Metagenomics is the study of the collection of all genomes and genes from all microorganisms present in a sample (the “metagenome”). This metagenome is subjected to random fragmentation and DNA sequencing followed by various computational steps (assembly, mapping, annotation). Also known as whole genome shotgun metagenomics, the analysis can be used to profile microbial community composition and examine functional genes to provide insight into “What microorganisms are present?” and “What are they capable of doing?”.
Also known as shotgun metagenomics, the approach is untargeted and utilizes the entire genomic content of the sample including taxonomic and functional genes for analysis. With other Next Generation Sequencing (NGS) approaches, a specific gene such the 16S rRNA gene is targeted and PCR amplified prior to sequencing. Shotgun metagenomics and NGS targeting the 16S rRNA gene each have distinct advantages and limitations that should be considered before selecting an approach.
Who is there? Metagenomics provides accurate identification of microorganisms present in a sample down to the species level with no prior knowledge of the microbial community.
Based on the community composition and specific metabolic processes of interest, reference genomes can be used to identify functional genes.
While not quantitative, metagenomics reports include the relative proportions of the microorganisms identified in the sample based on number of classified sequence reads. Results reported as number of reads and percent of classified reads.
Metagenomics reveals the overall microbial community composition. Knowing which microorganisms are present and their relative abundances provides insight into the types of microbial processes might be occurring such as fermentation or metals reduction.
Reports include brief descriptions of the top genera identified in each sample. The descriptions highlight the metabolic capabilities commonly associated with the genus.
Metagenomics provides much more comprehensive identification of the microorganisms present in a sample than other DNA based techniques (e.g. DGGE, T-RFLP) thus giving a much more complete profile of the microbial community.
Analysis can be performed on almost any type of sample (water, soil, sediments, Bio-Traps®, and others).
HOW TO USE METAGENOMICS:
Metagenomics is a powerful molecular biological tool that can generate a profile of the microbial community composition to the species level and provide direct insight into functional potential.
Use Metagenomics to help answer…
- What microorganisms are present?
- Can a functional gene of interest be detected?
- How diverse is the microbial community?
- How did the microbial community change in response to site activities?
- Which microbes were relatively more or less abundant after treatment?
- What are the differences in the microbial communities along the dissolved plume?
- What biogeochemical processes are likely in each zone?