Detection of Beer-spoilageLactobacillus brevisstrains by Reduction of Resazurin

Depiction of the In Vitro and Genomic Basis of Resistance to Hop and High Hydrostatic Pressure of Lactiplantibacillus plantarum Isolated from Spoiled Beer

Among the beer-spoiling microorganisms, the dominant ones belong to the genera Lactobacillus, Leuconostoc, Oenococcus, and Pediococcus. It is assumed that resistance to hop bitters correlates with resistance to other factors and can significantly impact the brewing industry. Beer preservation with high hydrostatic pressure eliminates the spoiling microorganisms while preserving all desired properties of the beer. Here, we present comprehensive in vitro and genomic analysis of the beer-spoiling Lactiplantibacillus plantarum KKP 3573 capacity to resist hop and high hydrostatic pressure. Lp. plantarum KKP 3573 is a strain isolated from spoiled beer. Our finding suggests that the growth rate of the strain depends on the medium variant, where a small concentration of beer (5 IBU) stimulates the growth, suggesting that the limited concentration has a positive effect on cell growth. At the same time, increased concentrations of 20 IBU, 30 IBU, and pure beer 43.6 IBU decreased the growth rate of the KKP 3573 strain. We observed that higher extract content in the pressurized beer increased microbial survivability. The wort and Vienna Lager beer can stimulate the baroprotective effect. The taxonomy of the novel strain was confirmed after whole genome sequencing (WGS) and comparative genomic analysis. More specifically, it contains a chromosome of 3.3 Mb with a GC content of 44.4%, indicative of the Lp. plantarum species. Accordingly, it possesses high genomic similarity (>98%) with other species members. Annotation algorithms revealed that the strain carries several genes involved in resistance to stress, including extreme temperature, hop bitters and high pressure, and adaptation to the brewing environment. Lastly, the strain does not code for toxins and virulence proteins and cannot produce biogenic amines.

Short-length Homologous Region exhaustive Search algorithm (SHRS): A primer design algorithm for differentiating bacteria at the species, subspecies, or strain level based on a whole genome sequence

In fields such as the food industry, it is very important to identify target bacteria at the species level or lower for optimal product quality control. Bacteria identification at the subspecies or lower level requires time-consuming and high-cost analyses such as multi-locus sequence typing and amplified fragment length polymorphism analyses. Herein, we developed a primer design algorithm for precisely identifying bacteria based on a whole genome DNA sequence that is easy to apply. The algorithm designs primer sets that produce fragments from all input sequences and maximizes the differences in the amplicon size or amplicon sequence among input sequences. We demonstrate that the primer sets designed by the algorithm clearly classified six subspecies of Lactobacillus delbrueckii, and we observed that the resolution of the method is equal to that of a multi-locus sequence analysis. The algorithm allows the easy but precise identification of bacteria within a short time. (SHRS is available freely from PyPI under the MIT license.).

Modeling the inactivation of Lactobacillus brevis DSM 6235 and retaining the viability of brewing pitching yeast submitted to acid and chlorine washing

This study aimed to model the inactivation of Lactobacillus brevis DSM 6235 while retaining the viability of yeasts during washing brewer's yeast with phosphoric acid and chlorine dioxide. The independent variables in the acid washing were pH (1-3) and temperature (1-9 °C), whereas in the washing with chlorine dioxide, concentration (10-90 mg/L) and temperature (5-25 °C) were assessed. The predictive models obtained for the four response variables γ_LA, γ_Cl (decimal reduction of L. brevis DSM 6235), V_f/V0_LA, and V_f/V0_Cl (brewer's yeast viability ratio) were found to have R² > 0.80 and values of F_calc > F_reference. Then, the models were considered predictive and statistically significant (p < 0.10). Our results indicated that phosphoric acid and chlorine dioxide washing resulted in up to 7 and 6.4 (log CFU/mL) decimal reductions of L. brevis DSM 6235, respectively. On the other hand, the viability of the brewer's yeast ranged from 22.3 to 99.4%. L. brevis DSM 6235 inactivation was significantly influenced by parameters pH(Q) and T°C(Q) when phosphoric acid was applied, and by parameters mg/L(L), mg/L(Q), T°C(Q), and mg/L × T°C when ClO₂ was applied. The validation of the models resulted in bias (γ_LA, 0.93/V_f/V_0LA, 0.99 - γ_Cl, 1.0/V_f/V_0Cl, 0.99) and accuracy values (γ_LA, 1.12/Vf/V_0LA, 1.01 - γ_Cl, 1.08/V_f/V_0Cl, 1.03). The results of this study indicate that it might be possible to decontaminate brewer's yeast through acid and chlorine dioxide washing while keeping its viability. This procedure will result in the reduction of costs and the lower generation of brewer's waste.

Comparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates

Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.

A rapid method to estimate NADH regeneration rates in living cells

We introduce a rapid whole cell assay for the estimation of NADH regeneration rates based on the fluorescent dye resazurin. A co-feed of formate and glucose, known to increase the intrinsic NADH regeneration rate of P. putida KT2440, was chosen as model system for the validation of this assay.

