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Metagenomic Shotgun Sequencing

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Metagenomic Shotgun Sequencing

CD Genomics is committed to providing unprecedented amounts of sequence data permitting rapid and profound de novo metagenomics shotgun analysis of a variety of microbial communities with cost-effective solutions.

Metagenomic de novo sequencing is using the shotgun methodology to fully sequence the majority of available genomes within a microbial community, is a very powerful technology as it targets the entirety of the microbial genetic information contained in an environmental sample. This creates a community taxonomic profile that can be further associated with the functional profile of known and unknown organism lineages. When performing metagenomics sequencing, the complete sequences of protein-coding genes as well as full operons in the sequenced genomes can offer invaluable functional knowledge about the microbial communities inhabiting practical ecosystems under study, for example, the genetic information on potentially novel biocatalysts or enzymes, genomic linkages between function and phylogeny for uncultured organisms, evolutionary profiles of community function and structure and much more. Metagenomics has a wide range of applications in countless fields including the food and medical industries. This approach has been applied to environmental studies as well as biomarker research.


The general workflow for metagenomic sequencing is outlined in Figure 1. Briefly, the sequencing library is constructed by DNA fragmentation, then the sheared DNA fragments are sequenced with Illumina HiSeq PE150 strategy. The raw data is processed by removal of adaptor, host genome sequence, and low-quality data.

Schematic workflow of metagenomic sequencing Figure 1. Schematic workflow of metagenomic sequencing.

Recommend Sequencing Platform and Sequencing Depth

  • HiSeq PE150
  • 6-10G raw data per sample

Data Analysis

Flowchart of our basic metagenomics data analysis steps is illuminated in Figure 2.

Flowchart of bioinformatics analysis to metagenomic sequencing data Figure 2. Flowchart of bioinformatics analysis to metagenomic sequencing data.

Our standard analysis package includes DNA assembly, sample complexity analysis, function annotation, alpha and beta diversity analysis, gene prediction (KEGG, GO, COG et al.), taxonomic annotation, mPATH, heatmaps, PCA and PCoA analysis, Krona, cluster analysis, MetaStats, and OG-Taxa et al.

Our advanced analysis package includes MRPP, ANOSIM, NMDS (Non-metric Multidimensional Scaling), CCA/RAD, and LEfSe (LDA Effect Size) and so on.

Sample Requirements

Small number and large number of microbiome samples from a wide variety of sources including human or animals, natural environments and industrial environments can be sequenced and analyzed. Customers may submit environmental samples for bacteria/fungi gDNA extraction services or submit extracted genomic DNA. All DNA samples are validated for purity and quantity and subject to quality control prior to processing. The recommended DNA amount for submission is 2 µg or more with a concentration of ≥ 30 ng/µl.

We provide the comprehensive service from DNA isolation to library preparation to next generation sequencing to de novo assembly & annotation, by harnessing our unique bioinformatics analysis capabilities, up-to-date software tools and databases, and microbiology based expertise.

We are also able to offer long read sequencing based shotgun metagenomics with the help of PacBio’s SMRT technology. You can choose a variety of options regarding the depth of coverage, the data analysis strategies and so on. At CD Genomics, with multiple specialists and years of experience in this area, we guarantee you with high-quality data and satisfying results. If you have additional requirements or questions, do not hesitate to contact us, our specialists would like to solve your problems.

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