Metagenomics

Genomics on a huge scale

Microbes affect human and animal health, support the growth of plants, are critical components of all terrestrial and aquatic ecosystems and can be exploited to produce food, fuels or chemicals. Estimating the presence and abundance of small animals, phytoplankton and zooplankton, metegenomics has proven a powerful tool to assess biodiversity and be used to monitor health of terrestrial and aquatic ecosystems.

Next-Generation Sequencing, with its ability to sequence thousands of organisms in parallel, has revolutionized microbiology by allowing concurrent analysis of whole microbial communities from complex samples and identification of strains that may not be found using other methods.

Applications of Metagenomics

• Environmental Microbiology: Explore soil, water, and air microbiomes.
• Human and Animal Health: Study gut microbiota and their impact on health.
• Agricultural Science: Improve crop yield by understanding soil microbes.
• Biotechnology: Discover new enzymes and biochemical pathways.
• Ecology and Conservation: Assess biodiversity and ecosystem health.

Shotgun metagenomic sequencing

Shotgun metagenomics allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. The method provides information both about which organisms are present and what metabolic processes are possible in the community.

Since the collection of DNA from an environment is largely uncontrolled, it is important to remember that the most abundant organisms in an environmental sample are most highly represented in the resulting sequence data. Thus, large sequencing efforts are required to achieve the high coverage needed to fully resolve the genomes of under-represented community members. However, the random nature of shotgun sequencing ensures that many of these organisms, which would otherwise go unnoticed using traditional culturing techniques, will be represented by at least some small sequence segments.

Key Deliverables

• Quality Control Reports: Detailed HTML reports on read quality and preprocessing steps.
• Assembled Metagenomes: High-quality contigs and scaffolds for each sample.
• Metagenome-Assembled Genomes (MAGs): Reconstructed genomes with completeness and contamination metrics.
• Functional Annotations:
  • Annotations Tables: Comprehensive data on gene functions and pathways.
  • Metabolic Summaries: Excel spreadsheets summarizing metabolic capabilities.
• Taxonomic Classifications: Accurate assignments from domain to species level.
• Phylogenetic Trees: Newick format trees illustrating microbial relationships.
• Abundance Profiles: Quantitative data on genome abundance across samples.
• Gene and Protein Catalogs: Non-redundant collections for further research.
• Alignment Files: Mapped reads to contigs, MAGs, and predicted genes.
• Antibiotic Resistance Genes hits:
  • by shotgun mapping mapping
  • by ORF match from assembled MAGs.