Predicting gut microbiota dynamics in obese individuals from cross-sectional data

• Published in: Frontiers in cellular and infection microbiology Vol. 15; p. 1485791
• Main Authors: Melvan, Ena, Allen, Andrew P., Vuckovic, Tea, Soljic, Irena, Starcevic, Antonio
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 10.06.2025
• Subjects: Adult; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteroidetes; Cellular and Infection Microbiology; Cross-Sectional Studies; dietary interventions; Dysbiosis - microbiology; Female; Firmicutes - genetics; Firmicutes - isolation & purification; Gastrointestinal Microbiome; GLV method; gut microbiota; Humans; Male; Microbial Interactions; obesity; Obesity - microbiology; personalized nutrition; RNA, Ribosomal, 16S - genetics; GLV method; dietary interventions; microbial interactions; microbiome dynamics; gut microbiota; obesity; personalized nutrition
• ISSN: 2235-2988; 2235-2988
• DOI: 10.3389/fcimb.2025.1485791

Obesity affects approximately 39% of adults worldwide. While gut microbiota has been linked to obesity, most research has focused on static taxonomic composition rather than the dynamic interactions between microbial taxa. We applied BEEM-Static, a generalized Lotka-Volterra model, to cross-sectional 16S rRNA gut microbiome data from six public datasets, comprising 2,435 profiles from lean and obese individuals. A total of 57 significant microbial interactions were identified in obese individuals (79% negative), compared to 37 in lean individuals (92% negative). For example, Bacteroidetes showed a stronger inhibitory effect on Firmicutes in obese individuals (-0.41) than in lean ones (-0.26). Firmicutes and Proteobacteria exhibited consistently higher carrying capacities in obese populations. These findings suggest that microbial interaction networks-not just taxonomic abundance-play a key role in obesity-related dysbiosis. Our approach enables the inference of microbiota dynamics from a single time point, paving the way for tailored dietary interventions, which we refer to as .