Physicochemical Properties and Microbiome of Vineyard Soils from DOP Ribeiro (NW Spain) Are Influenced by Agricultural Management.

Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of vineyards from DOP Ribeiro on the soil's condition. Samples from soils under three different management systems were collected, and the main soil physicochemical properties were evaluated. A selection of 50 pesticides were investigated by liquid chromatography with tandem mass spectrometry. The bacterial and fungal microbiomes were characterized through amplicon sequencing. The results show that organic agriculture positively influences soil pH and the concentration of some nutrients compared to conventional management. Our microbiome analysis demonstrated that transitioning from conventional to organic management significantly improves several BeCrop® indexes related to key microbial metabolism and soil bio-sustainability. Such a transition does not affect soil alpha diversity, but leads to a higher interconnected microbial network structure. Moreover, differential core genera and species for each management system are observed. In addition, the correlation of the microbiome with geographical distance is evidence of the existence of different microbial terroirs within DOP Ribeiro. Indeed, sustainable management leads to higher nutrient availability and enhances soil health in the short term, while lowering pesticide usage.

Short impact on soil microbiome of a Bacillus amyloliquefaciens QST713 based product that correlates with higher potato yield across USA.

Potato (Solanum tuberosum L.) is considered one of the most widely consumed crops worldwide, due to its high yield and nutritional profile, climate change-related environmental threats and increasing food demand. This scenario highlights the need of sustainable agricultural practices to enhance potato productivity, while preserving and maintaining soil health. Plant growth-promoting bacteria (PGPB) stimulate crop production through biofertilization mechanisms with low environmental impact. For instance, PGPB promote biological nitrogen fixation, phosphate solubilization, production of phytohormones, and biocontrol processes. Hence, these microbes provide a promising solution for more productive and sustainable agriculture. In this study, the effects of Bacillus amyloliquefaciens QST713 based-product (MINUET™, Bayer) were assessed in terms of yield, soil microbiome, potato peel and petiole nutrient profile as a promising PGPB in a wide range of potato cultivars across the United States of America. Depending on the location, potato yield and boron petiole content increased after biostimulant inoculation to maximum of 24% and 14%, respectively. Similarly, nutrient profile in potato peel was greatly improved depending on the location with a maximum of 73%, 62% and 36% for manganese, zinc and phosphorus. Notably, fungal composition was shifted in the treated group. Yield showed strong associations with specific microbial taxa, such as Pseudoarthrobacter, Ammoniphilus, Ideonella, Candidatus Berkiella, Dongia. Moreover, local networks strongly associated with yield, highlighting the important role of the native soil microbiome structure in indirectly maintaining soil health. Our results showed that treatment with B. amyloliquefaciens based product correlated with enhanced yield, with minor impacts on the soil microbiome diversity. Further studies are suggested to disentangle the underlying mechanisms of identified patterns and associations.

Exploring the Gut Microbiome and Metabolome in Individuals with Alopecia Areata Disease.

In recent years, heightened attention has been devoted to unravelling the intricate interplay between genetic and environmental factors shaping the gut microbiota and its significance for human health. This study delves into exploring the plausible connection between Alopecia Areata (AA), an autoimmune disease, and the dynamics of the gut microbiome. Examining a cohort of healthy adults and individuals with AA, both the gut microbiota composition and volatile organic compound (VOC) metabolites from faeces and urine were analysed. While overall microbiota composition showed no significant differences, intra-individual variability revealed distinctions related to age, gender, and pathology status, with AA individuals exhibiting reduced species richness and evenness. Differential abundance analysis identified microbial biomarkers for AA, notably Firmicutes, Lachnospirales, and Blautia, while Coprococcus stood out for healthy individuals. The Data Integration Analysis for Biomarker discovery using Latent Components (DIABLO) method further supported these findings including metabolite biomarkers, such as esters of branched chain fatty acids and branched chain amino acids as predictors for AA, suggesting potential links to oxidative stress. Despite certain limitations, the study highlights the complexity of the gut microbiome and its metabolites in the context of AA, while the biomarkers identified could be useful starting points for upcoming studies.

Identification and Selection of Prospective Probiotics for Enhancing Gastrointestinal Digestion: Application in Pharmaceutical Preparations and Dietary Supplements.

