Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways

BACKGROUND: Oenococcus oeni, a member of the lactic acid bacteria, is one of a limited number of microorganisms that not only survive, but actively proliferate in wine. It is also unusual as, unlike the majority of bacteria present in wine, it is beneficial to wine quality rather than causing spoilage. These benefits are realised primarily through catalysing malolactic fermentation, but also through imparting other positive sensory properties. However, many of these industrially-important secondary attributes have been shown to be strain-dependent and their genetic basis it yet to be determined. RESULTS: In order to investigate the scale and scope of genetic variation in O. oeni, we have performed whole-genome sequencing on eleven strains of this bacterium, bringing the total number of strains for which genome sequences are available to fourteen. While any single strain of O. oeni was shown to contain around 1800 protein-coding genes, in-depth comparative annotation based on genomic synteny and protein orthology identified over 2800 orthologous open reading frames that comprise the pan genome of this species, and less than 1200 genes that make up the conserved genomic core present in all of the strains. The expansion of the pan genome relative to the coding potential of individual strains was shown to be due to the varied presence and location of multiple distinct bacteriophage sequences and also in various metabolic functions with potential impacts on the industrial performance of this species, including cell wall exopolysaccharide biosynthesis, sugar transport and utilisation and amino acid biosynthesis. CONCLUSIONS: By providing a large cohort of sequenced strains, this study provides a broad insight into the genetic variation present within O. oeni. This data is vital to understanding and harnessing the phenotypic variation present in this economically-important species.Anthony R Borneman, Jane M McCarthy, Paul J Chambers and Eveline J Bartowsk

Acetic Acid Bacteria: Physiology and Carbon Sources Oxidation

Acetic acid bacteria (AAB) are obligately aerobic bacteria within the family Acetobacteraceae, widespread in sugary, acidic and alcoholic niches. They are known for their ability to partially oxidise a variety of carbohydrates and to release the corresponding metabolites (aldehydes, ketones and organic acids) into the media. Since a long time they are used to perform specific oxidation reactions through processes called “oxidative fermentations”, especially in vinegar production. In the last decades physiology of AAB have been widely studied because of their role in food production, where they act as beneficial or spoiling organisms, and in biotechnological industry, where their oxidation machinery is exploited to produce a number of compounds such as l-ascorbic acid, dihydroxyacetone, gluconic acid and cellulose. The present review aims to provide an overview of AAB physiology focusing carbon sources oxidation and main products of their metabolism

Comparison of near infrared and mid infrared spectroscopy to discriminate between wines produced by different Oenococcus Oeni strains after malolactic fermentation: a feasibility study

Abstract not availableD. Cozzolino, J. McCarthy, E. Bartowsk

Comparison of near infrared and mid infrared spectroscopy to discriminate between wines produced by different Oenococcus Oeni strains after malolactic fermentation: A feasibility study

The wine industry requires rapid, comprehensive methods and techniques to answer the new challenges driven by the market demands. Recent advances in spectroscopy technologies have brought about a revolution in the manner in which biological systems are visualised and analysed. The measurement of numerous small molecules (metabolites) metabolised by microorganisms during growth in wine, will benefit from techniques that require minimal sample preparation, permit the automatic analysis of many samples with negligible reagent costs, allow their rapid characterization against a stable database, and are easy to use. With recent developments in analytical instrumentation, these requirements are being fulfilled by vibrational spectroscopic methods, often referred to as "whole-organism fingerprinting" and more recently "metabolic fingerprinting" The objective of this study was to evaluate and compare the use of near (NIR) and mid infrared (MIR) spectroscopy as rapid methods to distinguish red and white wines obtained by using different strains of Oenococcus oeni following malolactic fermentation. Using NIR and MIR wines produced with different O. oeni strains could be distinguished both in red and white wines yielding correct classification rates between 67 and 100% depending on the strain. © 2012 Elsevier Ltd

Hydrolysis and transformation of grape glycosidically bound volatile compounds during fermentation with three saccharomyces yeast strains

Copyright © 2006 American Chemical SocietyMaurizio Ugliano, Eveline J. Bartowsky, Jane McCarthy, Luigi Moio and Paul A. Henschk

Microsatellite PCR profiling of Saccharomyces cerevisiae strains during wine fermentation

Aims: Use of microsatellite PCR to monitor populations of Saccharomyces cerevisiae strains during fermentation of grape juice. Method and Results: Six commercial wine strains of S. cerevisiae were screened for polymorphism at the SC8132X locus using a modified rapid PCR identification technique. The strains formed four distinct polymorphic groups that could be readily distinguished from one another. Fermentations inoculated with mixtures of three strains polymorphic at the SC8132X locus were monitored until sugar utilization was complete, and all exhibited a changing population structure throughout the fermentation. Conclusions: Rapid population quantification demonstrated that wine fermentations are dynamic and do not necessarily reflect the initial yeast population structure. One or more yeast strains were found to dominate at different stages of the fermentation. Significance and Impact of the Study: The population structure of S. cerevisiae during mixed culture wine fermentation is dynamic and could modify the chemical composition and flavour profile of wine

Broadening your winemaking yeast portfolio: Identification of an SO2 tolerant non-Saccharomyces

Non-Saccharomyces yeast are gaining winemaker interest worldwide because of their potential to improve wine quality (aroma, length, and texture). There are currently only a handful of commercial non-Saccharomyces strains available for winemakers to choose from and this project seeks to broaden their portfolio. Any new yeast isolate should be tolerant to the most common wine stressors e.g., pH, ethanol, and sulfur dioxide (SO2), a common antimicrobial and antioxidant. Additionally, their fermentation performance and desirable secondary metabolites are critical selection criteria. In this study, 480 indigenous yeasts were isolated from the Chalmers Merbein vineyard (Victoria, Australia) and identified by ITS sequencing. Nineteen of those isolates were chosen, based on species identification, for further assessment. These were screened for their ethanol and SO2 tolerance, using YPD agar spiked with increasing concentrations of both stressors. Only 13 isolates showed some degree of tolerance, and their ethanol production was evaluated in Chemically Defined Grape Juice Medium (CDGJM). Lastly, their SO2 tolerance was evaluated using CDGJM spiked with 20, 35, 50 and 65 ppm employing an automated fermentation platform. The most promising candidate, a Hanseniaspora opuntiae isolate, withstood 65 ppm SO2, similar to the Saccharomyces cerevisiae control. This isolate also consumed approximately 110 g/L of sugar and produced 6% v/v of ethanol. This isolate will be tested further for its assimilable nitrogen requirements and volatile production, with a view towards broadening the portfolio of winemaking starter cultures.Natalia Caliani, Krista Sumby, Joanna Sundstrom, Cassandra Collins, Kelsey Laverne, Eveline Bartowsky, Anthony Borneman, Kim Chalmers, Vladimir Jirane