Code and processed data for "Trophotypes of the human gut microbiome: discrete energetic states under a macroecological framework"

This deposit contains the complete code, processed data and supporting material required to reproduce the analyses reported in: Mendoza M. "Trophotypes of the human gut microbiome: discrete energetic states under a macroecological framework." mSystems (submitted, 2026). The pipeline starts from the public release of the American Gut Project (AGP, Qiita study 10317) and identifies four discrete functional configurations (Trophotypes) of the human gut microbiome using Average Membership Degree (AMD) analysis on the richness of twelve metabolic guilds. The deposit includes the R scripts that constitute the full analysis pipeline (AMD detection, sigma-equivalent bootstrap calibration, principal component analysis, diagnostic random forest, metadata-based predictive analyses with three independent classifiers, and Dirichlet-multinomial mixture benchmark), processed data files (guild-richness matrix, genus-to-guild dictionary, Trophotype labels, cleaned metadata for the n=4,260 analytic subset), the six figures of the manuscript (Figs. 1-5 and Supplementary Fig. S1, all in TIFF at 300 dpi), the supplementary materials document (Tables S1 and S2, and the legend of Supplementary Fig. S1), a README with usage instructions, and a session_info.txt with R package versions. The raw 16S rRNA gene sequences and original metadata are available via Qiita (study 10317) under the terms of the AGP open data agreement and are not redistributed here.