Our study investigated the effectiveness of 446 strains of lactic acid bacteria (LAB) belonging to different species and isolated from diverse sources (food, human, and animal) as potential probiotic candidates, with the perspective of producing dietary supplements or pharmacological formulations suitable for enhancing gastrointestinal digestion. The survival capability of all the isolates under harsh gastrointestinal tract conditions was evaluated, in which only 44 strains, named high-resistant, were selected for further food digestibility investigations. All 44 strains hydrolyzed raffinose and exhibited amino and iminopeptidase activities but at various extents, confirming species- and strain-specificity. After partial in vitro digestion mimicking oral and gastric digestive phases, food matrices were incubated with single strains for 24 h. Fermented partially digested matrices provided additional functional properties for some investigated strains by releasing peptides and increasing the release of highly bio-accessible free phenolic compounds. A scoring procedure was proposed as an effective tool to reduce data complexity and quantitively characterize the probiotic potential of each LAB strain, which could be more useful in the selection procedure of powerful probiotics.

Do nomadic lactobacilli fit as potential vaginal probiotics? The answer lies in a successful selective multi-step and scoring approach.

BACKGROUND: The goal of this study was to create a multi-strain probiotic gel that would foster a lactobacilli-dominated vaginal microbiota in pregnant women and ensure appropriate eubiosis for the newborn. Nomadic lactobacilli (95 strains), mostly isolated from food sources, were preliminarily screened for functional traits before being characterized for their capability to inhibit the two vaginal pathogens Streptococcus agalactiae and Candida albicans, which may lead to adverse pregnancy-related outcomes. Eight best-performing strains were chosen and furtherly investigated for their ability to produce biofilm. Lastly, the two selected potential probiotic candidates were analyzed in vitro for their ability to reduce the inflammation caused by C. albicans infection on the reconstituted human vaginal epithelium (HVE). RESULTS: Lactiplantibacillus plantarum produced both isomers of lactic acid, while Lacticaseibacillus paracasei produced only L-isomer. The production of hydrogen peroxide was strain-dependent, with the highest concentrations found within Lact. paracasei strains. The auto-aggregation capacity and hydrophobicity traits were species-independent. S. agalactiae 88II3 was strongly inhibited both at pH 7.0 and 4.0, whereas the inhibition of C. albicans UNIBZ54 was less frequent. Overall, L. plantarum strains had the highest pathogen inhibition and functional scoring. L. plantarum C5 and POM1, which were selected as potential probiotic candidates also based on their ability to form biofilms, were able to counteract the inflammation process caused by C. albicans infection in the HVE model. CONCLUSIONS: Our multi-step and cumulative scoring-based approach was proven successful in mining and highlighting the probiotic potential of two nomadic lactobacilli strains (L. plantarum C5 and POM1), being applicable to preserve and improve human vaginal health.

Effect of sequential or ternary starters-assisted fermentation on the phenolic and glucosinolate profiles of sauerkraut in comparison with spontaneous fermentation.

This study investigated the effectiveness of two novel started-assisted sauerkraut fermentations in comparison with spontaneous fermentation. Three lactic acid bacteria strains were selected as best starters for sauerkraut processing, based on the complementarity of pro-technological (kinetics of growth and acidification) traits, phenotypic fingerprints through OmniLog Phenotype MicroArray, and phenolics metabolism. The selected strains were applied according to two different fermentation methods based on steering sequential and temporally deferred inoculum of three strains, and ternary simultaneous inoculum. Sequential and ternary starters-assisted fermentations lasted 9 and 7 days, respectively, and were compared to conventional spontaneous fermentation lasting 35 days. Sequential and ternary fermentations resulted in a higher and constant number of lactic acid bacteria compared to spontaneous fermentation, which reflected on the acidification and sugar utilization. Ternary fermentation enhanced phenolic compounds conversion (hydrocaffeic acid, hydroferulic acid, 4-ethyl catechol), ensuring at the same time higher level of aliphatic (glucobrassicanapin) and indole glucosinolates (glucobrassicin) and derivatives(ascorbigen). Short fermentation of sequential and ternary starters-assisted processing caused only slight changes in the sensory profile compared to the spontaneous process, preserved the structural integrity of sauerkraut, and did not affect the colour lightness.

How water-soluble saccharides drive the metabolism of lactic acid bacteria during fermentation of brewers' spent grain.

