Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Acquisition and Processing
2.2. DNA Extraction and Shotgun Metagenomic Sequencing
2.3. Bioinformatics Analysis
2.3.1. Metagenomic Read Processing, Assembly and Functional Annotation
2.3.2. Identification of Biosynthetic Gene Clusters and Virulence/Resistance Genes
2.3.3. KEGG-Based Functional Annotation
2.3.4. Taxonomy Profiling
3. Results
3.1. Assembly Quality Reports
3.2. Identification of Biosynthetic Gene Clusters
3.3. Antimicrobial Resistance Genes Profile
3.4. Identification of Virulence Factor Genes (VFGs)
3.5. Functional Annotation of Metabolomic Compounds
3.6. Microbial Taxonomic Profiling of Intestinal Microbiomes Across Sample Sites
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Paired_Non.Host_Reads | Contigs | Avg_Len (pb) | N50 | L50 | ||
---|---|---|---|---|---|---|
Broiler 1 | CR | 413,410 | 10,846 | 623 | 680 | 2758 |
PR | 221,628 | 6881 | 576 | 611 | 2779 | |
VE | 417,875 | 12,591 | 5996 | 631 | 3560 | |
SI | 13,986 | 3717 | 515 | 528 | 1190 | |
LI | 405,471 | 9913 | 6293 | 691 | 2371 | |
CE | 24,098,100 | 500,066 | 9687 | 1516 | 50,213 | |
Broiler 2 | CR | 5796,495 | 46,447 | 10,205 | 2170 | 3167 |
PR | 374,194 | 11,295 | 6167 | 663 | 2950 | |
VE | 1,014,566 | 18,603 | 705 | 734 | 4043 | |
SI | 657,987 | 19,464 | 7914 | 937 | 3579 | |
LI | 3,519,182 | 32,411 | 10,936 | 3013 | 1693 | |
CE | 9,727,800 | 52,119 | 10,353 | 2788 | 2960 | |
Avg | 511,689.75 | 10,253 | 2141.16 | 1246.833 | 6771.91 |
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Peña, N.; Lafuente, I.; Sevillano, E.; Feito, J.; Allendez, G.; Muñoz-Atienza, E.; Crispie, F.; Cintas, L.M.; Cotter, P.D.; Hernández, P.E.; et al. Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics. Genes 2025, 16, 946. https://doi.org/10.3390/genes16080946
Peña N, Lafuente I, Sevillano E, Feito J, Allendez G, Muñoz-Atienza E, Crispie F, Cintas LM, Cotter PD, Hernández PE, et al. Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics. Genes. 2025; 16(8):946. https://doi.org/10.3390/genes16080946
Chicago/Turabian StylePeña, Nuria, Irene Lafuente, Ester Sevillano, Javier Feito, Gastón Allendez, Estefanía Muñoz-Atienza, Fiona Crispie, Luis M. Cintas, Paul D. Cotter, Pablo E. Hernández, and et al. 2025. "Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics" Genes 16, no. 8: 946. https://doi.org/10.3390/genes16080946
APA StylePeña, 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