Comparative Genomic, Metabolic and Transcriptomic Profiling of Bacterial Isolates Reveals Strain-Specific Adaptation and Safety Traits
- 1Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland
- 2Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
Abstract
Food-associated microorganisms represent a diverse reservoir of bacterial strains with functional traits potentially relevant to host–microbiome interactions, stress resilience, metabolic processes, and microbial competition. In this study, we performed a multi-omics characterization of food-origin bacterial isolates to identify a potential candidate strain for further studies on microbiome–microgreens interactions. Over one hundred bacterial isolates were initially recovered from various food products and subjected to molecular screening, followed by whole-genome sequencing, metabolic profiling, transcriptomic characterization and morphological analysis of selected strains. Comparative characterization revealed significant differences among the strains. Among the tested isolates, strain B107/23, identified as Priestia megaterium (formerly Bacillus megaterium), showed consistently high numbers of genes associated with stress responses, nutrient uptake, plant growth-promoting traits, and colonization mechanisms. Phenotypic characterization later demonstrated high metabolic flexibility and a low substrate stress index, while transcriptomic profiling revealed the expression of genes associated with stress responses and metabolic activity. Overall, the integration of genomic, phenotypic, and transcriptomic results distinguished B107/23 as the most promising candidate among the tested isolates and revealed the molecular traits potentially relevant to interactions between the microbe and the host. These findings provide a basis for the validation of the selected strain in microgreens systems, including studies addressing plant stress resilience and post-harvest quality.
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BibTeX
@article{baranska2026comparative,
title = {{Comparative Genomic, Metabolic and Transcriptomic Profiling of Bacterial Isolates Reveals Strain-Specific Adaptation and Safety Traits}},
author = {Daria Barańska and Jacek Panek and Giorgia Pertile and Agata Gryta and Sylwia Różalska and Magdalena Frąc},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = sep,
doi = {10.3390/ijms27198734},
url = {https://www.mdpi.com/1422-0067/27/19/8734},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Comparative Genomic, Metabolic and Transcriptomic Profiling of Bacterial Isolates Reveals Strain-Specific Adaptation and Safety Traits
AU - Daria Barańska
AU - Jacek Panek
AU - Giorgia Pertile
AU - Agata Gryta
AU - Sylwia Różalska
AU - Magdalena Frąc
PY - 2026
DA - 2026/09/30
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27198734
UR - https://www.mdpi.com/1422-0067/27/19/8734
AB - Food-associated microorganisms represent a diverse reservoir of bacterial strains with functional traits potentially relevant to host–microbiome interactions, stress resilience, metabolic processes, and microbial competition. In this study, we performed a multi-omics characterization of food-origin bacterial isolates to identify a potential candidate strain for further studies on microbiome–microgreens interactions. Over one hundred bacterial isolates were initially recovered from various food products and subjected to molecular screening, followed by whole-genome sequencing, metabolic profiling, transcriptomic characterization and morphological analysis of selected strains. Comparative characterization revealed significant differences among the strains. Among the tested isolates, strain B107/23, identified as Priestia megaterium (formerly Bacillus megaterium), showed consistently high numbers of genes associated with stress responses, nutrient uptake, plant growth-promoting traits, and colonization mechanisms. Phenotypic characterization later demonstrated high metabolic flexibility and a low substrate stress index, while transcriptomic profiling revealed the expression of genes associated with stress responses and metabolic activity. Overall, the integration of genomic, phenotypic, and transcriptomic results distinguished B107/23 as the most promising candidate among the tested isolates and revealed the molecular traits potentially relevant to interactions between the microbe and the host. These findings provide a basis for the validation of the selected strain in microgreens systems, including studies addressing plant stress resilience and post-harvest quality.
SN - 1422-0067
ER -