Contamination-Aware

For 15+ years, Vaiomer has developed contamination-aware methods specifically for challenging microbiome samples.

From sample-specific extraction to adapted PCR and systematic controls, every step is designed to maximize microbial signal and minimize contamination.

16S rRNA Gene Sequencing

16S rRNA gene sequencing (16S Metabarcoding) characterizes bacterial composition and diversity by targeting hypervariable regions of the 16S rRNA gene, ranging from short-read approaches (V3-V4, V1-V3, or a custom design) to long-read sequencing encompassing several regions or the complete gene (full 16S). This approach provides alpha diversity and beta diversity analyses, reliable taxonomic resolution up to the genus level and broad bacterial coverage, at a turnaround suited to the majority of microbiome studies.

Fungal Profiling: ITS Sequencing of the Mycobiome

Fungal communities, collectively termed the mycobiome, are characterized through sequencing of the Internal Transcribed Spacer regions (ITS1, ITS2, or both with full-length sequencing), providing species-level resolution across a wide range of tissue types. Because fungal cell walls are resistant to standard extraction methods, we employ our optimized protocols adapted to these structures. ITS Sequencing is particularly relevant wherever fungal communities are implicated, whether in health, safety or environmental contexts.

Microbiome Quantification: qPCR, dPCR & PCR Arrays

Profiling approaches identify which taxa are present and their proportions; quantification approaches determine their abundance. Using universal or taxon-specific markers, qPCR, digital PCR and PCR arrays enable precise measurement of microbial loads or functional gene content, valuable for validating microbiome findings, monitoring treatment effects, or conducting rapid, cost-effective multi-target screening. The three techniques are complementary:

• qPCR for robust, routine quantification of a small number of targets
• Digital PCR for ultra-sensitive, absolute quantification
• PCR arrays for simultaneous multi-target analysis

Targets range from universal bacterial markers (16S) to taxon-specific, fungal or other eukaryotic probes, and custom functional or virulence gene assays, including in-house primer and probe design.

Distinguishing Living Microbes from Residual DNA

Standard DNA extraction does not differentiate living microorganisms from relic DNA, genetic material that persists after cells are no longer viable, but is still amplified alongside DNA from living cells. When distinguishing viable from non-viable microorganisms is relevant to your research question, we offer viability-based analysis: a selective DNA-intercalating dye treatment, such as Propidium monoazide (PMA), excludes DNA from dead or membrane-compromised cells prior to extraction. This ensures that the results generated by our sequencing or quantification methods reflect only microorganisms that are genuinely present within the sample.

Bioinformatics & Statistical Analysis

All our sequencing-based analyses include bioinformatics processing structured around the biological groups defined for the study, with figures and differential statistics provided to support scientific conclusions. For analyses extending beyond standard deliverables, whether based on data generated by Vaiomer or by external sources, our bioinformatics team offers a comprehensive range of solutions, from established pipelines to fully customized analysis.
Our computational pipelines encompass taxonomic profiling, functional annotation, statistical analysis and multi-omics integration, across 16S/ITS amplicon, shotgun metagenomic, host genomic and transcriptomic (RNA-Seq) data. Deliverables include for instance diversity metrics, differential abundance testing, pathway enrichment and publication-ready figures, with statistical approaches matched to study design.

Scientific Support, From Design to Interpretation

The generation of reliable data represents only one component of a successful microbiome study. Across all Vaiomer services, a dedicated scientist remains engaged with each project to support the translation of data into a substantiated answer to the underlying research question.

Even once processed by our team, microbiome data can be time-consuming to fully exploit, and requires specific scientific expertise. When this expertise is not available internally or through your collaborators, our scientists, drawing on a range of scientific backgrounds, are available to partner with you and provide this support as a dedicated, stand-alone service:

• • Upstream, in experimental design. Guidance on tissue selection, sample numbers, group structure and standards, for studies still at the design stage.
  • Downstream, in results interpretation and valorization. Once your report has been delivered, our scientists can analyze the data generated in the context of your broader study, review the relevant literature, compare your results to previously available data, and help you identify the conclusions your dataset does, and does not, support.

