Dynamics of the Fermentation Products, Residual Non-structural Carbohydrates, and Bacterial Communities of Wilted and Non-wilted Alfalfa Silage With and Without Lactobacillus plantarum Inoculation

The aim of this study was to investigate effects of wilting and Lactobacillus plantarum inoculation on the dynamics of the fermentation products, residual non-structural carbohydrates, and bacterial communities in alfalfa silage. Fresh and wilted alfalfa were ensiled with and without L. plantarum for 10, 30, 60, and 90 days. A high-throughput sequencing method for absolute quantification of 16S rRNA was adopted to determine the bacterial community composition at different ensiling periods. For the wilted silage, the bacterial community, pH value, and ammonia nitrogen concentration remained stable in the silage at 30 days. L. plantarum inoculation accelerated lactic acid fermentation and altered the predominant genus in the wilted silage as compared with the non-inoculated group. For the non-wilted group, fast consumption of water-soluble carbohydrates (WSCs) was observed at 10 days in the non-inoculated silage along with rapid growth of undesirable Hafnia. L. plantarum inoculation inhibited growth of Hafnia at 10 days in the non-wilted silage. Clostridia fermentation occurred in the non-wilted silage at 90 days, as indicated by an increased pH, formation of butyric acid (BA), and apparent abundance of genera belonging to Clostridia. L. plantarum inoculation inhibited BA accumulation and growth of Garciella in the non-wilted silage at 90 days as compared with the non-wilted silage without inoculation, but had little effect on the growth of Clostridium sensu stricto. Overall, the high moisture content of the non-wilted alfalfa silage led to rapid consumption of WSCs and growth of harmful microorganisms at the early stage of ensiling, resulting in poor fermentation quality. Wilting and L. plantarum inoculation both improved fermentation quality and inhibited the growth of spoilage microorganisms in alfalfa silage, while L. plantarum inoculation alone failed to achieve optimum fermentation quality of non-wilted alfalfa silage.

Vegan Diet Is Associated With Favorable Effects on the Metabolic Performance of Intestinal Microbiota: A Cross-Sectional Multi-Omics Study

Background and Aim: Plant-based diets are associated with potential health benefits, but the contribution of gut microbiota remains to be clarified. We aimed to identify differences in key features of microbiome composition and function with relevance to metabolic health in individuals adhering to a vegan vs. omnivore diet.Methods: This cross-sectional study involved lean, healthy vegans (n = 62) and omnivore (n = 33) subjects. We assessed their glucose and lipid metabolism and employed an integrated multi-omics approach (16S rRNA sequencing, metabolomics profiling) to compare dietary intake, metabolic health, gut microbiome, and fecal, serum, and urine metabolomes.Results: The vegans had more favorable glucose and lipid homeostasis profiles than the omnivores. Long-term reported adherence to a vegan diet affected only 14.8% of all detected bacterial genera in fecal microbiome. However, significant differences in vegan and omnivore metabolomes were observed. In feces, 43.3% of all identified metabolites were significantly different between the vegans and omnivores, such as amino acid fermentation products p-cresol, scatole, indole, methional (lower in the vegans), and polysaccharide fermentation product short- and medium-chain fatty acids (SCFAs, MCFAs), and their derivatives (higher in the vegans). Vegan serum metabolome differed markedly from the omnivores (55.8% of all metabolites), especially in amino acid composition, such as low BCAAs, high SCFAs (formic-, acetic-, propionic-, butyric acids), and dimethylsulfone, the latter two being potential host microbiome co-metabolites. Using a machine-learning approach, we tested the discriminative power of each dataset. Best results were obtained for serum metabolome (accuracy rate 91.6%).Conclusion: While only small differences in the gut microbiota were found between the groups, their metabolic activity differed substantially. In particular, we observed a significantly different abundance of fermentation products associated with protein and carbohydrate intakes in the vegans. Vegans had significantly lower abundances of potentially harmful (such as p-cresol, lithocholic acid, BCAAs, aromatic compounds, etc.) and higher occurrence of potentially beneficial metabolites (SCFAs and their derivatives).

