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SMRT-Based 16S/18S/ITS Sequencing


CD Genomics is familiar with performing full-length 16S/18S/ITS sequencing by utilizing PacBio's single molecule real-time (SMRT) sequencing technology. SMRT-based 16S/18S/ITS sequencing can identify individual members of the complex microbial communities collected from human feces, mouse feces, soil, etc.

Our Advantages:
  • Deliver the highest consensus accuracy with unprecedented read lengths.
  • Streamline your workflow with rapid targeted (16S/18S/ITS) approaches.
  • Full-length 16S/18S/ITS sequencing containing more information compared with its variable regions.
  • Improve sequence assembly for large and complex genomes.
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Introduction to Our SMRT-based 16S/18S/ITS Sequencing Platform

The 16S rRNA, 18S rRNA, and internally transcribed spacer (ITS) are commonly used molecular markers for species identification and phylogenetic analysis in prokaryotes or eukaryotes. While 16S and 18S rRNAs contain several hypervariable regions that vary dramatically in length, ITS tends to be hypervariable and unique among fungal species, even strains. These hypervariable sequences can be used to identify and characterize microbial diversity, function, and evolution analysis. The PacBio SMRT technology is a long-read sequencing platform with an average read length of about 10~18 Kb, which can cover all variable regions of 16S/18S/ITS. Our SMRT-based 16S/18S/ITS sequencing service can accurately amplify the full-length 16S/18S/ITS with validated universal primer pairs that target the highly conserved regions flanking these sequences. Compared with short-read sequencing data only from variable regions, full-length 16S/18S/ITS sequencing enables more accurate species/strain classification and identification.

SMRT-based 16S/18S/ITS sequencing enables us to identify or characterize the prokaryotic species and explore microbial diversity in complex microbial communities. In addition, this sequencing platform can advance microbial taxonomy and phylogenetic studies. In the medical field, it can be used to analyze the global microbial communities in both healthy and diseased groups for biomarker discovery, disease diagnosis, and target discovery. SMRT-based 16S/18S/ITS sequencing has also been applied to genetic changes tracking, food sources monitoring, reflection of biomass concentration, marine environmental conservation, surveillance and response to infectious disease outbreaks, and industrial manufacturing.

SMRT-based 16S/18S/ITS sequencing workflow

Bioinformatics Analysis

Our general bioinformatics analysis workflow includes raw data processing, taxonomic assignment, diversity analysis, functional prediction, correlation analysis, and evolutionary analysis, which is flexible to your needs.


Pipeline Content
Raw data processing Filtering and trimming of poor-quality sequence
Taxonomic assignment Operation taxonomic unit (OTU) clustering and filtering, PCA, Venn diagram, rank abundance curve, etc.
Diversity analysis Alpha diversity, beta diversity, meta-analysis
Functional prediction PICRUSt, FAPROTAX, Tax4fun, FunGuild
Correlation analysis CCA analysis, VPA analysis, Network analysis
Evolutionary analysis Construction of phylogenetic trees

Sample Requirement

Sampling kits: We provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: Raw data files in BAM format, demultiplex CCS reads in FASTQ format, quality-control dashboard, statistic data, and your designated bioinformatics analysis report.

References

  1. BM. Jones and AB. Kustka. A quantitative SMRT cell sequencing method for ribosomal amplicons. Journal of Microbiological Methods. 2017; 135:77–84.
  2. H Mori, et al. VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics. 2010; 11:332.
  3. JJ. Mosher, et al. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing. Journal of Microbiological Methods. 2014; 104: 59-60.

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