Microbiome Targeted Sequencing: Definition and How It Works

3 July 2023by Manoj Dadlani

Have you heard of microbiome targeted sequencing? It’s a powerful tool for understanding the world around us, and it is becoming increasingly popular in the medical community.

Microbiome targeted sequencing is a process that uses DNA sequencing to identify specific microbial communities in different environments. By targeting these microorganisms, scientists can better understand how they interact with their environment and what effect they have on human health.

In this article, we will explore what microbiome targeted sequencing is, how it works, and why it’s so important for research today.

What does microbiome targeted sequencing mean?

Targeted microbiome sequencing is the selection and isolation of genetic region(s) of interest before sequencing to illustrate the genetic variation between the samples within the target region.

What this essentially means is that targeted sequencing could capture the genetic variation of microbial communities within a known genetic region which can then be compared between samples.

A common sequencing target gene is the 16s rRNA gene. The gene is ubiquitously conserved in bacteria, yet it contains multiple variable regions that allows for the ability to identify and quantify the various bacteria within each sample. Another commonly used region for sequencing is the Internal Transcribed Spacer (ITS) region, which allows for the profiling of fungal organisms, such as the 16s rRNA gene region does for bacterial organisms.

By utilizing targeted sequencing technology for microbiome samples, one can achieve a detailed and accurate profile with minimal sequencing data. This is because rather than sequencing the entire genetic content of a sample, only specific regions that are informative and relevant are targeted for sequencing and analysis.

How does targeted sequencing work?

Enrichment steps are essential for targeted sequencing to work. To enrich the target region contained in the sample, the target region is amplified with target sequence-specific primers. After amplifying the target region, the nucleic acid is then prepped and analyzed via Next-Generation Sequencing.

This provides an accurate and specific profile of the variation within the target region for each sample. These profiles can then be compared between samples to find patterns in microbiome signatures related to your specific scientific question.

1.    Choosing Your Targeted Gene Region

When choosing the gene region of interest for your research, a few factors need to be considered:

  1. Is the target region within all organisms of interest?
  2. Does the target region provide enough variability between organisms of interest to allow for differentiation?
  3. Does the target region overlap with any organisms that are not of interest?

2.    Amplifying Your Target Regions

One you’ve chosen your target region, either PCR primers specific to the target region could be designed and the target region could be amplified, or target region probes that could hybridize with the target sequence could be used to capture and filter the target region from the genetic material. Once this has been performed, genetic material from the target region will then be cleaned up and used for downstream prep and sequencing.

3.    Using NGS and targeted sequencing

After amplification and library preparation, samples are loaded into Next-Generation Sequencers to generate sequenced data for analysis. Depending on the target region of interest, the read length generated on these sequencers can be adjusted to capture greater variability within the region. Typical read lengths for targeted sequencing are either 250bp or 300bp, and are most commonly sequenced using the Illumina MiSeq platform.

Closing Thoughts

Whatever your research, CosmosID’s Microbiome HUB can help. As a state-of-the-art microbial sequencing platform, our sequencing technologies and services provide industry-leading insights into the microbial composition of your sample.

We are also committed to providing you with the best customer service and support possible to ensure that you get the most out of our platform. At CosmosID, we work hard to help you make the most of your research and truly unlock the power of the microbiome.
For your NGS and targeted sequencing service needs, please contact us today!

Targeted Microbiome Sequencing FAQs

What’s the difference between whole genome sequencing and targeted sequencing?

Whole genome sequencing involves sequencing the entire organism or sample’s DNA, while Targeted Sequencing specifically targets certain regions within the genome.

What are the applications of targeted sequencing?

From the gut microbiome and the wider human microbiome to environmental and crop-based microorganisms, Targeted Sequencing not only provides a view of the genetic variation between samples, but also provides the ability to sequence only the genetic regions your research cares about, which is useful in samples that have high amount of non-target DNA (such as skin, blood, etc). This can offer applications across clinical, biological, environmental, and many more settings.

What is targeted metagenomic sequencing?

Targeted Metagenomic Sequencing is a method of sequencing genetic material from an environment or microbial community in order to study the species present, their functions, and interactions. This involves sequencing the DNA region from organisms belonging to different taxonomic groups, usually focusing on specific genes.


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Manoj Dadlani

Mr. Manoj Dadlani serves as Chief Executive Officer at CosmosID, Inc., the Maryland based provider of industry-leading solutions for unlocking the microbiome. Previously, Mr. Dadlani served as a partner at Applied Value Group, a management consulting and investment firm, and was co-founder and CEO at Rasa Industries, Ltd., a leading beverage manufacturing company. Mr. Dadlani has substantial experience in strategy, M&A, supply chain management, product development, marketing and business development. Mr. Dadlani received his bachelor’s and master’s degrees in Biological Engineering from Cornell University. Services offered by CosmosID’s CLIA certified and GLP laboratory cover the entire workflow from study design to sample collection, extraction, library preparation, sequencing, data analysis and publication support. CosmosID’s cloud-based metagenomics application offers user-friendly access to the largest curated databases for microbial genomics, antimicrobial resistance and virulence data and has been independently validated to return metagenomic analyses at strain level resolution with industry-leading sensitivity and precision.