Bioinformatics & Genomics for Industrial Fermentation
Characterize microbial strains, secure their genetic identity and turn sequencing data into actionable decisions throughout fermentation development and scale-up.
Microbial strains are at the heart of industrial fermentation performance. Their identity, genetic content, stability and interaction with the process environment can directly influence productivity, quality and reproducibility.
Biomanda combines biological expertise, bioinformatics and data mining to help R&D and production teams understand their microorganisms and make evidence-based decisions from laboratory development to industrial scale-up.
Questions we help answer
Is the production strain correctly identified and free from unexpected organisms?
Which genes, pathways or genomic features may explain a phenotype of interest?
How does a candidate strain differ from reference, parental or competing strains?
Has the strain remained genetically stable after passaging, storage or scale-up?
Can a specific and robust PCR/qPCR assay be designed for monitoring?
Which microorganisms are present in the fermentation ecosystem or production environment?
R&D decision support
Our analyses are designed around your scientific and operational questions. Results are translated into clear conclusions, documented evidence and practical recommendations that can support strain selection, process investigation, quality strategy and further experimental work.
Microbial strain characterization
Whole-genome sequencing data provide a detailed view of the identity and functional potential of bacterial, yeast and fungal strains used in fermentation.
Identification and genome analysis
quality control and curation of sequencing reads;
de novo genome assembly and assembly assessment;
taxonomic identification and confirmation of strain identity;
genome annotation and functional interpretation;
detection of plasmids, mobile genetic elements and relevant genomic islands;
screening for genes associated with metabolic functions, resistance, virulence or safety;
search for contamination or mixed-strain signals;
integration of public scientific databases and literature-derived information.
Deliverables
Depending on the project, deliverables may include curated sequence files, assemblies, annotated genomes, quality metrics, strain identity results, tables of detected features, genome visualizations and a tailored interpretation report.
Comparative genomics and strain selection
Comparative genomics helps distinguish closely related strains, identify genetic differences and prioritize candidates for experimental validation or industrial development.
Comparative analyses
whole-genome comparisons and average nucleotide identity analysis;
phylogenomic positioning and relationship assessment;
core-genome, accessory-genome and pangenome analyses;
SNP, small insertion/deletion and structural variation detection;
presence/absence analysis of genes, pathways and mobile elements;
comparison with parental, reference, historical or competitor strains;
genotype-to-phenotype hypothesis generation;
selection of discriminating markers for traceability or monitoring.
From genomic differences to actionable hypotheses
We interpret relevant variations in their biological context to support the investigation of productivity, substrate use, stress tolerance, by-product formation, robustness and other fermentation-related traits.
Strain stability and process consistency
Repeated cultivation, long-term storage and industrial scale-up can select genetic changes. Genomic monitoring can reveal whether a production strain has diverged from its reference or master stock.
Stability studies
comparison of master, working and production cell banks;
analysis of isolates collected before and after serial passaging;
detection and annotation of mutations arising during fermentation development;
assessment of plasmid presence, loss or rearrangement;
investigation of unexpected phenotypic or performance changes;
definition of genomic markers for routine identity and stability monitoring.
Supporting risk assessment
We help distinguish biologically relevant changes from sequencing noise and neutral variation. The resulting evidence can guide confirmatory experiments, strain-bank management and decisions about process continuation or investigation.
Molecular detection, microbiome and metagenomics
PCR / qPCR
Design or improve primers and probes for strain-specific detection, identity confirmation, contamination monitoring or process follow-up. In silico specificity, inclusivity and exclusivity assessments reduce empirical trial and support robust assay development.
Microbiome analysis
Characterize bacterial or fungal communities using metabarcoding approaches, compare batches or process stages and identify organisms associated with performance, variability or contamination.
Metagenomics
Use shotgun metagenomics to investigate both taxonomic composition and functional potential, reconstruct microbial genomes and explore pathways involved in complex fermentation ecosystems.
Typical applications
routine verification of production strains;
detection and investigation of contaminants;
monitoring of mixed or spontaneous fermentations;
comparison of microbiomes across sites, batches, raw materials or process conditions;
identification of microbial indicators linked to product quality or process performance.
A project workflow adapted to your fermentation challenge
1. Scientific framing
We clarify the biological question, available samples and data, expected decisions, constraints and success criteria.
2. Study design
We recommend a suitable sequencing, molecular biology and bioinformatics strategy, independently of technology providers.
3. Data analysis
We build a reproducible workflow combining quality control, genomics, statistics, comparative analysis and biological databases.
4. Interpretation
We connect genomic and microbial results to the fermentation question and identify limitations, priorities and testable hypotheses.
5. Reporting
You receive clear results, documented methods, figures, data tables and a report tailored to both scientific and decision-making needs.
Industries and fermentation applications
Food & beverage
Industrial biotechnology
Enzymes & ingredients
Probiotics & cultures
Environmental biotechnology
Discuss your industrial fermentation project
Whether you need to characterize a new strain, compare production candidates, investigate instability, develop a PCR/qPCR assay or understand a complex fermentation microbiome, Biomanda can build a tailored analysis strategy around your objectives.
