Metagenomics NGS Sequencing (mNGS)

Metagenomics Solutions in Africa

In metagenomics, environmental samples are collected in their natural state and studied in order to make sense of the genetic material contained in the samples.

At KIBs, we provide a complete array of metagenomics services, from sequencing to bioinformatics analysis. Our mNGS services include targeted and shotgun metagenomics, metatranscriptomics, metaepigenomics, and bioinformatics analysis.

1. Targeted Metagenomics

mNGS sequencing of variable regions allows discrimination between bacteria (16S), fungi (18S, ITS), and archaea (ITS).

This involves sequencing the 16S rRna, 18S rRna and ITS regions which are shared across multiple organisms and samples. Targeted mNGS is a faster and more accurate method of identifying bacteria compared to culturing and cloning. It is also less costly than shotgun sequencing, requires less depth, and is highly sensitive as it enables identification of extremely low abundance bacteria.

2. Shotgun Metagenomics

mNGS sequencing of the total genomic complement.

Unlike the targeted metagenomics approach, the shotgun method sequences everything in your sample and not just the rRNA regions. This method provides greater resolution to genetic content.

3. Metatranscriptomics

Identification of transcript isoforms allows pathogens to be identified from metagenomic samples.

This involves the study of microbial gene expression in mixed microbial communities. Metatranscriptomics reveals the diversity of active genes within a natural microbial community, the expression profiles of these genes, and how these expression levels change because of alterations in environmental conditions.

4. Metaepigenomics

Identification of transcript isoforms allows pathogens to be identified from metagenomic samples.

Epigenetics refers to genetic changes that do not involve mutations. Epigenetic mechanisms involve alterations in DNA organization due to physical changes such as histone modification, or chemical alterations to nucleotides such as methylation, acylation, phosphorylation, or adenylation. Metaepigenomics studies epigenetic changes in microbial communities. In bacteria, epigenetics influences antimicrobial resistance (AMR), sporulation and formation of pilli and has an impact on human disease. Therefore, metaepigenomics is a clinically relevant tool.

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Applications of mNGS

Identification and differentiation of closely related microbial strains using long reads

Diagnosis of infectious diseases

Real-time study of antimicrobial resistance (AMR)

Outbreak tracking

Infection control surveillance

Mutation and pathogen discovery

Discovery of novel natural products, enzymes and antibiotics.

Research - to understand the interactions between microbes and their hosts, identification of active pathways, discovery of how microbial gene expression impacts host disease onset and progress, among others.

core microbiome


Cost of Metagenomic Sequencing in Kenya

Targeted mNGS

5,000 Kshs per sample

Shotgun mNGS


Targeted metatranscriptomics


Targeted metaepigenomics



Completed DNA Tests


Happy Clients


Customer Services



Success Rate

Samples for Metagenomic Sequencing

Expert Bioinformatics Analysis

PhD-level bioinformatics analysis is bundled with the sequencing services and involves:

  • Alpha diversity analysis
  • Beta diversity analysis
  • Core microbiome analysis
  • Phylogenetic analysis
  • Heatmap clustering
  • Univariate analysis - METASTATS, LefSE, T-test/ANOVA,
  • Random forest classification
  • Taxon set enrichment analysis (TSEA)
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Metagenomic Sequencing Features & Overviews

  • Long reads

    long read sequencing resolves structural variants, repeat regions and phasing with long reads.

  • Direct Sequencing

    Direct RNA sequencing eliminates bias, allowing for a comprehensive assessment of epigenetic modifications

  • DNA Sample Collection Instructions

    Sample collection instructions

  • Microbial DNA

    Pathogens can be detected accurately and strains typed precisely.

  • Short Turnaround Time

    Results are available in 10 working days.

  • Confidentiality

    Client information is held in struct confidence and all data is returned to the client or discrded unlesss the client asks us to store it.


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