Real-Time Monitoring of the Yeast Intracellular State During Bioprocesses With a Toolbox of Biosensors

Industrial fermentation processes strive for high robustness to ensure optimal and consistent performance. Medium components, fermentation products, and physical perturbations may cause stress and lower performance. Cellular stress elicits a range of responses, whose extracellular manifestations have been extensively studied; whereas intracellular aspects remain poorly known due to lack of tools for real-time monitoring. Genetically encoded biosensors have emerged as promising tools and have been used to improve microbial productivity and tolerance toward industrially relevant stresses. Here, fluorescent biosensors able to sense the yeast intracellular environment (pH, ATP levels, oxidative stress, glycolytic flux, and ribosome production) were implemented into a versatile and easy-to-use toolbox. Marker-free and efficient genome integration at a conserved site on chromosome X of Saccharomyces cerevisiae strains and a commercial Saccharomyces boulardii strain was developed. Moreover, multiple biosensors were used to simultaneously monitor different intracellular parameters in a single cell. Even when combined together, the biosensors did not significantly affect key physiological parameters, such as specific growth rate and product yields. Activation and response of each biosensor and their interconnection were assessed using an advanced micro-cultivation system. Finally, the toolbox was used to screen cell behavior in a synthetic lignocellulosic hydrolysate that mimicked harsh industrial substrates, revealing differences in the oxidative stress response between laboratory (CEN.PK113-7D) and industrial (Ethanol Red) S. cerevisiae strains. In summary, the toolbox will allow both the exploration of yeast diversity and physiological responses in natural and complex industrial conditions, as well as the possibility to monitor production processes.

Antioxidant Profile and Biosafety of White Truffle Mycelial Products Obtained by Solid-State Fermentation

Solid-state fermentation may produce therapeutic compounds with higher biomass or better product characteristics than those generated by submerged fermentation. The objectives of this study were to analyze the antioxidant activities and biosafety of products obtained by white truffle (Tuber magnatum) solid-state fermentation in media with different ratios of soybean and red adlay. High levels of antioxidant components and high antioxidant activities such as DPPH radical scavenging, ferrous ion chelation, and reducing power were measured in 20 mg/mL water and ethanol extracts of the white truffle fermentation products. When the solid-state fermentation medium contained soybean and red adlay in a 1:3 ratio (S1A3), the fermentation product had more uniform antioxidant compositions and activities by principal component analysis (PCA). In addition, a 200 ppm water extract of the mycelial fermentation product was able to protect zebrafish embryos from oxidative stress induced by 5 mM hydrogen peroxide. Sprague–Dawley rats were fed the mycelial fermentation product for 90 consecutive days, revealing a no-observed-adverse-effect level (NOAEL) of 3000 mg/kg BW/day. Therefore, mycelial products obtained by white truffle solid-state fermentation can be used instead of expensive fruiting bodies as a good source of antioxidant ingredients.

Saccharomyces cerevisiae Dehydrated Culture Modulates Fecal Microbiota and Improves Innate Immunity of Adult Dogs

Saccharomyces cerevisiae yeast culture can be dehydrated, and it has a potential prebiotic effect. This study evaluated the effects of supplementing increasing levels of dehydrated yeast culture (DYC) of Saccharomyces cerevisiae (Original XPC™, Diamond V, Cedar Rapids, IA, USA) on fecal microbiota, nutrient digestibility, and fermentative and immunological parameters of healthy adult dogs. Eighteen adult male and female dogs with a mean body weight of 15.8 ± 7.37 kg were randomly assigned to three experimental treatments: CD (control diet), DYC 0.3 (control diet with 0.3% DYC) and DYC 0.6 (control diet with 0.6% DYC). After 21 days of acclimation, fecal samples were collected for analysis of nutrient digestibility, microbiota and fecal fermentation products. On the last day, the blood samples were collected for the analysis of immunological parameters. The microbiome profile was assessed by the Illumina sequencing method, which allowed identifying the population of each bacterial phylum and genus. The statistical analyses were performed using the SAS software and the Tukey test for multiple comparison (p < 0.05). Our results suggest that the addition of DYC increased the percentage of the phyla Actinobacteria and Firmicutes (p = 0.0048 and p < 0.0001, respectively) and reduced that of the phylum Fusobacteria (p = 0.0008). Regardless of the inclusion level, the yeast addition promoted reduction of the genera Allobaculum and Fusobacterium (p = 0.0265 and p = 0.0006, respectively) and increased (p = 0.0059) that of the genus Clostridium. At the highest prebiotic inclusion level (DYC 0.6), an increase (p = 0.0052) in the genus Collinsella and decrease (p = 0.0003) in Prevotella were observed. Besides that, the inclusion of the additive improved the apparent digestibility of the crude fiber and decreased the digestibility of crude protein, nitrogen-free extract and metabolizable energy (p < 0.05). There were no significant changes in the production of volatile organic compounds. However, an increase in propionate production was observed (p = 0.05). In addition, the inclusion of yeast resulted in an increased phagocytosis index in both treatments (p = 0.01). The addition of 0.3 and 0.6% DYC to the diet of dogs wase able to modulate the proportions of some phyla and genera in healthy dogs, in addition to yielding changes in nutrient digestibility, fermentative products and immunity in healthy adult dogs, indicating that this additive can modulate fecal microbiota and be included in dog nutrition.

