# Bioactive Plasmid- and Phage-Encoded Antimicrobial Peptides (AMPs) in the Human Gut: A Metatranscriptome–Virome Profiling Reveals Exploratory Links to Metabolic Human Diseases

## TL;DR

This study explores how antimicrobial peptides from gut microbes and viruses may be linked to obesity and metabolic diseases.

## Contribution

The study identifies plasmid- and phage-encoded AMPs in the gut and links their overexpression to obesity and metabolic syndrome.

## Key findings

- Fifty-one high-confidence AMPs were identified, with eight originating from plasmids or bacteriophages.
- Overexpression of specific AMPs was negatively correlated with healthy gut bacteria and positively with obesity-associated taxa.
- A phage-encoded AMP (AMP-3020) showed broad-spectrum antibacterial activity without harming human immune cells.

## Abstract

Microbe-derived antimicrobial peptides (AMPs) can shape gut community structure; however, their contribution to disease-associated dysbiosis remains poorly understood. We assembled fecal metatranscriptomes from individuals with normal weight (NW), obesity (O), and obesity with metabolic syndrome (OMS), yielding 51,087 non-human transcripts. We screened 1,095 small open reading frames (smORFs) using AMP-prediction algorithms combined with stringent post-hoc bioinformatics filters identifying 51 high-confidence AMP candidates. Most matched bacterial homologs, predominantly Faecalibacterium prausnitzii, while eight mapped to plasmids or bacteriophages. Differential expression identified two and four AMPs overexpressed in O and OMS, respectively. Two of them were originated from chromosomes, three from phages, and one from plasmid. Notably, the over-expression of these AMPs was negatively correlated with healthy-associated bacteria and positively correlated with obesity-enriched taxa. Furthermore, these AMPs were broadly detectable across 372 external gut metatranscriptomes (prevalence up to 94% of the samples) indicating conservation within the human gut microbiome and highlighting mobile elements as an overlooked reservoir of transcriptionally active AMPs. Using DNA virome sequencing and prophage analyses, we suggested phage origin of the transcribed AMPs. We further synthesized a phage-encoded AMP (AMP-3020), demonstrating broad-spectrum activity against Gram-positive and Gram-negative bacteria, without detectable cytotoxicity toward human immune T cells. This supports the idea that phages could encode functional AMPs capable of shaping gut community structure by suppressing diverse bacteria without harming host immune cells. Our gut metatranscriptome–virome profiling revealed a conservative core of actively transcribed, plasmid- and phage-encoded AMPs with exploratory associations to obesity/MetS. These findings support mobile-element AMPs as candidate ecological regulators and motivate validation in larger cohorts and mechanistic models.

The online version contains supplementary material available at 10.1007/s00248-025-02620-2.