Ref H7
Computational Service
Confidence Reported
Scoped After Feasibility Review
Service Overview
Microbiome analysis spans amplicon surveys and deep shotgun metagenomics, and the two answer different questions. We process both: taxonomic profiling, diversity analysis, differential abundance testing with methods appropriate to compositional data, and, for shotgun data, functional pathway reconstruction and assembly of metagenome-assembled genomes. Compositionality, sparsity and contamination are handled explicitly, since ignoring them produces confident findings that do not replicate.
Key Features & Advantages
Compositional Statistics Applied Correctly
Differential abundance testing uses methods designed for compositional, sparse data, which materially changes which taxa are reported as significant.
Contamination Screened
Negative controls and prevalence-based decontamination are used where available, which matters greatly for low-biomass samples such as tissue and blood.
Function As Well As Taxonomy
Shotgun data is profiled for pathways and gene families, because functional capacity is often more biologically informative than a species list.
Design Constraints Stated
Confounders such as batch, extraction kit, diet and medication are identified up front, since they routinely dominate microbiome variation.
Where This Service Is Used
1Comparing microbial communities between disease and control groups
2Assessing microbiome change under an intervention, drug or dietary treatment
3Characterising the microbial composition of an environmental or industrial sample
4Reconstructing metabolic capacity within a community
5Identifying candidate microbial biomarkers for follow-up validation
Methods and Techniques Applied
1Quality control, adapter trimming and host read removal for shotgun data
2Amplicon processing to exact sequence variants with taxonomic assignment against curated references
3Shotgun taxonomic and functional profiling with read-based and assembly-based approaches
4Alpha and beta diversity analysis with appropriate ordination and permutational testing
5Differential abundance analysis using compositional-aware methods with covariate adjustment
6Assembly, binning and quality assessment of metagenome-assembled genomes where scoped
What We Need From You
1Raw sequencing data with the protocol, region amplified where applicable, and platform described
2Complete sample metadata including group, batch, collection method and relevant clinical covariates
3Negative and positive control samples where they were included in the run
4The biological question and which comparisons matter
What You Receive
1Taxonomic abundance tables at every taxonomic rank
2Diversity analyses with ordination plots and statistical testing
3Differential abundance results with effect sizes and adjusted significance
4Functional pathway profiles for shotgun datasets
5Full report with methods, reference database versions and reproducible analysis code
What We Compute and Report
1Taxonomic abundance tables at every rank, with classification confidence
2Alpha and beta diversity metrics with permutational test statistics
3Differential abundance results using compositional-aware statistics with effect sizes
4Functional pathway and gene family abundance profiles for shotgun data
5Assembly and bin quality statistics where genome reconstruction is in scope
Questions We Are Asked Before Scoping
Amplicon or shotgun sequencing?
▸Amplicon sequencing is cheaper and adequate for community composition at genus level. Shotgun sequencing is required for species and strain resolution and for functional profiling. We advise based on the question, ideally before sequencing.
Can microbiome findings establish causation?
▸No. Observational microbiome differences are associations, frequently confounded by diet, medication and collection procedure. Causal claims require intervention or gnotobiotic experiments.
How much sequencing depth is needed?
▸It depends on sample complexity and the question. Shallow shotgun sequencing suffices for composition; assembly and strain-level analysis need far deeper sequencing, which we specify during scoping.
Interpretation and Limitations
Computational predictions prioritise hypotheses; they do not independently establish binding, biological activity, therapeutic efficacy, safety or clinical validity. Performance depends on input quality, target class, the structural evidence available and the applicability domain of the selected methods. Scores used for ranking are comparative devices and should not be read as measured quantities. All deliverables are for research use only and are not intended for diagnostic or therapeutic use.
Is This the Right Service for You?
Choose this when
Microbial community composition differs between groups and needs proper statistics
Functional capacity, not just taxonomy, is part of the question
Low-biomass samples require contamination control to be taken seriously
Consider another service when
Host expression is the real readout
Bulk & Single-Cell RNA-Seq Analysis Metabolite-level consequences are the question
Metabolomics & Mass Spectrometry Analysis What Goes Wrong, and How We Handle It
These are the failure modes that produce confident-looking results which do not survive the next experiment. Each one is designed against rather than discovered afterwards.
Standard differential tests applied to compositional data
Compositional-aware methods are used, which materially changes which taxa come out as significant.
Reagent contamination read as biology in low-biomass samples
Negative controls and prevalence-based decontamination are applied where controls exist, and flagged as a limitation where they do not.
Diet, medication or extraction kit driving the apparent effect
Known confounders are identified at design review and adjusted for, or declared as unresolvable in the given design.
A Worked Example
A disease-associated genus that was a kit artefact
The situation
A study reported a strong disease association for a genus that the team planned to pursue mechanistically.
What the work involved
Negative controls were incorporated, prevalence-based decontamination was applied, and differential abundance was recomputed with compositional methods and covariate adjustment.
What came back
The genus was present in extraction blanks at comparable abundance and did not survive decontamination. Two other taxa, previously below the significance threshold, survived and became the follow-up targets.
Illustrative of the shape this work takes. Details are generalised, no client or target is identified, and scope and outcome vary with the system in question.
Service Workflow
1
Scientific Consultation
We discuss the objective, the decision it supports and the data you hold. Nothing is quoted before we understand what the result has to answer.
2
Feasibility Review
We check that the data, target class and available structural evidence can support the proposed approach, and say plainly where they cannot.
3
Technical Proposal
Scope, methods, deliverables, timeline and price are confirmed in writing, together with the limitations we expect to report.
4
Computation and QC
The analysis runs on pinned tool versions in a containerised environment, with quality checkpoints and method comparison where that is informative.
5
Report and Follow-Up
You receive the ranked results, the documented methods, the limitations and a proposed validation plan, plus support in interpreting them.
Service Process
1
Online Consultation
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2
Solution Matching
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3
Service Contract
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4
Project Execution
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5
Data Delivery
Specifications & Turnaround
Note: ICDMO delivers computational (in silico) services. Results prioritise hypotheses for testing; they do not by themselves establish binding, biological activity, efficacy or safety. All deliverables are for research use only and are not intended for diagnostic or therapeutic use. Downstream experimental work is scoped separately and executed through qualified partners.
Get a Custom Quote
Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your project.
Contact Us Online ConsultationStandard Deliverables
✓Sequence-verified final product
✓Full QC documentation
✓Certificate of Analysis (CoA)
✓Electronic data files
✓Project completion report
Why ICDMO?
Computational CDMO Focus
Reproducible, Versioned Pipelines
Confidence & Limitations Reported
Experiment-Aware Recommendations
Response Within One Business Day