Fig. 4: Features of reconstructed time-varying interaction networks over 110 days after start-up.

The time-varying interaction networks was reconstructed using the MDR-S map method. A Trace of the Jacobian matrix indicating the degree of community instability. B Proportions of positive and negative interaction edges. C Mean strength of positive and negative interaction edges. D Interaction complexity, as illustrated by the Shannon index of interaction types from all populations included in the MDR S-map; different interaction types are illustrated in panels (E) and (F) and Supplementary Fig. 4. Panels (E) and (F) indicate the 5-day moving average proportion of interaction types (E) commensalism (+/0) and (F) amensalism (−/0) within and between different trophic groups. The symbol “Overall” represents the sum proportion of each interaction type, calculated using all genus-level taxa in the network analysis. The proportion of interaction types between microbial taxa from various trophic groups is denoted by different colored lines, accompanied by the symbol name “XX_XX” (where XX represents the trophic group). The trophic groups included FB (Top 10 abundant fermentative bacteria), SB (syntrophic bacteria), and MA (methanogenic archaea). The taxa of FB, SB, and MA analyzed are listed in Fig. 3A. The dashed vertical lines partition the total time series into three phases according to the instability index in Panel (A). The interaction networks were reconstructed using 111 core genera (abundance > 0.01% in total samples and abundance > 0.01% in at least 60% of samples).