Shotgun Metagenomic Sequencing
Metagenomic analysis is performed to understand the dynamics of microbial communities from environmental samples. It provides classification of species-level taxonomy and the projection of metabolic pathway activities from microbial samples.
Shotgun Metagenome Analysis involves sequencing the complete metagenome samples followed by De novo assembly of multiple genomes from sequence reads of multiple species in an environmental sample. During assembly, the paired-end reads are compared, and overlapping reads are used to build longer contiguous sequences.
These sequences are further analysed for prediction of genes and functional annotations.
Why Choose Eurofins Genomics for Your Shotgun Metagenomic Analysis?
- Comprehensive Workflow
Eurofins offers a complete workflow from quality check to comparative analysis, ensuring thorough and accurate results.
- Custom Solutions
Eurofins provides tailored solutions to meet specific research needs, ensuring optimal results for diverse applications.
- Trusted Partner
As a globally recognized leader in bioanalysis, Eurofins offers reliable and professional services trusted by researchers worldwide.
Workflow and Deliverables
Bioinformatics workflow for Shotgun Metagenome Analysis:
- Quality Check of Raw Reads:
- The raw reads undergo quality filtration and adapter trimming. Primer sequences, poly(A) tails, and reads from ribosomal DNA templates are removed. High-quality data is used for downstream analysis.
- De novo Assembly:
- High-quality reads are assembled using various parameters like Kmer length, coverage cutoff, insert length, and expected coverage for scaffold assembly. The assembled scaffolds are then binned which helps in grouping reads/contigs and assign them to an individual genome.
- Gene Prediction:
- Ab initio gene predictors use statistical models to find gene features such as start and stop codons. The assembly contiguous sequences serve as input for predicting the coding regions in the sample.
- Taxonomic Analysis:
- Taxonomic analysis of predicted genes is performed using sensitive classification programs. This can involve complete genomes from NCBI RefSeq including fungi and microbial eukaryotes.
- Functional Annotation:
- Functional annotation is done using tools that provide COG, KEGG and Pfam annotations for metagenomic datasets.
Deliverables
- Quality filtration of data.
- De novo assembly of high-quality reads.
- Gene prediction.
- Taxonomic profiling and classification
- Taxonomical abundance at different level (Phylum, Class, Order etc.).
- Krona plot visualization.
- Sankey Plot
- Functional Analysis
- COG, Pfam and KEGG subsystem annotations.
- KEGG pathway analysis
- Statistical Analysis
- α and β diversity
- Box plot
- PCoA plot
- Comparative analysis (if multiple samples)
- NCBI submission (SRA)
- Comprehensive report with publication-standard methodology, graphs, and tables
Frequently Asked Questions(FAQ's)
What is Shotgun Metagenome Analysis?
Shotgun Metagenome Analysis involves sequencing and assembling the complete metagenome from environmental samples to understand microbial community dynamics, identify species, and predict metabolic activities.
Why is de novo assembly important in metagenomics?
De novo assembly is crucial as it allows the construction of longer contiguous sequences from sequence reads, enabling more accurate gene prediction and functional annotation without a reference genome.
What kind of samples can be analysed using Shotgun Metagenome Analysis?
Environmental samples such as soil, water, air, and biological samples like gut microbiota can be analyzed using this technique.
How does Eurofins ensure the quality of metagenome sequencing data?
Eurofins ensures quality through rigorous filtration and trimming processes, removing contaminants like primer sequences and ribosomal DNA reads, ensuring high-quality data for accurate analysis.
What are the applications of Shotgun Metagenome Analysis?
Applications include environmental monitoring, human health studies, agricultural research, and understanding microbial roles in various ecosystems.
Choose Eurofins for accurate, reliable, and comprehensive Shotgun Metagenome Analysis to advance your research and understanding of microbial communities.
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