, 2, or 4 weeks, and whole-mount immunostaining of iWAT was performed using antibodies against tyrosine hydroxylase (red) and UCP1 (blue). Images were acquired using a light sheet microscope. Representative images from two independent experiments are shown, with dashed lines indicating the iWAT boundaries. Source data

Fig 4: Down-selection of human-derived bacterial strains that promote LPD-mediated browning.a, Standardized uptake values (SUV) of FDG in the supraclavicular regions of each volunteer. Columns highlighted in red and blue indicate samples that were selected for follow-up analysis, and representative FDG-PET images are shown as inserts. b–f, GF B6 mice were colonized with faecal microbiota from the indicated individuals (b,c) or with defined bacterial consortia (d) and then fed either a CD or an LPD for 6 weeks. Relative iWAT Ucp1 expression, normalized to Ppib, was determined by qPCR (b–d). Plasma bile acids (e) and FGF21 (f) were quantified by LC–MS/MS and ELISA, respectively. g, iWAT Ucp1 expression in GF Nr1h4−/− and Fgf21−/− mice colonized with the T19-derived 33-mix and fed a CD or an LPD. h, List of the 33 T19-derived strains, as determined by 16S rRNA sequencing. i–m, GF B6 mice were colonized with the indicated bacterial consortia selected from the 33 T19-derived strains and fed a CD or an LPD for 4 weeks. In j, the presence (+) or absence (−) of each bacterial group in the consortium is indicated. Expression of Ucp1 in iWAT (i-k) and Fgf21 in the liver (l), normalized to Ppib, was measured by qPCR. m, Plasma bile acid concentrations in LPD-fed gnotobiotic mice were quantified by LC–MS/MS (n = 8 per group). Circles represent individual mice; bar heights indicate exact SUV values (a) or mean ± s.d. (b–d,f,g,i–l). Box plots show median, interquartile range and data range. Statistics: one-way ANOVA with Benjamini–Hochberg correction for multiple comparisons (b–d,f,g,i–l) or two-tailed Mann–Whitney test for each comparison (e,m).Source data

Fig 5: Mouse-derived microbial isolates promote LPD-induced browning.a, Schematic illustrating the strategy to isolate browning-inducing commensal strains from the gut microbiota of SPF mice. SI, small intestine. b,c,e,f, GF mice were colonized with ileal microbiota from LPD-fed SPF mouse A, SPF mouse B (b) or exGF mouse B28 (c), or with defined bacterial consortia (mu18-mix in e or mu20-mix in f). Mice were then fed an LPD for 6 weeks, and relative iWAT Ucp1 expression was measured by qPCR. d, The ileal microbiota compositions of mouse B, mouse B28 and mouse B28-1 were determined by 16S rRNA gene sequencing. The 20 strains isolated from mouse B28-1 are listed. g, Representative H&E-stained iWAT sections from the indicated groups. Scale bars, 50 μm. h,i, Plasma bile acid (h) and FGF21 (i) concentrations in the indicated mice were quantified by LC–MS/MS and by enzyme-linked immunosorbent assay (ELISA), respectively. j, iWAT Ucp1 expression in GF Nr1h4−/− or GF Fgf21−/− mice inoculated with mu20-mix or vehicle control and fed a CD or an LPD for 6 weeks. k, GF mice were colonized with the indicated mouse-derived bacterial consortia (mu20-mix, mu3-mix, mu5-mix or mu7-mix) and fed a CD or an LPD for 6 weeks. iWAT Ucp1 expression and hepatic Fgf21 expression were measured. Circles represent individual mice; data are mean ± s.d. Box plots show median, interquartile range and range. Statistics: one-way ANOVA with Benjamini–Hochberg correction for multiple comparisons (b,c,e,f,i–k) or two-tailed Mann–Whitney test for each comparison (h).Source data