Fig. 1: Inference of gut microbes affecting glucose metabolism in the host.

a The red and blue colors indicate higher and lower levels of metabolic parameters measured in mice fed normal diet (ND) or western diet (WD) at 4 and 8 weeks. Source data are provided as a Source Data file. b Principal Component Analysis of stool (triangle) and ileal (circle) microbial communities of mice on ND (blue) or WD (red). Source data are available at https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA558801. c The microbe and host parameter nodes are represented by circles and squares, respectively, in the transkingdom (TK) network. Red and blue colors of nodes indicate increased and decreased (WD/ND) fold change, respectively, whereas the size of circle represents frequency of microbe in stool of WD mice. The black and green node borders indicate the microbes were significantly increased or decreased, respectively, in ileum of WD mice compared with ND (Fisher’s p value across experiments <0.05). The orange and black edges indicate positive and negative correlations, respectively. The degree distribution of the TK-network follows a power law. The blue line indicates the fitted line. Source data are available at https://tinyurl.com/TK-NW-Fig-1C. d The left two figures allow inference of microbial candidates that are potentially improvers (left figure) or worseners (middle figure) using high values of TK-network property (bipartite betweenness centrality (BiBC) on the x axis) and significance of change in ileal (WD vs ND) abundance of microbes (log transformed Fisher’s p value across experiments on y axis). The horizontal green line indicates a log transformed value for Fisher’s p value of 0.05. The right figure shows the keystoneness score (x axis) of the microbial nodes (y axis). Source data are provided as a Source Data file. e Ileal abundance of potential candidate and keystone microbes in ND and WD-fed mice at 8 weeks. Asterisk indicate the change in abundance passed statistical significance threshold (two-tail Mann–Whitney p value <0.2 in each experiment, Fisher’s p value across experiments <0.05, and FDR < 10%. Each dot represents a mouse, bars present median of the group. Source data same as for b.