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Microbiome Sequencing

Understanding the microbiome using genomic sequencing and analysis

Microbiome study is vital for drug discovery as the microbiome significantly influences drug metabolism, efficacy, and safety. Understanding these interactions can optimize drug dosages, enhance treatment effectiveness, and enable personalized medicine based on an individual's unique microbiome profile. Moreover, the microbiome's impact on drug-induced toxicity and interactions between medications can be identified, leading to safer drug development. Microbiome-targeted therapies offer promising approaches, directly treating conditions or improving drug effects. Microbiome analysis also helps identify biomarkers for diseases and treatment response, advancing diagnostic tools and precision medicine. Integrating microbiome data into drug development can revolutionize healthcare by improving treatment outcome

Microbiome sequencing provids insights into complex microbial communities. Choose our microbiome sequencing services for:

  • Diverse service options: We offer multiple methods for comprehensive microbiome sequencing analysis, including full-length 16s rRNA sequencing, shotgun metagenomic sequencing, and metatranscriptomic sequencing

  • Superior data quality and advanced technology platforms: Our services utilize Illumina NovaSeq and PacBio platforms, ensuring accurate and high-quality sequencing for comprehensive microbiome analysis.

  • Expert data analysis: Our experienced bioinformatics team provides in-depth data interpretation and analysis.

  • In vivo service integration: Gain valuable insights into host-microbiome interactions through access to our in vivo service. 

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Full-length 16s rRNA Sequencing

Crown Bioscience leads in comprehensive and cost-effective full-length 16S rRNA analysis using PacBio's long-read third-generation sequencing. Our approach offers distinct advantages over short read sequencing. By capturing the entire 16S rRNA gene, we provide unparalleled insights into bacterial diversity and ensure precise taxonomic classification. Overcoming limitations of short read methods, such as primer bias and reduced taxonomic resolution, our full-length sequencing delivers a comprehensive and unbiased view of the microbial community. This empowers the identification of potential drug targets and deepens understanding of their functional roles.


Traditional 16S Sequencing

Full-Length 16S Sequencing

  Sequencing Platform

  Short Read Sequencing

  Long Read Sequencing 

  Targeted Region

  Short hypervariable region

  Entire 16S rRNA gene

  Taxonomic Resolution



  Primer Bias



  Secondary Structure

  Not captured



Fig. Commonly used DNA regions in short-read and long-read 16S rRNA sequencing

Shotgun Metagenomic Sequencing

Metagenomic sequencing provides a significant advantage over 16S rRNA sequencing by capturing comprehensive genomic information. This empowers higher taxonomic resolution, direct functional profiling, and the identification of novel or rare species. While it comes at a higher cost and requires specialized bioinformatics expertise, shotgun sequencing is an ideal choice for researchers looking to delve into a smaller number of samples with greater depth compared to amplicon sequencing. Embrace the power of metagenomic sequencing to unlock a wealth of valuable insights about microbial communities and their functional potential.

Metatranscriptomic Sequencing 

Metatranscriptomic sequencing studies the gene expression profiles of microbial communities, providing insights into their functional activities and responses to the environment. By analyzing RNA molecules, researchers can identify actively expressed genes, revealing the metabolic pathways and biological processes within the microbiome. This approach enhances our understanding of how microbes interact with their surroundings and contribute to ecosystem functions and host-associated processes.

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Full-length 16S rRNA 

  • Identification, classification, and quantification of microbes (bacteria) within complex biological mixtures
  • Microbial contamination detection
  • Cost-effective
  • Established pipeline for data analysis
  • Well-developed database
  • Potential PCR amplification bias
  • Relatively low taxonomic resolution (genus-species)
  • Focuses on bacterial microbes only

Shotgun Metagenomic

  • Comprehensive sequencing of all genes in all organisms (bacteria, fungi, etc.) present in a given complex sample
  • High taxonomic resolution (species-strains)
  • Improved sequencing depth and accuracy
  • Increased detection of microbial diversity
  • Functional profiling
  • Relatively higher cost
  • Longer sequencing period
  • Challenges with database completeness and reference availability


  • Capturing and studying the expressed transcripts within a microbiome at a specific time and environmental condition
  • Whole gene expression profiling
  • Functional enrichment analysis
  • Insight into active members of the microbiome
  • Study of microbiome-host and microbiome-environment interactions
  • Relatively higher cost
  • Longer sequencing period
  • Limited availability of reference genomes

Related Resources

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