MGS sequences the entire genomic content of both known and unculturable microorganisms.

Shotgun MGS

Shotgun MGS is ideal for complete gene-sampling from all organisms within a complex sample so that microbiologists can evaluate the types and concentration of microorganisms in their environment. Further, it can trace the diversity of unculturable microorganisms that would otherwise be unstudied or impossible to analyze.

In contrast to capillary sequencing or PCR-based methods, a single NGS sequencing run can sequence hundreds, sometimes thousands of organism side-by-side. Furthermore, because hundreds or even thousands of samples can be combined into a single sequencing run and sequence coverage is high per sample, members with very low relative abundance of the microbial communities can be detected by NGS-based metagenomic sequencing that might go unnoticed or be too costly to identify by other techniques.

Fig. 1 Shotgun Metagenome Sequencing Analysis of Four Mangrove Root-Compartments Microbiota.¹

Shotgun Metagenomic Sequencing vs. 16S rRNA Gene Sequencing

16S rRNA gene sequencing is one of the most important techniques used for microbial community analysis. It's the microbial analysis equivalent of trying to identify a kind of tree by looking at its molecular fingerprint. If you chop out a chloroplast from a leaf, digest it, and sequence the genetic sequence within the conserved and variable region of the 16S rRNA gene, you can classify and distinguish species between very different taxa (in terms of their ecology, biochemistry and symbiosis). This is because you're able to amplify and sequence the conserved and variable regions of 16S rRNA within the microbial cell so that you can identify the bacteria involved.

The table below illustrates the fundamental differences between shotgun metagenomic sequencing and 16S rRNA gene sequencing, on important factors such as taxonomic coverage, sequencing depth, computational needs, and cost implications. This comparison aims to clearly show the pros and cons of the two techniques so that researchers can make a more informed choice about the technique they should apply in their work, without compromising their research goals or their bank account.

Tab. 1 Comparison of Shotgun Metagenome Sequencing and 16S rRNA Gene Sequencing.

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Applications of Shotgun MGS

• Microbiome biomarker discovery.
• Research and discovery across a wide variety of human health areas such as gut, oral and skin health.
• Clinical study analysis of antibiotic resistance genes.
• Clinical study analysis for linking the microbiome to clinical outcomes in drug, probiotic and nutritional intervention studies.
• Clinical study analysis of potential microbiome factors determining responders and non-responders.
• Microbiome data mining for identifying disease-associated strains.
• Engraftment and colonization analysis for fecal microbial transplant (FMT) studies and probiotic studies.

If you are interested in our shotgun metagenomic sequencing service, please do not hesitate to contact us for any discussion.

Reference

1. Zhuang, Wei, et al. "Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale." npj Biofilms and Microbiomes 6.1 (2020): 52. Distributed under Open Access license CC BY 4.0, without modification.

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