RT Journal Article
T1 Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics
A1 Peña Vidal, Nuria
A1 Lafuente, Irene
A1 Sevillano, Ester
A1 Feito Hermida, Javier
A1 Allendez, Gastón
A1 Crispie, Fiona
A1 Cintas Izarra, Luis Miguel
A1 Cotter, Paul D.
A1 Hernández Cruza, Pablo Elpidio
A1 Borrero Del Pino, Juan
A1 Muñoz Atienza, Estefanía
AB Background/Objectives: Antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics in livestock, offering a sustainable strategy for controlling bacterial pathogens in food production systems. In addition to their direct antimicrobial effects, AMPs play a key role in modulating host-associated microbiomes, influencing both microbial composition and function. Advances in metagenomic sequencing and bioinformatic tools now enable comprehensive exploration of AMP diversity and activity within complex microbial ecosystems.  Methods: In this study, we employed Illumina-based next-generation sequencing (NGS) to analyze intestinal contents from six gut sections of broiler chickens obtained from a Spanish slaughterhouse.Results: Through de novo assembly and bioinformatic annotation, we identified biosynthetic gene clusters (BGCs) encoding ribosomally synthesized and post-translationally modified peptides (RiPPs), other specialized bioactive secondary metabolites, antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and a diverse microbial community. Among all gut sections, the cecum exhibited the highest genetic richness, characterized by a high diversity of RiPP-like clusters and antimicrobial resistance determinants.Conclusions: These findings highlight the poultry gut, particularly the cecum, as a significant reservoir of antimicrobial peptides (AMPs) with potential implications in antibiotic-free poultry production and enhanced food safety
PB MDPI
YR 2025
FD 2025
LK https://hdl.handle.net/20.500.14352/124895
UL https://hdl.handle.net/20.500.14352/124895
LA eng
NO Peña, N., Lafuente, I., Sevillano, E., Feito, J., Allendez, G., Muñoz-Atienza, E., Crispie, F., Cintas, L. M., Cotter, P. D., Hernández, P. E., & Borrero, J. (2025). Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics. Genes, 16(8), 946. https://doi.org/10.3390/genes16080946
NO Author Contributions: Conceptualization, P.D.C., E.M.-A., L.M.C., P.E.H. and J.B.; methodology, P.D.C., F.C., E.M.-A. and J.B.; validation, N.P., F.C. and G.A.; formal analysis, N.P. and G.A.; investigation, N.P., I.L., E.S. and J.F.; resources, P.D.C., E.M.-A., L.M.C., P.E.H. and J.B.; data curation, N.P. and G.A.; writing—original draft, N.P.; writing—review and editing, P.D.C., F.C., G.A., P.E.H. and J.B.; visualization, N.P., P.E.H. and J.B.; supervision, P.D.C., F.C., L.M.C., P.E.H. and J.B.; project administration, P.D.C., F.C. and J.B.; funding acquisition, E.M.-A., L.M.C., P.E.H. and J.B. All authors have read and agreed to the published version of the manuscript
NO This research was funded by the Atracción de Talento Program of the Comunidad de Madrid [2018-T1/BIO-10158; 2022-5A/BIO-24232] and the Ministerio de Ciencia e Innovación [PID2019-104808RAI00]. N.P., I.L. and J.B. were supported by the Atracción de Talento Program of the Comunidad de Madrid [2018-T1/BIO-10158; 2022-5A/BIO-24232]. E.S. was supported by the Empleo Juvenil Program of the Comunidad de Madrid [PEJ-2020-AI/BIO-17758] and the Ministerio de Ciencia e Innovación [PID2019-104808RAI00].
NO Ministerio de Ciencia e Innovación y Universidades ( España)
NO Comunidad de Madrid
DS Docta Complutense
RD 18 dic 2025