Chagas disease induces gut microbial metabolic stress: Disruption of energy and nucleotide pathways and partial reversal by antiparasitic therapy (TRIPOBIOME-2 study)

• Published in: Travel medicine and infectious disease Vol. 67; p. 102881
• Main Authors: Pérez-Molina, José A., Moreno, Elena, Crespillo-Andújar, Clara, Chamorro-Tojeiro, Sandra, Arsuaga, Marta, Olavarrieta, Leticia, Martín, Oihane, Monge-Maillo, Begoña, Norman, Francesca, Lanza, Val F., Serrano-Villar, Sergio
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Ltd 01.09.2025; Elsevier
• Subjects: Benznidazole; Chagas disease; Infectious Disease; Metabolic pathways; Microbiota; Migrants; Surrogate marker; Chagas disease; Surrogate marker; Microbiota; Metabolic pathways; Migrants; Benznidazole
• ISSN: 1477-8939; 1873-0442; 1873-0442
• DOI: 10.1016/j.tmaid.2025.102881

Chagas disease (CD) can alter gut microbiota composition, although its functional impact is poorly defined. We conducted whole-genome metagenomic sequencing of stool samples from 55 adults with chronic CD (23 treated with benznidazole) and 17 non-infected controls. Functional pathways were annotated with HUMAnN 3, and their differential abundance was assessed using ANCOM-BC2. Diversity metrics (Chao1/ACE indices and multidimensional scaling) and sPLS-DA modelling were used to explore community structure. No significant group differences were observed for alpha- and beta-diversity of bacterial functions; only 6–7 % of variance was attributable to infection status or prior benznidazole therapy. Nevertheless, chronic CD produced a distinctive functional signature marked by depletion of energy-yielding pathways (reductive and canonical tricarboxylic-acid cycles, fatty-acid β-oxidation, haem and 2-methylcitrate metabolism) and modest enrichment of purine and pyrimidine biosynthetic routes. These shifts may imply a microbiome adapting to hypoxia, nutrient scarcity, and metabolic competition with Trypanosoma cruzi. Compared with untreated patients and controls, benznidazole-treated individuals exhibited partial metabolic restoration, namely, up-regulated nucleotide and carbohydrate-degradation pathways, enhanced (5Z)-dodecenoate synthesis, and reduced reliance on the reductive tricarboxylic acid cycle, suggesting renewed microbial growth and improved short-chain-fatty-acid potential. Collectively, our results seem to portray a resource-limited, metabolically stressed gut ecosystem in chronic CD whose functional imbalance is partially reversible with antiparasitic therapy. The affected pathways, particularly those governing energy and nucleotide metabolism, could be used as candidate surrogate markers for disease monitoring and therapeutic response and as targets for microbiota-directed adjuvant strategies. •Whole-genome stool sequencing shows gut microbiome metabolic stress in Chagas patients•Energy-yielding TCA, β-oxidation, and haem pathways fall during chronic infection•Benznidazole partly restores nucleotide and carbohydrate metabolism in microbiota•Gut-microbiome metabolic pathways may act as biomarkers and targets for future therapies