Fig. 4: Translationally active community and RACS isolated strains after XOS supplementation. | Nature Communications

Fig. 4: Translationally active community and RACS isolated strains after XOS supplementation.

From: Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting

Fig. 4

a BONCAT-FACS: log2 fold changes for each donor are shown at the genus level. Bubble size indicates relative abundance in the starting sample. Asterisks indicate significantly enriched taxa after supplementation with XOS, as calculated with the Wald test (2-sided, p < 0.05, n = 36 samples). Genera with relative abundance >0.5% were considered. b Example of fluorescence microscopy images showing BONCAT-positive cells (pink, Cy5) after 6 h incubation with XOS. All cells are stained with DAPI (blue). c No amendment control shows no BONCAT signal. Both images were recorded using identical settings, and imaging was performed for all 6 donors. d Percentage of active cells measured by Raman microspectroscopy. The x-axis represents 6 stool samples collected from 6 donors and incubated for 6 h in D2O-containing media in the presence of XOS. The y-axis represents the level of D incorporation of randomly selected cells measured by %CD. Each dot represents a random single-cell measurement (water control: n = 40 cells, donor 18 nothing added (NA): n = 40 cells, donor 18: n = 40 cells, donor 19 NA: n = 30 cells, donor 19: n = 40 cells, donor 20 NA: n = 40 cells, donor 20: n = 40 cells, donor 21 NA: n = 40 cells, donor 21: n = 40 cells, donor 22 NA: n = 40 cells, donor 22: n = 40 cells, donor 23 NA: n = 40 cells, donor 23: n = 40 cells). The red dashed line at 2.55% indicates the threshold for considering a cell labeled. Boxplot: boxplot medians (center lines), interquartile ranges (box ranges), whisker ranges. e Phylogenetic analysis of representative strains isolated with RACS after XOS supplementation (OP183499-OP183547). The tree was generated with the maximum likelihood algorithm using IQtree, with the optimal model identified by modelFinder as TN+F+G4 and rooted at mid-point. Each color in the tree denotes the different genera isolated and each color code represented as a color strip shows the different phyla. Source data are provided as a Source Data file.

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