Gut metatranscriptome–virome profiling reveals active antimicrobial peptides (AMPs) encoded in plasmids and phages linked to human diseases

Microbe-derived antimicrobial peptides (AMPs) play a crucial role in shaping the microbiota composition; however, their contribution to disease-associated dysbiosis remains poorly understood. Here, we assembled fecal metatranscriptomes from individuals with normal weight, obesity, and obesity plus metabolic syndrome, yielding 51,087 non-human transcripts. We screened 1,095 small open reading frames (smORFs) using AMP-prediction algorithms and identified 112 AMP candidates. Most of them were associated with bacterial homologs, predominantly Faecalibacterium prausnitzii , while twelve aligned with plasmid or bacteriophage sequences. Differential expression analysis identified nine AMPs that were overexpressed among our groups, of which five originated from chromosomes, one from a plasmid, and three from phages. The expression of these AMPs was inversely correlated with specific bacterial taxa, linking them to disease-associated shifts in microbiota. Additionally, we also examined the presence of these nine AMPs in 372 external gut metatranscriptomes, discovering that they were highly prevalent in up to 98% of the samples, suggesting their conservation within the human gut microbiome and highlighting mobile elements as an often-overlooked reservoir of active AMPs. Finally, through virome sequencing and prophage genome analyses, we suggest that mobile-derived AMPs were transcribed from phage particles. We synthesized a phage-encoded AMP and demonstrated its broad-spectrum antibacterial activity against Gram-positive and Gram-negative bacteria, with no detectable cytotoxicity toward human immune cells. These findings illustrate that the human gut harbors a conserved set of microbe-derived AMPs associated with mobile genetic elements, whose overexpression was linked to obesity and metabolic syndrome, underscoring their role as ecological regulators of the microbiota in disease.