SMRT-Based Metagenomics

Overview

CD Genomics' comprehensive metagenomics service is based on a single molecule, real-time (SMRT) sequencing from PacBio Biosciences. The SMRT-based metagenomics is a culture-free, long-read sequencing strategy that can effectively reduce some splicing errors and visibly improve the resolution of microbial community profiling. This service aims to examine thousands of microorganisms in parallel and comprehensively obtain all genes, providing insight into community biodiversity and function.

Our Advantages:

High throughput and high coverage, allowing to detect low abundance members of microbial communities.
Full-length genes profiling within a microbial community using long-read metagenomic technologies.
Unbiased structural and functional characterization of microbial communities.
High-quality assembly for metagenomes with low-bias sequence context and high consensus accuracy.

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Introduction to our SMRT-based metagenomics platform

Microorganisms are almost everywhere. But to study them, more than 99% cannot be cultured in vitro. Our SMRT-based metagenomics, using PacBio RSII or Sequel from PacBio Biosciences, is a highly accurate, culture-independent metagenome profiling approach to study the microbial communities despite the culture limitations. The PacBio SMRT sequencing technology is characterized by unparalleled read length and accuracy, which is helpful for the reconstruction of the high-quality draft and metagenomic analysis.

SMRT-based metagenomics can be used to study the species composition and abundance, identify differentially expressed genes (DEGs) among samples, explore gene functions and metabolic pathways, and mine gene resources for bioactive products. The technology can also be used to elucidate and understand the relations between microbes and their habitat/host, like the microenvironments within the human body in healthy or diseased states. SMRT-based metagenomics has been widely applied to research and biotech industry.

SMRT-based metagenomics workflow

Bioinformatics Analysis

Our bioinformatics analysis includes four parts: raw data processing, assembly, binning, annotation. We are flexible to your needs.

Pipeline	Contents
Raw data processing	Filtering and trimming of poor-quality sequence.
Assembly	Reference-based assembly, de novo assembly, and quality assessment of metagenomics assemblies.
Binning	Phylogenetic binning using tools like LikelyBin, PHYSCIMM, MetaWatt, CONCOCT, etc.
Annotation	Metagenome gene prediction using tools like MetaGeneAnnotator, Orphelia, and Glimmer-MG; protein function prediction using InterProScan software pipeline; pathway annotation using databases like KEGG, WikiPathways, and MetaCyc.

Sample Requirement

1. gDNA ≥ 5 ug, 1.8 < OD_260/280 < 2.0, without degradation or contamination.

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

Connor B. Driscoll, et al. Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture. Standards in Genomic Sciences. 2017; 12:9.
Torsten Thomas, et al. Metagenomics - a guide from sampling to data analysis. Microbial Informatics and Experimentation. 2012; 2:3.
anastasis oulas, et al. Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies. Bioinformatics and Biology Insights. 2015;9: 75–88.
Roumpeka D D, Wallace R J, Escalettes F, et al. A review of bioinformatics tools for bio-prospecting from metagenomic sequence data. Frontiers in genetics, 2017, 8: 23.

* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.