With more than 15 years of microbiome experience and over 50 publications, our team supports both internally generated data and datasets originating from external or partner laboratories, from experimental design through final interpretation.

Thanks to our recognized scientific expertise, Vaiomer is also accredited under France’s Crédit d’Impôt Recherche (CIR) scheme, allowing private companies based in France to include part of their spending on our services in their research tax credit claim.

DOCUMENTARY RESOURCES

Bio-informatics Services

Vaiomer provides advanced bioinformatics support to help you unlock the full value of your data and accelerate your research projects.

Our bioinformatics services cover a wide range of applications, from NGS data analysis and custom assay design to pipeline development and data management.

Advanced Data Analysis

Whether you have newly generated data, historical datasets to reanalyse using the latest tools and databases, or publicly available data to leverage for exploratory or confirmatory studies, Vaiomer can support you throughout the analysis process.

Our expertise covers a broad range of NGS and omics applications, including:

• • Metagenomics, including shotgun metagenomics, metabarcoding (targeted sequencing such as 16S or ITS) and functional profiling
  • Transcriptomics and RNA sequencing (RNA‑seq)
  • Genome assembly and annotation
  • Polymorphism and variant detection
  • Comparative and integrative analysis of multiple datasets
  • Custom assay design
  • Statistical analysis, data visualisation and biological interpretation

DOCUMENTARY RESOURCES

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Microbiome Analysis Services

Beyond the gut, tissue and environmental microbiomes are among the most demanding samples to analyze. A reliable result depends on two factors: a methodology specifically developed for these challenging samples, and the continued involvement of an expert scientist to support rigorous interpretation of the resulting data.

Why Microbiome Analysis Demands Rigor

Most tissue and environmental microbiomes correspond to mid- or low-biomass samples, which present significantly greater analytical challenges than stool samples. Three factors are consistently at play:

• A low microbial-to-host DNA ratio. Microbial DNA can represent a very small fraction of the total DNA extracted, with host DNA predominating. A standard protocol, developed for higher-biomass samples, frequently fails to capture the limited microbial signal present.
• PCR inhibitors. These samples are frequently rich in compounds that inhibit PCR amplification. The lower the microbial biomass, the more amplification efficiency depends on overcoming these inhibitors, and the more a generic protocol is likely to underperform or fail entirely.
• Contamination risk. Low biomass renders these samples highly susceptible to exogenous microbial DNA introduced via reagents, consumables or the environment. At low biomass, such contamination can exceed the biological signal itself, resulting in false positives that may be indistinguishable from an authentic finding.

The method selected, and the rigor with which it is controlled for these three factors, can determine whether a study yields conclusive results or a misleading one. We assist in this choice prior to any laboratory work on your samples, whether they are high, mid or low biomass.

How Vaiomer’s unique technology “contamination-aware approach” overcomes conventional limitations?

Our Contamination-Aware Approach

At the core of every Vaiomer service is a contamination-aware methodology, developed and refined over 15 years specifically for mid- and low-biomass samples. This methodology was designed to address each of the three challenges described above:

• Reagents adapted against contamination. We employ molecular reagents, modified in-house, to reduce background contaminant DNA before it can affect the analysis.
• Sample-specific extraction. Tissue, biofluid, swab and environmental matrices each require a distinct combination of reagents and steps. We select and validate this combination for each project, rather than relying on a single standardized kit, to maximize microbial DNA recovery while limiting host DNA and inhibitor carryover.
• PCR protocols adapted for low input. Our library preparation and PCR quantification protocols are optimized specifically for mid- and low-biomass amplification, with inputs and cycling conditions adjusted according to each sample’ type.
• Controls at each stage of the pipeline. Except for high biomass samples, we apply negative controls systematically throughout our pipeline, and directly at sampling whenever protocol allows, enabling eventual contamination to be identified and, where necessary, subtracted rather than reported as a result.
• 15 years of accumulated experience. Interpretation of high, mid- and low-biomass data remains inherently complex, regardless of protocol quality. Our team draws on 15 years of results across sample types to assess the significance of borderline signals, and to identify results warranting further verification prior to inclusion as study conclusions.

This contamination-aware approach underlies each of the microbiome analysis services presented below, which address different scientific questions and different technical constraints related to the starting sample.