Comprehensive Gene and Protein Catalog for Antimicrobial Environments: A Metagenomic Approach to Mitigate Antimicrobial Resistance

Currently, the rise of antibiotic-resistant microorganisms presents substantial challenges to critical sectors such as healthcare, agriculture, and poultry production. Tackling this issue requires the discovery of new antimicrobial agents, such as enzybiotics, that are capable of bypassing resistance mechanisms. A promising approach to identify such agents involves exploring biomolecules found in extreme microbiome environments, where microbial communities compete for survival and develop powerful antimicrobial properties. The role of antimicrobial-exposed environment microbiomes is pivotal for identifying microbes and enzymes to enhance antimicrobial resistance mitigation. Integrating computational methods and metagenomic approaches is essential to improve current strategies for combating antimicrobial resistance. Catalogs of genes, proteins, and metagenome-assembled genomes facilitate taxonomic and functional analysis of antimicrobial metagenome samples. To the best of our knowledge, no integrated gene and protein catalogs exist for environments containing antimicrobial agents. In this study, ۱۵ whole-metagenome samples (including soil, seawater, groundwater, and plastic-contaminated metagenome samples) were combined. A total of ۵۵۰ Gb of high-quality data were obtained with an average library fragment size. A comprehensive gene and protein catalog was generated by expanding a computational workflow comprising the quality control of reads, trimming, assembly, and binning of contigs from ۱۵ source environments for antimicrobial agents. This catalog comprises ۴۶.۸ million nonredundant genes and proteins. Among the carbohydrate-active enzymes (CAZymes), glycoside hydrolases (GHs) were the most abundant, as determined using the dbCAN۲ software. The dbCAN۲ analysis identified ۴۶۵,۳۲۵ CAZyme-encoding genes in the catalog. Our workflow and the catalog generated from ۱۵ source environment samples provide an efficient resource for identifying antimicrobial enzymes and microorganisms, enabling researchers to enhance their understanding of genes and proteins in this metagenomic environment with minimal time and cost.

کلیدواژه ها:

Enzybiotics ، gene catalog ، genome ، metagenomic analysis ، environments for antimicrobial agents