Metagenomic Analysis    

Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Currently, metagenomics projects are facilitated by the rapid development of NGS techniques, which provide lowered experimental costs inherent in conventional sequencing methods.

Mass sequencing of uncultured, unpurified microbial or viral populations, followed by bioinformatics analyses permits the identification and characterization of unknown pathogens necessary for clinical, medicinal and ecosystem applications. Metagenomics approaches in medicine are poised to deliver information of high diagnostic value for infectious diseases and many chronic health conditions.

Metagenomic analysis falls into two broad categories. Large-scale shotgun metagenomics typically involve complete (whole genome) sequencing of the entire metagenome in the sample, and then assembling individual genomes using complex algorithms and massive computational power. Targeted metagenomics, as the name suggests, typically aim at smaller-scale goals, such as the 16S rRNA-based surveys for microbe identification, or acquiring sequence reads with specific protein functions, such as antibiotic resistance genes.

At ACGT, Inc. we offer primarily Targeted Metagenomics services.

How it works

Total DNA is extracted from the sample, followed by any number of selected PCR reactions. The short PCR products (300 bp maximum size) are purified and are converted to Illumina libraries by the ligation of adapters. Multiplex barcoding is typically used to maximize sample processing efficiency (See Important Considerations and Guidelines for Sample Submission). The libraries are analyzed using long paired-end reads to fully sequence each PCR product in the cluster. The reads are sorted, counted, and non-identical sequences are BLASTed against selected databases for sequence identification.