From a microbial community to actionable conclusions: which species are present, which genomes make it up, and which genes (resistance, virulence, function) they encode. Contract research with the rigor of a clinical lab, validated against certified reference material.
Microbiome analysis powers translational research, intervention trials and pathogen characterization. We work as a research CRO; we do not issue regulated clinical diagnostics.
Associate microbial species and functions with clinical phenotypes to uncover candidate biomarkers.
Effect of probiotics, diet or drug on the microbiota: before/after and longitudinal analysis with statistics.
Genome, strain typing and resistance of an isolate or of the community in a clinical sample.
How the microbiota metabolizes or modulates treatment response (pharmacomicrobiomics).
Resistome of a patient or cohort: which resistance genes circulate and in which organisms.
Gut, oral, skin, vaginal or respiratory: niche-specific composition and function.
Species identification and abundance from shotgun sequencing, culture-free. Fast, sensitive and with expert noise filtering.
K-mer classification (Kraken2) and abundance re-estimation (Bracken): species table and percentages.
Marker-gene confirmation (MetaPhlAn) to reduce false positives in species-level calls.
Differential abundance between groups or timepoints (before/after, treatment) with statistics.
Alpha and beta diversity indices, ordinations (PCoA) and community structure.
Navigable Krona charts and MultiQC report, plus CSV tables for your own analysis.
Expert criteria (relatedness, threshold, multi-method consensus) to separate real signal from database noise.
From raw FASTQ to species table and figures, with host DNA removal.
FastQC + fastp; quality trimming
Remove human DNA
Kraken2 (+MetaPhlAn)
Bracken
Krona, MultiQC, statistics
| Parameter | Default specification |
|---|---|
| Technology | Shotgun metagenomics (Illumina paired-end); 16S amplicon on request |
| Input formats | FASTQ (also BAM/CRAM); or reanalysis of public data (SRA/ENA) |
| Tools | Kraken2 + Bracken + Krona; optional MetaPhlAn for high specificity |
| Deliverables | Species table (CSV), Krona charts, MultiQC and interpreted report (PDF) |
| Validation | Pipeline validated against certified reference material (ATCC MSA-1003) |
De novo assembly and reconstruction of complete genomes of the community members, culture-free. Enables strain typing and reliable functional analysis.
MEGAHIT and metaSPAdes to reconstruct contigs from the reads.
Six binners (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, COMEBin, MetaBinner) to group contigs into genomes.
Completeness and contamination of each genome per MIMAG standard.
GTDB-Tk + ANI identity: species and strain-level comparison.
Prokka (Prodigal): gene catalogue, products, tRNA/rRNA.
Bin refinement (DAS_Tool) and chimera detection (GUNC) for publication-grade genomes.
Screening of the genomes against curated databases to deliver real capabilities —resistance, virulence, biosynthesis— not gene-name predictions.
Confirmed resistance genes per genome and per antibiotic class.
Confirmed virulence factors: toxins, adhesins, capsule, secretion.
Mining of biosynthetic clusters and peptides: candidates against multidrug-resistant bugs.
The microbiome challenge isn't producing a species list, it's knowing which ones to trust. We apply the rigor of a clinical lab to any sample: characterized limit of detection, false-positive filtering and full traceability.