Dynamic modelling of brewers’ yeast and Cyberlindnera fabianii co-culture behaviour for steering fermentation performance

Optimal experimental design (OED) for the growth rate of microbial populations. Are they really more "optimal" than uniform designs?

Secondary growth models from predictive microbiology can describe how the growth rate of microbial populations varies with environmental conditions. Because these models are built based on time and resource consuming experiments, model-based Optimal Experimental Design (OED) can be of interest to reduce the experimental load. In this study, we identify optimal experimental designs for two common models (full Ratkowsky and Cardinal Parameters Model (CPM)) for a different number of experiments (10-30). Calculations are also done fixing one or more model parameters, observing that this decision strongly affects the layout of the OED. Using in silico experiments, we conclude that OEDs are more informative than conventional (equidistant) designs with the same number of experiments. However, OEDs cluster the experiments near the growth limits (Xmin and Xmax) resulting in impractical designs with aggregated experimental runs ~10 times longer than conventional designs. To mitigate this, we propose a novel optimality criterion (i.e., the objective function) that accounts for the aggregated time. The novel criterion provides a reduction in parameter uncertainty with respect to the conventional design, without an increase in the experimental load. These results underline that an OED is only based on information theory (Fisher information), so the results can be impractical when actual experimental limitations are considered. The study also emphasizes that most OED schemes identify where to measure, but do not give an indication on how many experiments should be made. In this sense, numerical simulations can estimate the parameter uncertainty that would be obtained for a particular experimental design (OED or not). These results and methodologies (available in Open Code) can guide the design of future experiments for the development of secondary growth models.

Assessment of Tannin Tolerant Non-Saccharomyces Yeasts Isolated from Miang for Production of Health-Targeted Beverage Using Miang Processing Byproducts

This research demonstrated an excellent potential approach for utilizing Miang fermentation broth (MF-broth), a liquid residual byproduct from the Miang fermentation process as a health-targeted beverage. One hundred and twenty yeast strains isolated from Miang samples were screened for their potential to ferment MF-broth and four isolates, P2, P3, P7 and P9 were selected, based on the characteristics of low alcoholic production, probiotic properties, and tannin tolerance. Based on a D1/D2 rDNA sequence analysis, P2 and P7 were identified to be Wikerhamomyces anomalus, while P3 and P9 were Cyberlindnera rhodanensis. Based on the production of unique volatile organic compounds (VOCs), W. anomalus P2 and C. rhodanensis P3 were selected for evaluation of MF-broth fermentation via the single culture fermentation (SF) and co-fermentation (CF) in combination with Saccharomyces cerevisiae TISTR 5088. All selected yeasts showed a capability for growth with 6 to 7 log CFU/mL and the average pH value range of 3.91-4.09. The ethanol content of the fermented MF-broth ranged between 11.56 ± 0.00 and 24.91 ± 0.01 g/L after 120 h fermentation, which is categorized as a low alcoholic beverage. Acetic, citric, glucuronic, lactic, succinic, oxalic and gallic acids slightly increased from initial levels in MF-broth, whereas the bioactive compounds and antioxidant activity were retained. The fermented MF-broth showed distinct VOCs profiles between the yeast groups. High titer of isoamyl alcohol was found in all treatments fermented with S. cerevisiae TISTR 5088 and W. anomalus P2. Meanwhile, C. rhodanensis P3 fermented products showed a higher quantity of ester groups, ethyl acetate and isoamyl acetate in both SF and CF. The results of this study confirmed the high possibilities of utilizing MF-broth residual byproduct in for development of health-targeted beverages using the selected non-Saccharomyces yeast.

A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay

Background

Although the yeast Cyberlindnera fabianii (C. fabianii) has been rarely reported in human infections, nosocomial outbreaks caused by this organism have been documented. Here we report a pseudo-outbreak of C. fabianii in a urology department of a Chinese hospital over a two-week period.

Methods

Three patients were admitted to the urology department of a tertiary teaching hospital in Beijing, China, from Nov to Dec 2018, for different medical intervention demands. During the period Nov 28 to Dec 5, funguria occurred in these three patients, and two of them had positive urine cultures multiple times. Sequencing of rDNA internal transcribed spacer (ITS) region and MALDI-TOF MS were applied for strain identification. Further, sequencing of rDNA non-transcribed spacer (NTS) region and whole genome sequencing approaches were used for outbreak investigation purpose.

Results

All the cultured yeast strains were identified as C. fabianii by sequencing of ITS region, and were 100% identical to the C. fabianii type strain CBS 5640T. However, the MALDI-TOF MS system failed to correctly identify this yeast pathogen. Moreover, isolates from these three clustered cases shared 99.91%-100% identical NTS region sequences, which could not rule out the possibility of an outbreak. However, whole genome sequencing results revealed that only two of the C. fabianii cases were genetically-related with a pairwise SNP of 192 nt, whilst the third case had over 26,000 SNPs on its genome, suggesting a different origin. Furthermore, the genomes of the first three case strains were phylogenetically even more diverged when compared to a C. fabianii strain identified from another patient, who was admitted to a general surgical department of the same hospital 7 months later. One of the first three patients eventually passed away due to poor general conditions, one was asymptomatic, and other clinically improved.

