Metagenomics Analysis Services

Complete metagenomics and microbiome analysis

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples, allowing an entire microbial community to be characterised without the need for culturing. It encompasses both marker-gene approaches, such as 16S, 18S and ITS amplicon sequencing, and whole-genome shotgun sequencing, which together reveal who is present in a community and what they are capable of doing.

We provide end-to-end microbiome and metagenomics analysis for human, environmental, agricultural and clinical studies, turning raw sequencing reads into clear taxonomic and functional insight.

Our Services

• 16S, 18S and ITS amplicon processing (DADA2 / QIIME 2)
• Whole-genome shotgun metagenomic profiling
• Taxonomic classification and abundance estimation
• Alpha- and beta-diversity analysis
• Functional and metabolic pathway annotation
• Differential-abundance testing between groups
• Metagenome-assembled genome (MAG) recovery and binning
• Antimicrobial-resistance and virulence-gene screening

These analyses connect microbial composition and function with health, disease and ecosystem processes, supported by clear visualisations and robust statistics.

What you receive

• Taxonomic abundance tables at every rank, from phylum to species or strain where the data supports it
• Alpha- and beta-diversity results with the statistical tests appropriate to compositional data
• Differential-abundance results identifying which taxa genuinely differ between your groups
• Functional and pathway annotation, plus resistance and virulence gene screening where relevant
• Metagenome-assembled genomes with completeness and contamination scores, for shotgun projects
• Publication-ready figures: ordination plots, stacked composition bars, heatmaps and diversity boxplots
• A written interpretation and the full analysis code

Choosing between amplicon and shotgun sequencing

If you have not yet sequenced, this decision matters more than any analysis choice that follows. Amplicon sequencing of 16S, 18S or ITS is inexpensive and well suited to large cohorts and comparative questions, but resolves reliably only to genus and infers function indirectly from reference genomes.

Shotgun metagenomics reaches species and strain level and measures functional content directly — resistance genes, metabolic pathways, virulence factors, and viruses and fungi that amplicon primers miss entirely. It costs substantially more per sample and requires far more compute.

We are happy to advise on this before you commit budget, including designs that use amplicon sequencing across a full cohort and shotgun on a targeted subset.

How the analysis runs

• Quality control, adapter and quality trimming, and removal of host reads
• For amplicon data: exact sequence variant inference with DADA2 or Deblur, rather than clustering into OTUs
• Taxonomic assignment against SILVA, Greengenes2, UNITE or RDP as appropriate to the marker
• For shotgun data: read-based profiling with Kraken2 and Bracken or MetaPhlAn, and assembly with metaSPAdes or MEGAHIT where genome recovery is the goal
• Binning into metagenome-assembled genomes with quality assessment via CheckM
• Functional annotation against KEGG, COG, CAZy and CARD
• Diversity analysis and differential abundance using compositionally aware methods

Why compositional statistics matter here

Sequencing measures relative, not absolute, abundance. If one taxon blooms, every other taxon appears to decrease as a proportion even when its true cell count has not changed. Applying standard tests to this kind of data produces false positives, and it is one of the most common errors in published microbiome work.

We use methods designed for compositional data — ALDEx2, ANCOM-BC or centred log-ratio transformation — and will tell you when a question genuinely requires absolute quantification by qPCR or flow cytometry instead.

Data we accept

Raw FASTQ from Illumina, Nanopore or PacBio; existing feature or OTU tables; or public accessions from SRA, ENA and MG-RAST. Human gut, skin and oral microbiome, soil, marine, rhizosphere, built environment, food and industrial samples are all routine.