Different culture media and purification methods unveil the core proteome of <i>Propionibacterium freudenreichii</i>-derived extracellular vesicles

Rodovalho, Vinícius de Rezende; Luz, Brenda Silva Rosa da; Nicolas, Aurélie; Jardin, Julien; Briard‐Bion, Valérie; Folador, Edson Luiz; Santos, Anderson; Jan, Gwénaël; Loir, Yves Le; Azevedo, Vasco; Guédon, Éric

doi:10.1093/femsml/uqad029

Cited by 5 publications

(1 citation statement)

References 129 publications

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“…Interestingly, the majority of the differentially abundant ribosomal proteins identified here have previously been identified from the vesicles produced by PFR (5, 55, 56). In these studies, the proteins delivered by vesicles contributed to translation, ribosomal structure, and biogenesis.…”

Section: Resultsmentioning

confidence: 82%

Aerobic Adaptation and Metabolic Dynamics ofPropionibacterium freudenreichiiDSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis

Loivamaa,

Sillanpää,

Deptula

et al. 2024

Preprint

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Propionibacterium freudenreichii(PFR) DSM 20271 is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271 to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably of B12 vitamin, pseudovitamin-B12, propionate and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, TCA cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for sensing and adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and α-ketoglutarate availability. Furthermore, in liquid culture, FeSO4supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding ofPFR's physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications.

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Section: Resultsmentioning

confidence: 82%

Aerobic Adaptation and Metabolic Dynamics ofPropionibacterium freudenreichiiDSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis

Loivamaa,

Sillanpää,

Deptula

et al. 2024

Preprint

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Bacterial extracellular vesicles at the interface of gut microbiota and immunity

Melo-Marques,

Cardoso,

Empadinhas

2024

Gut Microbes

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Bacterial extracellular vesicles (BEVs) are nano-sized lipid-shielded structures released by bacteria and that play an important role in intercellular communication. Their broad taxonomic origins and varying cargo compositions suggest their active participation in significant biological mechanisms. Specifically, they are involved in directly modulating microbial ecosystems, competing with other organisms, contributing to pathogenicity, and influencing the immunity of their hosts. This review examines the mechanisms that underlie the modulatory effects of BEVs on gut dynamics and immunity. Understanding how BEVs modulate microbiota composition and functional imbalances is crucial, as gut dysbiosis is implicated not only in the pathogenesis of various gastrointestinal, metabolic, and neurological diseases, but also in reducing resistance to colonization by enteric pathogens, which is particularly concerning given the current antimicrobial resistance crisis. This review summarizes recent advancements in the field of BEVs to encourage further research into these enigmatic entities. This will facilitate a better understanding of intra- and interkingdom communication phenomena and reveal promising therapeutic approaches.

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A comprehensive review of the characterization, host interactions, and stabilization advancements on probiotics: Addressing the challenges in functional food diversification

Fentie,

Lim,

Jeong

et al. 2024

Comp Rev Food Sci Food Safe

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The demand for functional food is rising in tandem with the prevalence of chronic diseases. Probiotics play a crucial role in functional food development, yet their ability to confer health benefits to the host remains a topic of debate according to Food and Agriculture Organization/World Health Organization requirements. The application of culturomics, innovative isolation techniques, within the realm of probiotics is increasingly deemed essential for fully harnessing the latent potential of microbial reservoirs. Nevertheless, its application remains confined predominantly to human fecal sources. Following the integration of probiogenomics, significant advancements have been made in the safety assessment of probiotics. However, the adoption of novel probiotic microorganisms has yet to match the requisite pace. Progress in research concerning host–probiotic interactions by employing omics technologies, particularly in animal models, is notable. Nonetheless, the comprehensive elucidation of mechanisms of action and human trial studies are lagging behind. Additionally, the viability of probiotics, spanning from their production as functional foods to their transit to the human colon, has markedly improved through encapsulation techniques. Nevertheless, opportunities for exploration persist regarding alternative coating materials and diverse encapsulation methodologies. Furthermore, there is a discernible transition in the domain of probiotic‐based functional foods, shifting away from a primarily dairy‐centric focus toward inclusion in a broader array of food categories. This comprehensive review addresses critical issues ranging from isolation sources and novel techniques to the final functional food developments. while doing so, it explores probiogenomics applications for probiotic characterization, investigations into host–probiotic interactions, and strategies for probiotic stabilization under harsh environmental conditions.

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Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles

Cited by 5 publications

References 129 publications

Aerobic Adaptation and Metabolic Dynamics ofPropionibacterium freudenreichiiDSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis

Aerobic Adaptation and Metabolic Dynamics ofPropionibacterium freudenreichiiDSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis

Bacterial extracellular vesicles at the interface of gut microbiota and immunity

A comprehensive review of the characterization, host interactions, and stabilization advancements on probiotics: Addressing the challenges in functional food diversification

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