Global transcriptomic analysis of functional oligosaccharide metabolism in Pediococcus pentosaceus

Symbiotic microparticles produced through spray-drying-induced in situ alginate crosslinking for the preservation of Pediococcus pentosaceus viability

Probiotic microorganisms are a promising alternative to antibiotics in preventing and treating bacterial infections. Within the probiotic group, the lactic acid bacteria (LAB)stand out for their health benefits and for being recognized as safe by regulatory agencies. However, these microorganisms are sensitive to various environmental conditions, including the acidic environment of the stomach. Faced with these obstacles, this work aimed to promote the symbiotic microencapsulation of LAB in a composite matrix of alginate and prebiotics to enhance their survival and improve their probiotic activity during gastrointestinal transit. We evaluated the effect of inulin, fructo-oligosaccharides (FOS) and mannan-oligosaccharides (MOS) as prebiotic sources on the growth of Pediococcus pentosaceus LBM34 strain, finding that MOS favored LAB growth and maintenance of microencapsulated cell viability. The symbiotic microparticles were produced using the spray-drying technique with an average size of 10 μm, a smooth surface, and a composition that favored the stabilization of live cells according to the FTIR and the thermal analysis of the material. The best formulation was composed of 1 % of alginate, 10 % MOS and 1 % M10 (% w/v), which presented notable increases in the survival rates of the probiotic strain in both alkaline and acidic conditions. Therefore, this industrially scalable approach to symbiotic LAB microencapsulation can facilitate their growth and colonization within the host. This effort aims to contribute to reducing antibiotic reliance and mitigating the emergence of new zoonotic diseases, which pose significant challenges to public health.

The rise of the sourdough: Genome-scale metabolic modeling-based approach to design sourdough starter communities with tailored-made properties

Sourdough starters harbor microbial consortia that benefit the final product's aroma and volume. The complex nature of these spontaneously developed communities raises challenges in predicting the fermentation phenotypes. Herein, we demonstrated for the first time in this field the potential of genome-scale metabolic modeling (GEMs) in the study of sourdough microbial communities. Broad in-silico modeling of microbial growth was applied on communities composed of yeast (Saccharomyces cerevisiae) and different Lactic Acid Bacteria (LAB) species, which mainly predominate in sourdough starters. Simulations of model-represented communities associated specific bacterial compositions with sourdough phenotypes. Based on ranking the phenotypic performances of different combinations, Pediococcus spp. - Lb. sakei group members were predicted to have an optimal effect considering the increase in S. cerevisiae growth abilities and overall CO2 secretion rates. Flux Balance Analysis (FBA) revealed mutual relationships between the Pediococcus spp. - Lb. sakei group members and S. cerevisiae through bidirectional nutrient dependencies, and further underlined that these bacteria compete with the yeast over nutrients to a lesser extent than the rest LAB species. Volatile compounds (VOCs) production was further modeled, identifying species-specific and community-related VOCs production profiles. The in-silico models' predictions were validated by experimentally building synthetic sourdough communities and assessing the fermentation phenotypes. The Pediococcus spp. - Lb. sakei group was indeed associated with increased yeast cell counts and fermentation rates, demonstrating a 25 % increase in the average leavening rates during the first 10 fermentation hours compared to communities with a lower representation of these group members. Overall, these results provide a possible novel strategy towards the de-novo design of sourdough starter communities with tailored-made characterizations, including a shortened leavening period.

Synergy between oligosaccharides and probiotics: From metabolic properties to beneficial effects

Synbiotic is defined as the dietary mixture that comprises both probiotic microorganisms and prebiotic substrates. The concept has been steadily gaining attention owing to the rising recognition of probiotic, prebiotics, and gut health. Among prebiotic substances, oligosaccharides demonstrated considerable health beneficial effects in varieties of food products and their combination with probiotics have been subjected to full range of evaluations. This review delineated the landscape of studies using microbial cultures, cell lines, animal model, and human subjects to explore the functional properties and host impacts of these combinations. Overall, the results suggested that these combinations possess respective metabolic properties that could facilitate beneficial activities therefore could be employed as dietary interventions for human health improvement and therapeutic purposes. However, uncertainties, such as applicational practicalities, underutilized analytical tools, contradictory results in studies, unclear mechanisms, and legislation hurdles, still challenges the broad utilization of these combinations. Future studies to address these issues may not only advance current knowledge on probiotic-prebiotic-host interrelationship but also promote respective applications in food and nutrition.

