Tag: Shotgun metagenomics

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.

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.

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.

Antimicrobial resistance surveillance monitors resistance genes, resistant microorganisms, resistomes, and resistance patterns across human, animal, agricultural, food, wastewater, and environmental systems. Learn how metagenomics, genomic epidemiology, resistome analysis, and One Health approaches support AMR detection, monitoring, and surveillance.

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.

Resistome profiling characterizes antimicrobial resistance genes within microbial communities. Learn how resistomes are detected, quantified, compared, and interpreted using metagenomic sequencing, resistance databases, abundance analysis, diversity analysis, statistical methods, and genomic context.

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.

Metagenomic resistome analysis examines the collection of antimicrobial resistance genes within microbial communities. Learn how resistomes are detected, profiled, quantified, compared, and interpreted using metagenomic sequencing, resistance databases, assembly, genome-resolved analysis, statistical methods, and genomic context.

Metagenomic DNA extraction is a critical step in recovering microbial DNA from complex biological and environmental samples. Learn about extraction methods, cell lysis, purification, DNA quality control, contamination, extraction bias, and sequencing requirements.

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.