METAGENOMICS
High-Resolution Microbiome Profiling and Functional Interpretation
At Nucleome, we unravel the complexity of microbial communities through high-resolution metagenomic and metatranscriptomic analyses. Our solutions enable genome-resolved insights into microbiomes, revealing not just who is present, but what they are capable of and actively doing within diverse environments.
From comprehensive shotgun sequencing to targeted amplicon profiling, we transform complex microbial data into functional, ecological, and clinically relevant insights.
Partner with Nucleome to explore microbial ecosystems with precision, depth, and impact—from environmental research to clinical and industrial applications.
Why Metagenomics Matters
Microbial communities play a critical role in health, disease, agriculture, and environmental sustainability.
Metagenomics enables:
- Identification of microbial diversity and community composition.
- Reconstruction of metagenome-assembled genomes (MAGs) for genome-level insights.
- Discovery of functional pathways and metabolic potential.
- Detection of antimicrobial resistance (AMR) genes and resistomes.
- Understanding of microbiome-host and microbiome-environment interactions.
At Nucleome, we go beyond taxonomic profiling to deliver genome-resolved and functionally interpretable microbiome insights.
Next-Generation Metagenomics Ecosystem
At Nucleome, our metagenomics ecosystem integrates advanced shotgun sequencing, targeted amplicon profiling, and metatranscriptomic approaches to comprehensively characterize microbial communities across diverse environments. We enable both taxonomic and functional resolution, moving beyond community composition to uncover the genetic and metabolic potential of microbiomes.
Our workflows combine deep shotgun metagenomics for genome-resolved analysis, enabling reconstruction of metagenome-assembled genomes (MAGs) and strain-level variation, with 16S rRNA and ITS sequencing for high-throughput microbial profiling of bacterial and fungal communities. In parallel, metatranscriptomic sequencing captures actively expressed genes, providing insights into real-time microbial activity and functional dynamics.
This integrated approach allows precise identification of microbial diversity, functional pathways, antimicrobial resistance genes (resistome), and host–microbiome interactions, delivering high-resolution insights into ecosystem function, disease associations, and environmental adaptation.
Bioinformatics & Data Analysis
At Nucleome, we implement robust, scalable bioinformatics pipelines to convert complex metagenomic sequencing data into high-resolution, functionally interpretable insights. Our workflows begin with stringent quality control, host read removal, and optimized assembly or direct read-based profiling, ensuring accurate downstream analysis across diverse sample types.
We perform comprehensive analyses including taxonomic profiling (species- and strain-level), metagenome assembly, and binning for reconstruction of metagenome-assembled genomes (MAGs).
Functional characterization is enabled through gene prediction, pathway annotation (e.g., KEGG, GO), and metabolic reconstruction, providing insights into microbial roles and ecosystem function.
Advanced modules include resistome analysis (antimicrobial resistance genes), virulence factor identification, and comparative microbiome analysis across conditions or cohorts.
For metatranscriptomic datasets, we quantify actively expressed microbial genes, linking community composition to functional activity.
Our Key Solutions
Shotgun Metagenome Sequencing
Comprehensive sequencing of all genetic material present in a sample, enabling unbiased profiling of entire microbial communities at species and strain level, along with functional potential.
Why it should be done: Provides deep insights into microbial diversity, metabolic pathways, resistome, and genome-resolved analysis (MAGs) for clinical, environmental, and industrial applications.
16S Ribosomal RNA (rRNA) Sequencing
Targeted amplicon sequencing of the 16S rRNA gene for profiling bacterial community composition and relative abundance.
Why it should be done:
Cost-effective and efficient for microbiome diversity studies, comparative analysis, and large-scale microbial profiling
across samples.
Metatranscriptome Sequencing
Sequencing of total RNA from microbial communities to capture actively expressed genes and functional activity.
Why it should be done: Reveals real-time microbial function, enabling understanding of active pathways, host–microbiome interactions, and environmental responses.
Microbial Genome Sequencing
High-resolution sequencing of individual microbial genomes, including bacteria and fungi, for complete genomic characterization.
Why it should be done:
Essential for strain-level identification, functional annotation, comparative genomics, and evolutionary studies.
Viral Genome Sequencing
Targeted sequencing of viral genomes for detection, characterization, and mutation analysis across diverse viral populations
Why it should be done:
Critical for viral surveillance, outbreak tracking, mutation analysis, and vaccine or therapeutic research.