Metagenome Sequencing
Shotgun Metagenomic Sequencing
Variant Genetics offers metagenomic sequencing services targeted for microbial genomic sequencing on environmental samples. Sequence based examination of the metagenome is a powerful technique for examination of uncultured/ unculturable/ previously unknown species.
Shotgun metagenomic sequencing enables comprehensive sampling of all genes of organisms present in complex sample. It is a highly sophisticated method for evaluation of bacterial diversity and detection of abundance of microbes in various environmental samples. It is an excellent method to study uncultured microorganisms that are otherwise difficult to examine.
Shotgun metagenomic sequencing is based on next generation sequencing that allows sequencing of thousands of organisms in parallel. This technique is able to detect low abundant samples also if sequencing is done on high sequence coverage.
- Applications
- Identification of multiple species in environmental samples
- Characterization of microbiota
- Environmental and geographic region-based characterization of microbial species diversity
Sample Requirements
| Sample Type | Amount | Purity |
|---|---|---|
| Genomic DNA | ≥200ng | OD260/280 = 1.8-2.0 |
Sequencing Parameters:
| Recommended Read Length | Paired End 250 bp or 350 |
|---|---|
| Recommended Sequencing Data | 2G data per sample |
| Sequencing platform targeted sequencing | Illumina Platform |
| Sequencing platform full length sequencing | PacBio SMRT sequencing technology |
Data Analysis
- Data quality test
- Taxonomic profiles
- Functional profiles
- BioBakery analysis
- HUMAnN2
- MetaPhIAn2
- StrainPhIAn
- Custom analysis based on project requirement
Data Analysis Work Flow
16a rRNA / 18a rRNA / ITS Amplicon Metagenomic Sequencing
Variant Genetics offers solutions for metagenomic sequencing of 16s rRNA, 18s rRNA and ITS amplicons. Our services are cost effective, state of art technology, reliable and highly scalable that help you identify and investigate the microbial sample.
Ribosomal RNA is predominant form of RNA that makes up to 80% of total cellular RNA. These have multiple conserved and variable regions. 16s rRNA are highly conserved elements of transcriptional machinery of all life forms. They are most widely used markers for genus and species identification and taxonomical classification of bacteria and archaea.
16s/18s/ITS amplicon sequencing uses shot >500 bp hypervariable regions of conserved genes or intergenic regions for differentiation among microbial species. 16s rRNA hypervariable region are used for bacteria and archaea and 18s rRNA is for fungi. ITS (internal transcribed spacer) is located between 16s and 23s rRNA genes in microbes. Eukaryotes have two ITS (ITS1 and ITS2) located adjacent to 5.8s rRNA gene. ITS is sequenced mostly in fungi for determination of molecular ecology of fungi and characterization of molecular systematics at genus and species level. These regions are amplified by PCR and analyzed using next generation sequencing (NGS) technology. Sequencing data is compared against microbial database.
- Applications:
- Identification of single species in culture
- Characterization of microbiota of animals and plants
- Environmental and geographic region-based characterization of microbial species diversity
- Gut microbial environment-based identification and characterization
Sample Requirements
| Sample Type | Amount | Purity |
|---|---|---|
| Genomic DNA | ≥200ng | OD260/280 = 1.8-2.0 |
Sequencing Parameters:
| Recommended Read Length | Paired End 250 bp |
|---|---|
| Recommended Sequencing Depth | 30 / 50 / 100 K reads |
| Sequencing platform targeted sequencing | Illumina Platform |
| Sequencing platform full length sequencing | PacBio SMRT sequencing technolog |
Data Analysis
- Data quality test
- OTUs cluster construction
- Phylogenic relationship construction
- Species annotation
- α diversity analysis
- β diversity analysis
- Ternary Plots
- NMDS analysis
- LefSE analysis
- Metastats analysis
- Species T test analysis
- Custom analysis based on project requirement
Project Workflow
