Metagenome sequencing is a method of identifying microbial communities in different environments. It is used primarily to analyze distribution and type of different species of bacteria and fungi – and to identify their interactions and roles.

Metagenome data can benefit a large number of scientific fields. These include environmental sampling of soil and water, wastewater analysis and food testing. It is also highly relevant to human microbiome samples such as gut and skin.

Amplicon vs shotgun sequencing

The two most common ways to study the metagenome are  shotgun and amplicon sequencing.

Shotgun metagenomic sequencing is a comprehensive method of looking at all genes of all microorganisms present in a sample, similar to whole genome sequencing. The method enables you to evaluate the microbial diversity and detect the abundance of species under different conditions. In shotgun sequencing, a sample’s total DNA is isolated and randomly sheared into smaller fragments before sequencing.

Amplicon metagenomic sequencing is similar to targeted sequencing and enables efficient identification of microorganism diversity in a sample through analyzing operational taxonomic units (OTUs). It works by PCR amplification of conserved genes such as 16S, 18S, ITS and CO1 and sequencing the resulting amplicons.

Explore our Sanger sequencing-based 16S, 18S and ITS rRNA services here.

Library preparation kits

• TruSeq DNA PCR-free
• TruSeq Nano DNA
• Nextera XT DNA
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• PCR + Illumina index kits (amplicon)

Sequencing platforms

• Illumina: NovaSeq 6000, HiSeq, MiSeq (amplicon and shotgun sequencing)
• PacBio: Sequel II (long amplicon sequencing, e.g. full-length 16S rRNA)

Data analysis

Amplicon OTU analysis

• assembly
• clustering
• taxonomy assignment
• diversity analysis

Shotgun sequencing

• read classification
• read pathway
• co-assembly and binning
• gene prediction and annotation