Tag: Metagenomic analysis

Antimicrobial resistance mechanisms allow microorganisms to survive antimicrobial exposure through processes such as drug inactivation, target modification, target protection, reduced permeability, active efflux, metabolic bypass, and genetic mutation. Learn how metagenomic sequencing can identify and investigate these mechanisms across microbial communities.

Plasmid reconstruction recovers and characterizes plasmid DNA from sequencing data. Learn how metagenomic assembly, short- and long-read sequencing, plasmid detection, host association, genomic context, and resistance-gene analysis are used to investigate plasmids and genetic mobility.

The wastewater resistome contains antimicrobial resistance genes and associated genetic determinants found in wastewater and wastewater-associated microbial communities. Learn how metagenomic sequencing is used to detect, quantify, and characterize resistance genes, mobile genetic elements, plasmids, microbial hosts, and potential resistance pathways across municipal, hospital, agricultural, and environmental wastewater systems.

Horizontal gene transfer enables microorganisms to acquire genetic material from other organisms outside normal parent-to-offspring inheritance. Learn how conjugation, transformation, transduction, plasmids, transposons, integrons, and other mobile genetic elements contribute to microbial evolution and antimicrobial resistance, and how metagenomics can investigate genetic mobility.

Antimicrobial resistance databases provide reference sequences and annotations for detecting and interpreting resistance genes. Learn about AMR database types, resistance gene resources, database selection, curation, sequence matching, metagenomic applications, and limitations.

Mobile genetic elements are DNA structures that can move within genomes or between microorganisms and can carry antimicrobial resistance, virulence, metabolic, and adaptive genes. Learn about plasmids, transposons, integrons, insertion sequences, genomic islands, bacteriophages, horizontal gene transfer, and metagenomic methods for studying genetic mobility.

One Health antimicrobial resistance recognizes that resistance develops and spreads across interconnected human, animal, food, agricultural, wastewater, and environmental systems. Learn how metagenomics can investigate antimicrobial resistance genes, resistomes, mobile genetic elements, resistance reservoirs, and potential dissemination pathways across these connected ecosystems.

Agricultural antimicrobial resistance occurs across livestock, poultry, aquaculture, manure, agricultural soils, water, crops, farm environments, and food systems. Learn how metagenomic sequencing can detect and characterize resistance genes, resistomes, mobile genetic elements, plasmids, microbial hosts, and potential resistance pathways across agricultural environments.

The human resistome is the collection of antimicrobial resistance genes and associated genetic determinants within the human microbiome. Learn how metagenomic sequencing is used to detect, quantify, and characterize resistance genes across the gut, oral, skin, respiratory, and other human-associated microbial communities, including their abundance, genomic context, mobility, and potential clinical relevance.

Environmental antimicrobial resistance occurs across soil, freshwater, sediments, marine ecosystems, wastewater, agricultural environments, and other microbial habitats. Learn how metagenomic sequencing is used to detect, quantify, and characterize resistance genes, resistomes, mobile genetic elements, plasmids, microbial hosts, and potential resistance pathways across interconnected environmental systems.

Resistance gene detection identifies genetic determinants associated with antimicrobial resistance in microbial genomes and communities. Learn how metagenomic sequencing, resistance databases, read-based and assembly-based analysis, gene prediction, abundance profiling, and genomic context are used to detect and characterize antimicrobial resistance genes.

Resistance gene abundance analysis measures the representation of antimicrobial resistance genes within microbial communities. Learn how resistance genes are quantified using metagenomic sequencing, relative and absolute abundance methods, normalization, prevalence analysis, statistical testing, and genomic context.

Antimicrobial resistance genes enable microorganisms to survive antimicrobial exposure through mechanisms such as drug modification, target protection, reduced permeability, and active efflux. Learn how resistance genes are detected and analyzed using metagenomic sequencing, resistance gene databases, gene prediction, assembly, abundance analysis, and genomic context.

Metagenomic databases provide the reference information needed to interpret microbial DNA sequences. Explore database types, selection strategies, taxonomic and functional resources, specialized databases, applications, challenges, and best practices for reproducible metagenomic analysis.

Metagenomic gene prediction identifies potential protein-coding genes and genomic features within metagenomic sequences and reconstructed microbial genomes. Learn how gene prediction works, how gene catalogs are created, major methods, challenges, and applications in functional metagenomics.