Comparative Genomics of Microbial Strains

Understand what differentiates your microbial strains

Closely related microorganisms can display major differences in performance, safety, resistance, stability or ecological adaptation. Comparative genomics identifies the genetic features that strains share and those that make each strain unique.

Biomanda designs tailored comparative analyses for bacteria, yeasts, fungi and other microorganisms. We combine rigorous bioinformatics with biological interpretation to produce results that can directly support research, strain selection and product development.

Questions we help answer

How closely related are the strains under investigation?
Which genes or genomic regions are specific to a strain or group?
Which mutations may explain a phenotypic difference?
Has a strain changed during storage, passaging or production?
Are genes associated with safety, resistance or virulence present?
Which genomic markers can distinguish and monitor selected strains?

Decision-oriented analysis

The analysis strategy is built around your biological question, experimental design and intended decision. We help separate relevant signals from background diversity and translate genomic findings into testable hypotheses and practical recommendations.

Genome assembly and strain characterization

Reliable comparisons depend on consistent, high-quality genomic data. We evaluate each dataset and apply an analysis workflow adapted to the sequencing technology, organism and expected resolution.

From sequencing reads to curated genomes

quality control, trimming and filtering of sequencing reads;
de novo assembly from short reads, long reads or hybrid datasets;
assembly quality, completeness and contamination assessment;
taxonomic identification and confirmation of strain identity;
consistent structural and functional genome annotation;
detection of plasmids, prophages and mobile genetic elements;
search for mixed cultures, contamination or unexpected sequences;
selection and curation of suitable public reference genomes.

Comparable data, robust conclusions

All genomes are processed using harmonized criteria to limit methodological bias. Publicly available genomes can be incorporated after quality and metadata review to provide a broader taxonomic or functional context.

Phylogenomics, core genome and pangenome

Genome-wide comparisons provide the resolution needed to position strains, study their evolutionary relationships and describe the diversity of a species or collection.

Relationship and population analyses

average nucleotide identity and genome similarity measurements;
whole-genome and core-genome phylogenetic reconstruction;
core-genome multilocus sequence typing and strain clustering;
identification of clades, lineages and closely related isolates;
assessment of genetic distances within a collection;
comparison with reference, historical or environmental strains.

Pangenome analysis

definition of core, accessory and strain-specific genes;
gene presence/absence matrices and strain clustering;
identification of functions enriched in a phenotype or group;
exploration of genome plasticity and horizontal gene transfer;
selection of discriminating genomic markers.

Genetic variants and functional interpretation

Biologically meaningful differences can involve a single nucleotide, a gene gain or loss, a mobile element or a larger genome rearrangement. We select the appropriate level of analysis for your strains and sequencing data.

Variant detection

SNP and small insertion/deletion analysis;
structural variant and genome rearrangement detection;
copy-number and gene presence/absence assessment;
plasmid and mobile element comparison;
mutation analysis across passages, time points or conditions;
prioritization of variants according to their predicted impact.

Functional analysis

comparison of genes, pathways and metabolic capabilities;
screening for resistance, virulence and safety-related determinants;
analysis of functions associated with stress tolerance or adaptation;
investigation of genotype-to-phenotype associations;
scientific database and literature mining;
design of PCR/qPCR markers to validate or track genomic differences.

Comparative genomics applications

Strain selection

Compare candidate strains, identify distinctive functions and prioritize microorganisms for laboratory validation, product development or industrial use.

Identity & traceability

Confirm strain identity, distinguish closely related isolates and identify specific markers for molecular detection, traceability or routine monitoring.

Genotype & phenotype

Connect genomic differences with observed traits such as productivity, resistance, metabolism, host interaction, quality or environmental adaptation.

Genetic stability

Compare master, working and production strains or serial passages to detect genetic drift and investigate unexpected performance changes.

Safety assessment

Screen genomes for relevant resistance, virulence, toxin or mobile genetic elements and place findings in an appropriate biological context.

Source tracking

Investigate relationships among isolates, identify clusters and support contamination, epidemiology or environmental source-tracking studies.

A comparative genomics workflow tailored to your objectives

1. Project framing

We define the biological question, strains, metadata, reference genomes, sequencing data and decision criteria.

2. Data assessment

We evaluate data quality and comparability, then recommend any additional sequencing or controls required.

3. Comparative analysis

We implement a reproducible workflow combining genome characterization, phylogenomics, variants and functional analyses.

4. Biological interpretation

We prioritize differences according to your phenotype, scientific knowledge and intended application.

5. Results and recommendations

We provide clear conclusions, limitations, follow-up priorities and direct discussion of the results with your team.

Typical deliverables

quality-control and genome assembly reports;
curated genome annotations and comparison tables;
phylogenetic trees and genome similarity matrices;
core, accessory and strain-specific gene results;
annotated SNP and structural variant tables;
functional profiles and prioritized candidate features;
publication-quality figures and a tailored interpretation report;
processed data and documented analysis methods.

Fields of application

Industrial biotechnology
Food & fermentation
Probiotics & cultures
Animal health
Environmental microbiology
Microbial R&D

Discuss your comparative genomics project

Whether you need to compare a few candidate strains or analyze a large microbial collection, Biomanda can design a study adapted to your data, scientific question and required level of resolution.

Contact Biomanda to discuss your strains, sequencing data and research objectives.