We used barcoded sequencing to analyze the eukaryotic population in the grape berries at different ripening states in four Australian vineyards. Furthermore, we used an innovative compositional data analysis for assessing the diversity of microbiome communities. The novelty was the introduction of log-ratio balances between the detected genera. Altogether, our results suggest that fungal communities were more impacted by the geographical origin of the Australian vineyards than grape variety and harvest time. Even if the most abundant genera were Aureobasidium and Mycosphaerella, they were ubiquitous to all samples and were not discriminative. In fact, the balances and the fungal community structure seemed to be greatly affected by changes of the genera Penicillium, Colletotrichum, Aspergillus, Rhodotorula, and Botrytis. These results were not evident from the comparison of relative abundance based on OTU counts alone, remarking the importance of the balance analysis for microbiome studies.

Wine aged in barrels or bottles is susceptible to alteration by microorganisms that affect the final product quality. However, our knowledge of the microbiota during aging and the factors modulating the microbial communities is still quite limited. The present work uses high-throughput sequencing (HTS) techniques to deal with the meta-taxonomic characterization of microbial consortia present in red wines along 12 months aging. The wines obtained from two different grape varieties were aged at two different cellars and compared based on time of wine aging in the barrels, previous usage of the barrels, and differences between wine aging in oak barrels or glass bottles. The aging in barrels did not significantly affect the microbial diversity but changed the structure and composition of fungal and bacterial populations. The main microorganisms driving these changes were the bacterial genera Acetobacter, Oenococcus, Lactobacillus, Gluconobacter, Lactococcus, and Komagataeibacter and the fungal genera Malassezia, Hanseniaspora, and Torulaspora. Our results showed that the oak barrels increased effect on the microbial diversity in comparison with the glass bottles, in which the microbial community was very similar to that of the wine introduced in the barrels at the beginning of the aging. Furthermore, wine in the bottles harbored higher proportion of Lactobacillus but lower proportion of Acetobacter. Finally, it seems that 1 year of previous usage of the barrels was not enough to induce significant changes in the diversity or composition of microbiota through aging compared with new barrels. This is the first meta-taxonomic study on microbial communities during wine aging and shows that the microorganism composition of barrel-aged wines was similar at both cellars. These results hint at the possibility of a common and stable microbiota after aging in the absence of exogenous alterations. Further corroborations on the current outcome would be valuable for the comparison and detection of microbial alterations during aging that could potentially prevent economic losses in the wine industry.

Wine origin and ageing are two factors related to wine quality which in turn is associated to wine metabolome. Currently, new metabolomic techniques and proper statistics procedures allow accurate profiling of wine metabolome. Thus, the main goal was to evaluate different metabolomic methodologies on their ability to provide patterns on the wine metabolome based on selected factors, such as ageing of barrel-aged wine (factor time), prior usage of the barrels (factor barrel-type), and differences between wine ageing in barrels or glass bottles (factor bottled-wine). In the current study, we implement NMR, targeted and untargeted GC-MS and LC-MS metabolomic analytical techniques so as to gain insights into the volatile and nonvolatile wine metabolome composition of red wines from two cellars located in the only two Spanish Qualified Appellations of Origin; DOQ Priorat and DOCa Rioja regions. Overall, 95 differentially significant metabolites were identified facilitating the evaluation of the analytical methodologies performance and finding common trends of those metabolites depending on the considered factor. The results did not favor NMR as an effective technique on the current dataset whereas suggested LC-MS as an adequate technique for revealing differences based on the factor time, targeted GC-MS on the factor barrel-type, and untargeted GC-MS on the factor bottled-wine. Thus, a combination of different metabolomic techniques is necessary for a complete overview of the metabolome changes. These results ease the selection of the correct methodology depending on the specific factor investigated.

In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.

Metataxonomic analysis represents a fast and cost-effective approach for acquiring informative insight into the composition of the microbiome of samples with variable diversity, such as wine samples. Nevertheless, it comprises a vast amount of laboratory procedures and bioinformatic frameworks each one associated with an inherent variability of protocols and algorithms, respectively. As a solution to the bioinformatic maze, QIIME bioinformatic framework has incorporated benchmarked, and balanced parameters as default parameters. In the current study, metataxonomic analysis of two types of mock community standards with the same microbial composition has been performed for evaluating the effectivess of QIIME balanced default parameters on a variety of aspects related to different laboratory and bioinformatic workflows. These aspects concern NGS platforms, PCR protocols, bioinformatic pipelines, and taxonomic classification algorithms. Several qualitative performance expectations have been the outcome of the analysis, rendering the mock community a useful evaluation tool.