Conclusion

In conclusion, nosocomial outbreaks caused by emerging and uncommon fungal species are increasingly being reported, hence awareness must be raised. Genotyping with commonly used universal gene targets may have limited discriminatory power in tracing the sources of infection for these organisms, requiring use of whole genome sequencing to confirm outbreak events.

Application of yeast in plant-derived aroma formation from cigar filler leaves

Introduction: There are various degrees of defects of cigar filler leaves after air drying. Methods: In order to improve the quality and plant-derived aroma content of cigar filler leaves, nine aroma-producing yeasts were applied in artificially solid-state fermentation of cigar filler leaves in this study. The differences with various yeasts application were compared by chemical composition and GC-MS analysis. Results and discussion: The results showed that 120 volatile components were identified and quantified in cigar filler leaves after fermentation, including aldehydes (25 types), alcohols (24 types), ketones (20 types), esters (11 types), hydrocarbons (12 types), acids (4 types) and other substances (23 types). Based on the analysis of odor activity value (OAV), the OVA of fruity and floral aroma components were higher. It was found that floral aroma are the representative aroma types of cigar filler leaves treated with Clavispora lusitaniae, Cyberlindera fabianii, Saccharomycosis fibuligera and Zygosaccharomyces bailii R6. After being inoculated with Hanseniaspora uvarum J1, Hanseniaspora uvarum J4 and Pichia pastoris P3, the OAV of fruity aroma in cigar filler leaves was the highest, followed by tobacco aroma and woody aroma. The correlation between volatile components of cigar filler leaves with different yeasts was revealed after PCA analysis. It was concluded that the quality of cigar filler leaves was improved, and cigar filler leaves fermented with different yeasts showed different flavor.

Sourdough cultures as reservoirs of maltose-negative yeasts for low-alcohol beer brewing

De novo sourdough cultures were here assessed for their potential as sources of yeast strains for low-alcohol beer brewing. NGS analysis revealed an abundance of ascomycete yeasts, with some influence of grain type on fungal community composition. Ten different ascomycete yeast species were isolated from different sourdough types (including wheat, rye, and barley) and seven of these were screened for a number of brewing-relevant phenotypes. All seven were maltose-negative and produced less than 1% (v/v) alcohol from a 12 °Plato wort in initial fermentation trials. Strains were further screened for their bioflavouring potential (production of volatile aromas and phenolic notes, reduction of wort aldehydes), stress tolerance (temperature extremes, osmotic stress and ethanol tolerance) and flocculence. Based on these criteria, two species (Kazachstania servazzii and Pichia fermentans) were selected for 10 L-scale fermentation trials and sensory analysis of beers. The latter species was considered particularly suitable for production of low-alcohol wheat beers due to its production of the spice/clove aroma 4-vinylguaiacol, while the former showed potential for lager-style beers due to its clean flavour profile and tolerance to low temperature conditions.

Evaluation of Immunogenicity, Protective Immunity on Aquaculture Pathogenic Vibrio and Fermentation of Vibrio alginolyticus Flagellin FlaC Protein

Background:

Vibrio are the main pathogenic bacteria in aquaculture. The flagellin protein C (FlaC) of Vibrio alginolyticus has good immunogenicity and the prospect of potential application in a vaccine.

Objectives:

We aimed to evaluate the immunogenicity, protective immunity, and prokaryotic expression fermentation of V. alginolyticus FlaC protein for the vaccine in aquaculture.

Material and Methods:

A molecular cloning method was used to construct the expression strain of FlaC protein, and the protein was purified with Ni-affinity chromatography. Polyclonal antiserum was prepared via mice immunized with the FlaC protein. The Western blot and enzyme-linked immunosorbent assay (ELISA) were used to check the specificity and titre of the antiserum. ELISA and pull-down assay detected the interaction between FlaC protein antiserum and Vibrio. The immune protection function of FlaC protein was detected with mice actively immunized with FlaC protein and challenged by V. alginolyticus and V. parahaemolyticus. The optimal expression conditions for FlaC protein were detected using an L₉(3⁴) orthogonal design model.

Results:

The expression strain of FlaC protein was obtained successfully, and purified FlaC protein was prepared using a mice polyclonal antibody. The FlaC protein antiserum held a high specificity, and the titre was 13200. The antiserum directly interacted with V. alginolyticus and V. parahaemolyticus, and the FlaC protein demonstrated a significant immune protection function (50%) against V. alginolyticus infection and some immune protection function (41.66%) against V. parahaemolyticus. The optimal expression conditions for FlaC protein included a strain OD₆₀₀ value of 0.8, final isopropyl-β-d-thiogalactoside (IPTG) concentration of 0.1 mmol/L, an inducing time of 8 hours, and an inducing temperature of 28°C.

Conclusions:

This study showed that the FlaC protein possesses a significant immunogenicity and immune protection effect and obtained the optimal fermentation conditions. It is expected to be a potential vaccine against V. alginolyticus and V. parahaemolyticus.