We proposed a novel phenomic approach to track the effect of short-term exposures of Lactiplantibacillus plantarum and Leuconostoc pseudomesenteroides to environmental pressure induced by brewers' spent grain (BSG)-derived saccharides. Water-soluble BSG-based medium (WS-BSG) was chosen as model system. The environmental pressure exerted by WS-BSG shifted the phenotypes of bacteria in species- and strains-dependent way. The metabolic drift was growth phase-dependent and likely underlay the diauxic profile of organic acids production by bacteria in response to the low availability of energy sources. Among pentosans, metabolism of arabinose was preferred by L. plantarum and xylose by Leuc. pseudomesenteroides as confirmed by the overexpression of related genes. Bayesian variance analysis showed that phenotype switching towards galactose metabolism suffered the greatest fluctuation in L. plantarum. All lactic acid bacteria strains utilized more intensively sucrose and its plant-derived isomers. Sucrose-6-phosphate activity in Leuc. pseudomesenteroides likely mediated the increased consumption of raffinose. The increased levels of some phenolic compounds suggested the involvement of 6-phospho-ß-glucosidases in ß-glucosides degradation. Expression of genes encoding ß-glucoside/cellobiose-specific EII complexes and phenotyping highlighted an increased metabolism for cellobiose. Our reconstructed metabolic network will improve the understanding of how lactic acid bacteria may transform BSG into suitable food ingredients.

Feeding with Sustainably Sourdough Bread Has the Potential to Promote the Healthy Microbiota Metabolism at the Colon Level.

The contribution of sustainably food processing to healthy intestinal microbial functions is of recent acquisition. The sourdough fermentation fits well with the most sustainable bread making. We manufactured baker's yeast (BYB) and sourdough (t-SB30) breads, which first underwent to an in-depth characterization. According to nutritional questionnaires, we selected 40 volunteers adhering to the Mediterranean diet. Data on their fecal microbiota and metabolome allowed the selection of two highly representative fecal donors to separately run the Twin Mucosal-SHIME (Twin M-SHIME) under 2-week feeding with BYB and t-SB30. Bread feeding did not affect the microbial composition at phylum and family levels of both donors, in all Twin M-SHIME colon tracts, and lumen and mucosal compartments. The genus core microbiota showed few significant fluctuations, which regarded the relative abundances of Lactobacillus and Leuconostoc according to feeding with BYB and t-SB30, respectively. Compared with BYB, the content of all short chain fatty acids (SCFA), and isovaleric and 2-methylbutyric acids significantly increased with t-SB30 feeding. This was evident for all Twin M-SHIME colon tracts and both donors. The same was found for the content of Asp, Thr, Glu, GABA, and Orn. The bread characterization made possible to identify the main features responsible for this metabolic response. Compared with BYB, t-SB30 had much higher contents of resistant starch, peptides, and free amino acids, and an inhomogeneous microstructure. We used the most efficient approach to investigate a staple food component, excluding interferences from other dietary factors and attenuating human physiology overlaps. The daily consumption of sourdough bread may promote the healthy microbiota metabolism at colon level. IMPORTANCE Knowledge on environmental factors, which may compose the gut microbiota, and drive the host physiology and health is of paramount importance. Human dietary habits and food compositions are pivotal drivers to assemble the human gut microbiota, but, inevitably, unmapped for many diet components, which are poorly investigated individually. Approximately 30% of the human diet consists of fermented foods and beverages. Bread, a fermented/leavened food, is a basic component of the human diet. Its potential effect on gut microbiota composition and functionality is challenging. In this study, we industrially made baker's yeast and sourdough breads, which were used to feed the Twin Mucosal-SHIME, a worldwide scientifically validated gastrointestinal simulator. Only the consumption of sourdough bread has the potential to enhance the synthesis of short chain fatty acids and free amino acids at the colon level.

Bioprocessed Brewers' Spent Grain Improves Nutritional and Antioxidant Properties of Pasta.

Brewers' spent grain (BSG), the by-product of brewing, was subjected to a xylanase treatment followed by fermentation with Lactiplantibacillus plantarum PU1. Bioprocessed BSG has been used as ingredient to obtain a fortified semolina pasta which can be labeled as "high fiber" and "source of protein" according to the European Community Regulation No. 1924/2006. Compared to native BSG, the use of bioprocessed BSG led to higher protein digestibility and quality indices (essential amino acid index, biological value, protein efficiency ratio, nutritional index), as well as lower predicted glycemic index. Bioprocessing also improved the technological properties of fortified pasta. Indeed, brightfield and confocal laser scanning microscopy revealed the formation of a more homogeneous protein network, resulting from the degradation of the arabinoxylan structure of BSG, and the release of the components entrapped into the cellular compartments. The extensive cell wall disruption contributed to the release of phenols, and conferred enhanced antioxidant activity to the fortified pasta. The persistence of the activity was demonstrated after in vitro-mimicked digestion, evaluating the protective effects of the digested pasta towards induced oxidative stress in Caco-2 cells cultures. The fortified pasta showed a peculiar sensory profile, markedly improved by the pre-treatment, thus confirming the great potential of bioprocessed BSG as health-promoting food ingredient.