Pediococcus pentosaceus: Screening and Application as Probiotics in Food Processing

Lactic acid bacteria (LAB) are vital probiotics in the food processing industry, which are widely spread in food additives and products, such as meat, milk, and vegetables. Pediococcus pentosaceus (P. pentosaceus), as a kind of LAB, has numerous probiotic effects, mainly including antioxidant, cholesterol-lowering, and immune effects. Recently, the applications in the probiotic- fermentation products have attracted progressively more attentions. However, it is necessary to screen P. pentosaceus with abundant functions from diverse sources due to the limitation about the source and species of P. pentosaceus. This review summarized the screening methods of P. pentosaceus and the exploration methods of probiotic functions in combination with the case study. The screening methods included primary screening and rescreening including gastric acidity resistance, bile resistance, adhesion, antibacterial effects, etc. The application and development prospects of P. pentosaceus were described in detail, and the shortcomings in the practical application of P. pentosaceus were evaluated to make better application of P. pentosaceus in the future.

Mammalian gut metabolomes mirror microbiome composition and host phylogeny

In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.

Discovering the Influence of Microorganisms on Wine Color

Flavor, composition and quality of wine are influenced by microorganisms present on the grapevine surface which are transferred to the must during vinification. The microbiota is highly variable with a prevalence of non-Saccharomyces yeasts, whereas Saccharomyces cerevisiae is present at low number. For wine production an essential step is the fermentation carried out by different starter cultures of S. cerevisiae alone or in mixed fermentation with non-Saccharomyces species that produce wines with significant differences in chemical composition. During vinification wine color can be influenced by yeasts interacting with anthocyanin. Yeasts can influence wine phenolic composition in different manners: direct interactions—cell wall adsorption or enzyme activities—and/or indirectly—production of primary and secondary metabolites and fermentation products. Some of these characteristics are heritable trait in yeast and/or can be strain dependent. For this reason, the stability, aroma, and color of wines depend on strain/strains used during must fermentation. Saccharomyces cerevisiae or non-Saccharomyces can produce metabolites reacting with anthocyanins and favor the formation of vitisin A and B type pyranoanthocyanins, contributing to color stability. In addition, yeasts affect the intensity and tonality of wine color by the action of β-glycosidase on anthocyanins or anthocyanidase enzymes or by the pigments adsorption on the yeast cell wall. These activities are strain dependent and are characterized by a great inter-species variability. Therefore, they should be considered a target for yeast strain selection and considered during the development of tailored mixed fermentations to improve wine production. In addition, some lactic acid bacteria seem to influence the color of red wines affecting anthocyanins’ profile. In fact, the increase of the pH or the ability to degrade pyruvic acid and acetaldehyde, as well as anthocyanin adsorption by bacterial cells are responsible for color loss during malolactic fermentation. Lactic acid bacteria show different adsorption capacity probably because of the variable composition of the cell walls. The aim of this review is to offer a critical overview of the roles played by wine microorganisms in the definition of intensity and tonality of wines’ color.

Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice

The drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products. In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae , members of which produce propionate as a primary fermentation product.