Microbial Whole Genome Sequencing

N2Jenomics Lab Pvt. Ltd. provides accurate and cost-effective microbial whole genome sequencing solutions using advanced Illumina short-read and PacBio long-read technologies. Our integrated sequencing strategies and bioinformatics expertise support complete genome assembly, microbial re-sequencing, and in-depth genomic analysis.

What Is Microbial Whole Genome Sequencing?

Microbial whole genome sequencing analyzes the complete genetic makeup of microorganisms, including bacteria, fungi, yeast, and viruses. Unlike targeted sequencing approaches, it provides a comprehensive view of genes, plasmids, genomic variations, and functional elements within an organism.

Using shotgun sequencing, microbial genomes are fragmented, sequenced, and computationally assembled to generate complete genome information. Long-read technologies such as PacBio improve genome continuity and enable high-quality de novo assembly without requiring a reference genome.

This approach supports accurate microbial identification, genome annotation, comparative genomics, evolutionary studies, and discovery of novel genes and pathways relevant to biotechnology, medicine, and environmental research.

Advantages of Microbial Whole Genome Sequencing

• • Fast and cost-effective microbial genome analysis
• • Complete genome characterization and annotation
• • Supports de novo sequencing and comparative genomics
• • Identifies genetic variations and evolutionary relationships
• • Enables discovery of genes linked to resistance, metabolism, and biological functions

Applications of Microbial Whole Genome Sequencing

• Pathogen Identification

Rapid identification and characterization of microorganisms for clinical and epidemiological studies.

• Antibiotic Resistance Analysis

Detection of resistance genes and mobile genetic elements to understand resistance mechanisms and transmission.

• Comparative Genomics

Comparison of microbial strains to study genetic diversity, evolution, and population structure.

• Functional Genomics

Identification of genes, metabolic pathways, and biological functions.

• Environmental Microbiology

Analysis of microbial genomes to monitor ecosystem changes and pollutant responses.

• Drug Discovery & Biotechnology

Discovery of novel targets, enzymes, and bioactive compounds for research and development.

• Biosecurity Monitoring

Detection and surveillance of potentially harmful microorganisms.

• Food Safety Testing

Identification of microbial contaminants to support food quality and safety.

Microbial Whole Genome Sequencing Workflow

N2Jenomics Lab Pvt. Ltd. provides end-to-end genome sequencing services for bacteria, yeast, fungi, phages, and viruses.

1. Sample Preparation & Quality Control

• - Sample collection and documentation
• - DNA extraction and quality assessment

2. Library Preparation

• - Genome fragmentation and library construction
• - Quality validation before sequencing

3. High-Throughput Sequencing

• - Illumina short-read sequencing
• - PacBio long-read sequencing for complete genome assembly

4. Bioinformatics Analysis

• - Genome assembly
• - Gene prediction and annotation
• - Comparative genomic analysis
• - Functional characterization

5. Data Delivery

• - Sequencing data
• - Genome reports
• - Analytical results and visualizations

With advanced sequencing platforms and expert bioinformatics pipelines, N2Jenomics Lab Pvt. Ltd. delivers reliable microbial genome insights for research, diagnostics, and biotechnology applications.

Service Specification

	Sample Requirements Pure cultured microorganisms or extracted genomic DNA sample The recommended DNA amount≥2 µg, Concentration ≥ 20 ng/µl. OD260/280=1.8~2.0 All DNA samples are validated for purity and quantity and subject to quality control prior to processing. Short-insert or long-insert libraries are then generated using TruSeq or Nextera protocols.
	Sequencing HiSeq platforms PE150, PacBio SMRT and MGI DNBSEQ-T7/DNBSEQ-G400 Sequencing coverage ≥ 100X PacBio SMRT achieves ~10 kb average read lengths, with some as long as 60 kb.
	Data Analysis We provide customized bioinformatics analysis: Raw data quality control De novo assembly, reference genome mapping Genome annotation (pathogenic and susceptibility genes prediction, non-coding RNA prediction) Gene function annotation (COG/ GO/ KEGG) SNP/InDel identification and comparative genomics analysis Evolutionary analysis and divergence time estimation More data mining upon your request

Analysis Pipeline

Deliverables

• • The original sequencing data
• • Experimental results
• • Data analysis report
• • Details in Microbial Whole Genome Sequencing for your writing (customization)

1. How should samples be prepared for microbial whole genome sequencing?

You can submit purified microbial cultures or extracted genomic DNA samples.

• For microbial cultures:

• - Provide purified cell pellets without growth media.
• - A minimum of approximately 1 million cells is recommended.

• For genomic DNA:

• - Recommended quantity: ≥2 µg
• - Concentration: >20 ng/µL
• - Purity (OD260/280): 1.8–2.0

Samples should be stored and shipped under appropriate frozen conditions (such as dry ice). For stool samples, storage below -80°C is recommended to preserve DNA quality.

2. How does PacBio improve genome assembly accuracy?

PacBio long-read sequencing generates highly continuous genome assemblies, including challenging regions with high GC content or repetitive sequences. Advanced error correction and integration with short-read sequencing data improve final assembly accuracy, achieving highly reliable complete genomes.

3. Can complete genome assemblies be achieved without gaps?

Yes. Combining Illumina short reads with PacBio long reads enables complete genome reconstruction for most bacterial genomes. Additional sequencing approaches may be used for highly complex genomes when required.

4. Can sequencing handle high/low GC regions and repetitive sequences?

Yes. PacBio long-read technology effectively resolves complex genomic regions, including repetitive sequences and GC-rich areas, enabling accurate microbial genome assembly.

5. What are the clinical benefits of microbial whole genome sequencing?

Whole genome sequencing supports rapid microbial identification, outbreak tracking, evolutionary analysis, and antibiotic resistance characterization. Compared with traditional workflows, it provides deeper genomic insights and can improve microbial surveillance, diagnosis, and treatment strategies.