In the blood and gut environment, decreased butyrate abundance in the short-term patient was indicated by: A) significantly reduced plasma isobutyrate normalized abundance; B) decreased predicted gut isobutyrate in patients, especially in short-term patients. Boxes show median relative abundance and interquartile ranges (IQR); whiskers specify ±1.5*IQR from the box’s quartile. P-values were computed by Wilcoxon rank-sum test. C) The reduced abundance of most key enzymes in the butanoate mechanism (KEGG pathway map00650) indicated a more limited microbial butyrate biosynthesis capacity in ME/CFS. Differentiating enzymes were colored and annotated on the map (decreased in blue and increased in red). D) Correlation of plasma metabolite normalized abundance and relative abundance of microbial butyrate biosynthesis features, with fold changes. Heatmap shows significant correlations (Spearman, p < 0.05) with the top bar indicating the metabolite superfamily. The top half shows the key enzymes in the KEGG butanoate pathway. On the left, different fold changes between the two patient cohorts (short-term vs. control and long-term vs. control, respectively) indicated a significant decrease in butyrate biosynthetic capacity in the early stages of ME/CFS. P-values were calculated in each group with Wilcoxon rank-sum test. Finally, the bottom half shows the correlation between the relative abundance of predicted butyrate producers and plasma metabolites. Microbes were ordered by relative abundance. For each microbe, the size of the dot indicates the mean abundance in each group and the color indicated fold change over the control group. P-value was computed by Kruskal–Wallis H test. p-value annotation legend: *: 0.01 < p <= 0.05, **: 0.001 < p <= 0.01, ***: 1e-04 < p <= 0.001. See also Table S6.