Metabolic strategies of beer spoilage lactic acid bacteria in beer

Beer contains only limited amounts of readily fermentable carbohydrates and amino acids. Beer spoilage lactic acid bacteria (LAB) have to come up with metabolic strategies in order to deal with selective nutrient content, high energy demand of hop tolerance mechanisms and a low pH. The metabolism of 26 LAB strains of 6 species and varying spoilage potentialwas investigated in order to define and compare their metabolic capabilities using multivariate statistics and outline possible metabolic strategies. Metabolic capabilities of beer spoilage LAB regarding carbohydrate and amino acids did not correlate with spoilage potential, but with fermentation type (heterofermentative/homofermentative) and species. A shift to mixed acid fermentation by homofermentative (hof) Pediococcus claussenii and Lactobacillus backii was observed as a specific feature of their growth in beer. For heterofermentative (hef) LAB a mostly versatile carbohydrate metabolism could be demonstrated, supplementing the known relevance of organic acids for their growth in beer. For hef LAB a distinct amino acid metabolism, resulting in biogenic amine production, was observed, presumably contributing to energy supply and pH homeostasis.

Differentiation of Lactobacillus brevis strains using Matrix-Assisted-Laser-Desorption-Ionization-Time-of-Flight Mass Spectrometry with respect to their beer spoilage potential

Lactobacillus (L.) brevis is one of the most frequently encountered bacteria in beer-spoilage incidents. As the species Lactobacillus brevis comprises strains showing varying ability to grow in beer, ranging from growth in low hopped wheat to highly hopped pilsner beer, differentiation and classification of L. brevis with regard to their beer-spoiling ability is of vital interest for the brewing industry. Matrix-Assisted-Laser-Desorption-Ionization-Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) has been shown as a powerful tool for species and sub-species differentiation of bacterial isolates and is increasingly used for strain-level differentiation. Seventeen L. brevis strains, representative of different spoilage types, were characterized according to their tolerance to iso-alpha-acids and their growth in wheat-, lager- and pilsner beer. MALDI-TOF MS spectra were acquired to perform strain-level identification, cluster analysis and biomarker detection. Strain-level identification was achieved in 90% out of 204 spectra. Misidentification occurred nearly exclusively among strains belonging to the same spoilage type. Though spectra of strongly beer-spoiling strains showed remarkable similarity, no decisive single markers were detected to be present in all strains of one group. However, MALDI-TOF MS spectra can be reliably assigned to the corresponding strain and thus allow to track single strains and connect them to their physiological properties.

Optimization of Matrix-Assisted-Laser-Desorption-Ionization-Time-Of-Flight Mass Spectrometry for the identification of bacterial contaminants in beverages

The growth of microbial contaminants in industrially produced beverages can cause turbidity, haze and off-flavors resulting in quality loss often rendering the product undrinkable. In this work Matrix-Assisted-Laser-Desorption-Ionization-Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) based on the generation of peptide mass fingerprints, which form a distinctive protein peak pattern, is presented as a rapid, reliable and powerful tool for the identification of spoilage bacteria encountered in beverages. Lactobacillus brevis, Pediococcus claussenii and Leuconostoc mesenteroides were used to optimize sample preparation and MALDI-TOF MS-settings. Different sample preparation methods ranging from plain cell smears to more elaborate extraction procedures including mechanical and enzymatical disruption of cells were investigated. The effects of culturing time and the availability of oxygen and nutrients on the acquired protein peak patterns were studied. While cell smears at times hampered the acquisition of spectra for strain L. brevis all other procedures constantly delivered good quality spectra for all three strains. The extraction procedure allowed good reproducibility of spectra with high information content and enabled differentiation on the species level regardless of the culture conditions used. The application of specific culture conditions to microorganisms resulted in minor but stable changes in spectra, which were not sufficient to impair identification of isolates on the species level.

RT-qPCR analysis of putative beer-spoilage gene expression during growth of Lactobacillus brevis BSO 464 and Pediococcus claussenii ATCC BAA-344(T) in beer

Lactic acid bacteria (LAB) contamination of beer presents a continual economic threat to brewers. Interestingly, only certain isolates of LAB can grow in the hostile beer environment (e.g., as studied here, Lactobacillus brevis BSO 464 (Lb464) and a non-ropy isolate of Pediococcus claussenii ATCC BAA-344(T) (Pc344NR)), indicating that significant genetic specialization is required. The genes hitA, horA, horB, horC, and bsrA, which have been proposed to confer beer-spoiling ability to an organism, are suspected of counteracting the antimicrobial effects of hops. However, these genes are not present in the same combination (if at all) across beer-spoiling organisms. As such, we sought to investigate the extent to which these genes participate during Lb464 and Pc344NR mid-logarithmic growth in beer through reverse transcription quantitative PCR analysis. We first determined the optimal reference gene set needed for data normalization and, for each bacterium, established that two genes were needed for accurate assessment of gene expression. Following this, we found that horA expression was induced for Pc344NR, but not for Lb464, during growth in beer. Instead, horC expression was dramatically increased in Lb464 when growing in beer, whereas no change was detected for the other putative beer-spoilage-related genes. This indicates that HorC may be one of the principle mediators enabling growth of Lb464 in beer, whereas in Pc344NR, this may be attributable to HorA. These findings not only reveal that Lb464 and Pc344NR are unique in their beer-specific genetic expression profile but also indicate that a range of genetic specialization exists among beer-spoilage bacteria.