Organelle 16S rRNA amplicon sequencing enables profiling of active gut microbiota in murine model

High-throughput sequencing of ribosomal RNA (rRNA) amplicons has served as a cornerstone in microbiome studies. Despite crucial implication of organelle 16S rRNA measurements to host gut microbial activities, genomic DNA (gDNA) was overwhelmingly targeted for amplicon sequencings. Although gDNA could be a reliable resource for gene existing validation, little information is revealed in regard to the activity of microorganisms owing to the limited changes gDNA undertaken in inactive, dormant, and dead bacteria. We applied both rRNA- and gDNA-derived sequencings on mouse cecal contents. Respective experimental designs were verified to be suitable for nucleic acid (NA) purification. Via benchmarking, mainstream 16S rRNA hypervariable region targets and reference databases were proven adequate for respective amplicon sequencing study. In phylogenetic studies, significant microbial composition differences were observed between two methods. Desulfovibrio spp. (an important group of anaerobic gut microorganisms that has caused analytical difficulties), Pediococcus spp., and Proteobacteria were drastically lower as represented by gDNA-derived compositions, while microbes like Firmicutes were higher as represented by gDNA-derived microbiome compositions. Also, using PICRUSt2 as an example, we illustrated that rRNA-derived sequencing might be more suitable for microbiome function predictions since pathways like sugar metabolism were lower as represented by rRNA-derived results. The findings of this study demonstrated that rRNA-derived amplicon sequencing could improve identification capability of specific gut microorganisms and might be more suitable for in silico microbiome function predictions. Therefore, rRNA-derived amplicon sequencings, preferably coupled with gDNA-derived ones, could be used as a capable tool to unveil active microbial components in host gut. KEY POINTS: • Conventional pipelines were adequate for the respective amplicon sequencing study • Groups, such as Desulfovibrio spp., were differently represented by two methods • Comparative amplicon sequencings could be useful in host active microbiota studies.

Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress

Stress physiology of lactic acid bacteria (LAB) is crucial to their ecological fitness and applicational implications. As a self-imposed stress, lactic acid is the major final metabolic product of LAB and its accumulation can be detrimental to bacterial cells. However, the relationship between LAB carbohydrate metabolism, the primary energy supplying bioactivities, and lactic acid stress responses is not fully understood. Pediococcus pentosaceus has been recognized as an important cell factory and demonstrated probiotic activities. This study investigated behavior of P. pentosaceus under lactic and acetic acid stresses, particularly with supplementations of metabolizable carbohydrates. Lactic and acetic acid retain similar growth stagnation effect, and both resulted in cell death in P. pentosaceus. All metabolizable carbohydrates improved bacterial survival compared to lactic acid control, while xylooligosaccharides (XOS) exerted the highest viability protective efficacy, 0.82 log CFU/mL higher population survived than other carbohydrates after 30 h of incubation. RNA-seq pipeline showcased the intensive global transcriptional responses of P. pentosaceus to lactic acid, which caused significant regulations (more than 2 Log₂ fold) of 16.5% of total mRNA coding genes. Glucose mainly led to gene suppressions (83 genes) while XOS led to gene up-regulations (19 genes) under lactic acid stress. RT-qPCR study found that RNA polymerase-centered transcriptional regulation is the primary regulatory approach in evaluated culture conditions. The synergy between lactic acid stress and carbohydrate metabolism should be attentively contemplated in future studies and applications.

Pediocin PA-1 production by Pediococcus pentosaceus ET34 using non-detoxified hemicellulose hydrolysate obtained from hydrothermal pretreatment of sugarcane bagasse

Listeria monocytogenes is one of the foodborne pathogens of most concern for food safety. To limit its presence in foods, bacteriocins have been proposed as natural bio-preservatives. Herein, a bacteriocin was produced on hemicellulose hydrolysate of sugarcane bagasse by Pediococcus pentosaceous ET34, whose genome sequencing revealed an operon with 100% similarity to that of pediocin PA-1. ET34 grown on hydrolysate-containing medium led to an increase in the expression of PA-1 genes and a non-optimized purification step sequence resulted in a yield of 0.8 mg·L^-1 of pure pediocin (purity > 95%). Culture conditions were optimized according to a central composite design using temperature and hydrolysate % as independent variables and validated in 3-L Erlenmeyers. Finally, a process for scaled-up implementation by sugar-ethanol industry was proposed, considering green chemistry and biorefinery concepts. This work stands up as an approach addressing a future proper sugarcane bagasse valorisation for pediocin production.