Role of Lactic Acid Bacteria Phospho-ß-Glucosidases during the Fermentation of Cereal by-Products.

Bioprocessing using lactic acid bacteria (LAB) is a powerful means to exploit plant-derived by-products as a food ingredient. LAB have the capability to metabolize a large variety of carbohydrates, but such metabolism only relies on few metabolic routes, conferring on them a high fermentation potential. One example of these pathways is that involving phospho-ß-glucosidase genes, which are present in high redundancy within LAB genomes. This enzymatic activity undertakes an ambivalent role during fermentation of plant-based foods related to the release of a wide range of phenolic compounds, from their ß-D-glycosylated precursors and the degradation of ß-glucopyranosyl derived carbohydrates. We proposed a novel phenomic approach to characterize the metabolism drift of Lactiplantibacillus plantarum and Leuconostoc pseudomesenteroides caused by a lignocellulosic by-product, such as the brewers' spent grain (BSG), in contrast to Rich De Man, Rogosa and Sharpe (MRS) broth. We observed an increased metabolic activity for gentiobiose, cellobiose and ß-glucoside conjugates of phenolic compounds during BSG fermentation. Gene expression analysis confirmed the importance of cellobiose metabolism while a release of lignin-derived aglycones was found during BSG fermentation. We provided a comprehensive view of the important role exerted by LAB 6-phospho-ß-glucosidases as well the major metabolic routes undertaken during plant-based fermentations. Further challenges will consider a controlled characterization of pbg gene expression correlated to the metabolism of ß-glucosides with different aglycone moieties.

Microbial high throughput phenomics: The potential of an irreplaceable omics.

The phenotype-genotype landscape is a projection coming from detailed phenotypic and genotypic data under environmental pressure. Although phenome of microbes or microbial consortia mirrors the functional expression of a genome or set of genomes, metabolic traits rely on the phenotype. Phenomics has the potential to revolution functional genomics. In this review, we discuss why and how phenomics was developed. We described how phenomics may extend our understanding of the assembly of microbial consortia and their functionality, and then we outlined the novel applications within the study of phenomes using Omnilog platform together with a revision of its current application to study lactic acid bacteria (LAB) metabolic traits during food processing. LAB were proposed as a suitable model system to analyze and discuss the implementation and exploitation of this emerging omics approach. We introduced the 'phenotype switching', as a new phenotype microarray approach to get insights in bacterial physiology. An overview of methodologies and tools to manage and analyze the generated data was provided. Finally, pro and cons of pipelines developed so far, including the most innovative ones were critically analyzed. We propose an R pipeline, recently deposited, which allows to automatically analyze Omnilog data integrating the latest approaches and implementing the new concepts described here.

How fructophilic lactic acid bacteria may reduce the FODMAPs content in wheat-derived baked goods: a proof of concept.

BACKGROUND: FODMAPs (Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) intake is associated with the onset of irritable bowel syndrome symptoms. FODMAPs in wheat-derived baked goods may be reduced via bioprocessing by endogenous enzymes and/or microbial fermentation. Because of the inherent enzyme activities, bread made by baker's yeast and sourdough may result in decreased levels of FODMAPs, whose values are, however, not enough low for people sensitive to FODMAPs. RESULTS: Our study investigated the complementary capability of targeted commercial enzymes and metabolically strictly fructophilic lactic acid bacteria (FLAB) to hydrolyze fructans and deplete fructose during wheat dough fermentation. FLAB strains displayed higher fructose consumption rate compared to conventional sourdough lactic acid bacteria. Fructose metabolism by FLAB was faster than glucose. The catabolism of mannitol with the goal of its reuse by FLAB was also investigated. Under sourdough conditions, higher fructans breakdown occurred in FLAB inoculated doughs compared to conventional sourdough bacteria. Preliminary trials allowed selecting Apilactobacillus kunkeei B23I and Fructobacillus fructosus MBIII5 as starter candidates, which were successfully applied in synergy with commercial invertase for low FODMAPs baking. CONCLUSIONS: Results of this study clearly demonstrated the potential of selected strictly FLAB to strongly reduce FODMAPs in wheat dough, especially under liquid-dough and high oxygenation conditions.