What is 16S rRNA Sequencing?

The 16S ribosomal RNA gene is highly conserved yet contains variable regions unique to different bacteria and archaea. Sequencing this ~1500 bp gene allows accurate taxonomic classification, species-level identification in many cases, and construction of phylogenetic trees to understand evolutionary relationships.

At Yaazh Xenomics, we use universal primers (27F/1492R or similar) + Sanger sequencing (with 518F/800R internal) for gold-standard accuracy on pure isolates or simple communities. For complex microbiomes, we guide toward our NGS metagenome options.

Better and More Comprehensive Results

Our 16S rRNA Sequencing Workflow – Full Service Package

  1. Sample Receipt & DNA Extraction – Optimized kits for diverse samples (soil, water, clinical, food, plant-associated, etc.)
  2. PCR Amplification – Universal bacterial primers + gel verification
  3. Purification & Sanger Sequencing – Forward + Reverse reads for high-quality contigs (~1400 bp+)
  4. Bioinformatics Analysis (Free of cost):
    • Sequence assembly & quality check (Q16/Q20 lengths, GC content)
    • BLAST against NCBI/GenBank + comprehensive databases
    • Contig coverage visualization
    • Phylogenetic tree construction (customer-specific gene analysis included)
  5. Deliverables:
    • Raw files: .ab1 (chromatogram), .pdf, .txt, .fasta
    • Assembled contig sequence
    • BLAST results & top hits
    • Full summary report (methodology + results)
    • Phylogeny tree (Newick + visual)

Key Benefits of Choosing Yaazh Xenomics for 16S rRNA Sequencing

  • Affordable pricing – competitive with top labs in India
  • High success rate on difficult templates (high GC, low biomass)
  • Free advanced bioinformatics including phylogenetic tree
  • Coimbatore-based ISO-certified lab – fast local pickup & nationwide shipping support
  • Expert support for actinomycetes, environmental bacteria, probiotics, pathogen ID
  • Results suitable for publications & regulatory needs

Why Sequencing Coverage & Contamination Control Matter in 16S Analysis

Sequencing Coverage

High coverage ensures detection of rare species and accurate diversity estimates. We optimize read length & quality; rarefaction guidance available for complex samples.

Contamination Mitigation

  • Stringent sterilization & clean-room protocols
  • Negative controls to detect reagent/kit contaminants
  • Positive controls with known microbial mixes
  • Expert review to flag & filter artifacts

Pros & Cons of 16S rRNA Sequencing

Advantages

  • Gold standard for bacterial & archaeal identification
  • Cost-effective compared to shotgun metagenomics
  • Large, curated databases for reliable matches

Limitations

  • Limited to bacteria/archaea (use ITS/18S for fungi, eukaryotes)
  • May not resolve very closely related strains to species level
  • No direct functional gene information
  • Sensitive to contamination in low-biomass samples

For functional profiling or strain-level resolution, explore our shotgun metagenome sequencing.

Applications of 16S rRNA Sequencing

  • Microbiome studies (gut, soil, water, skin)
  • Bacterial identification from pure cultures
  • Phylogenetic analysis & novel species discovery
  • Probiotics & fermented food validation
  • Environmental monitoring & bioremediation
  • Clinical & veterinary pathogen research

Get Started with 16S rRNA Sequencing in India

Ready for precise microbial identification? Contact Coimbatore’s trusted genomics partner today.

Yaazh Xenomics Pvt Ltd
Module No. 103, TICEL BIOPARK Phase – III,
Maruthamalai Road, Coimbatore – 641046, Tamil Nadu

Phone: +91 99431 32020 | +91 95002 45454
Email: info@yaazhxenomics.com

Request Quote | View All Sequencing Services

Yaazh Xenomics – Crack the Microbial Code with Precision & Affordability.

The Technique- A Complete Solution

PCR amplification

After the bacteria is isolated and DNA extracted, we amplify the 16s rRNA sequence. We rely on 27F/1492R or 27F/1525R, the universal primers that complement the region. Once we have multiple copies of the target DNA, we utilise them as sequence templates. 

DNA sequencing

This step uses the common Sanger sequence method. Each strand - 3' to 5' and 5' to 3' – undergoes separate sequencing. We use forward and reverse primers. Often they are the same universal primers from amplification. Internal primers are used when entire regions need to be sequenced. The common primers Yaazh wields for 16s rRNA are 518F/800R.

Sequence comparison

The last stage is creating a phylogenetic tree using bioinformatic tools to visualise the result. The tree shows either the similarity or distance between the clustered calculation. It also helps compare sequences.

Power of Functional Genomics

The only whole-genome sequencing lab you will ever need for 16s rRNA sequencing services!
Get Started
Yaazh Xenomics,
Module No. 103,
TICEL BIOPARK Phase – III,
1st floor, Maruthamalai Road,
Coimbatore - 641046.
Tamil Nadu, India
Yaazh Xenomics,
No.9-6, Sritej Nagar,
Anandapuram, 
Visakhapatnam -531022
Andhra Pradesh

Yaazh Xenomics is a leading biotechnology company based in Coimbatore, Tamil Nadu, India, specializing in comprehensive genomic solutions. As a DNA testing laboratory, we offer a broad spectrum of services, including DNA sequencing, RNA Sequencing, Sanger Sequencing, 16s rRNA, 18s rRNA, ITS, COI, RBCL, Matk gene Sequencing for DNA Barcoding, gene expression analysis, SNP analysis, Next-Generation Sequencing (NGS), Various Medical Genome testing, Exome Sequencing, Gut Microbiome Test, Metagenome Sequencing, Whole Genome Sequencing (WGS), Transcriptome Sequencing using advance NGS platforms like Nanopore, Illumina, MGI, Thermo. Also, we provide advance Bioinformatics, Customized Bioinformatics and a variety of other genetic testing and Molecular testing.

 

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