Metagenomics studies the collective genomes of microbial communities directly from environmental or clinical samples – without culturing. It reveals microbial diversity, composition, interactions, and functions in their natural habitats (environmental genomics, eco-genomics, community genomics).

We offer two main approaches:

• Amplicon Metagenomics (targeted): Sequences specific marker genes like 16S rRNA (bacteria/archaea), 18S rRNA (eukaryotes), ITS (fungi) for cost-effective taxonomic profiling and diversity studies.
• Shotgun Metagenomics (untargeted): Sequences all DNA/RNA in the sample for species/strain-level resolution, functional gene prediction, metabolic pathways, and resistance/virulence profiling.

Our Metagenome Sequencing Platforms

• Illumina (NovaSeq/NextSeq) – High-throughput, short-read accuracy for deep coverage
• Oxford Nanopore – Long reads for better assembly, strain resolution, and real-time analysis
• MGI & Thermo – Flexible options for cost-effective high-output projects

Amplicon Metagenomics Workflow (16S/18S/ITS)

1. Sample Receipt & gDNA Extraction – Optimized for soil, water, gut, clinical, food, etc.
2. PCR Amplification – Hypervariable regions (e.g., V3-V4 for 16S, ITS1/ITS2 for fungi)
3. Library Prep & Sequencing – High-quality reads on Illumina/Nanopore
4. Bioinformatics Analysis (Free basic + custom):
   • Quality filtering, denoising, OTU/ASV clustering
   • Taxonomic classification (SILVA, Greengenes, UNITE databases)
   • Alpha/beta diversity, rarefaction, phylogenetic trees
   • Differential abundance & visualization (PCoA, heatmaps)
5. Deliverables: Raw FASTQ, ASV/OTU tables, taxonomy reports, diversity plots, summary PDF

Shotgun Metagenomics Workflow

1. Sample Receipt & High-Quality gDNA/Total RNA Extraction
2. Library Preparation – Fragmentation, adapter ligation (no PCR bias in host-depleted options)
3. Deep Sequencing – Paired-end or long reads for comprehensive coverage
4. Advanced Bioinformatics (Free basic + custom):
   • Host depletion, read assembly (MEGAHIT/metaSPAdes)
   • Taxonomic profiling (MetaPhlAn, Kraken2, Bracken)
   • Functional annotation (HUMAnN, eggNOG, KEGG, MetaCyc pathways)
   • Antibiotic resistance/virulence gene detection (CARD, VFDB)
   • Binning for MAGs (metagenome-assembled genomes)
5. Deliverables: FASTQ/BAM, taxonomic/functional tables, pathway maps, MAGs, custom reports

Why Choose Yaazh Xenomics for Metagenome Sequencing in India?

• Affordable pricing – competitive with top labs, high-value full packages
• Fast TAT – Efficient automated workflows for quick results
• High-quality data – Strict QC, controls, contamination mitigation
• Expert bioinformatics – Free standard analysis + publication/custom support
• Coimbatore-based ISO lab – Nationwide sample shipping/pickup
• Versatile sample types – Gut, soil, water, skin, food, clinical, probiotics

Applications of Metagenome Sequencing

• Gut microbiome analysis & health insights (dysbiosis, probiotics validation)
• Environmental monitoring (soil biodiversity, water quality, bioremediation)
• Agriculture (plant-microbe interactions, rhizosphere studies)
• Clinical research (infectious diseases, pathogen detection, AMR)
• Food safety & fermentation (microbial profiling in dairy, probiotics)
• Novel microbe/gene discovery & industrial biotechnology

Amplicon vs Shotgun Metagenomics: Which to Choose?

Amplicon (16S/18S/ITS)

• Advantages: Cost-effective, high taxonomic depth, great for diversity screening
• Limitations: Limited to marker genes, no functional info, PCR bias possible

Shotgun Metagenomics

• Advantages: Strain-level resolution, functional pathways, resistance/virulence genes, unculturable microbes
• Limitations: Higher cost/depth needed, more complex analysis

For targeted bacterial ID, start with our 16S rRNA Sequencing. For full functional profiling, choose shotgun.