Caister Academic Press

Brewing Microbiology: Current Research, Omics and Microbial Ecology | Book

Publisher: Caister Academic Press
Edited by: Nicholas A. Bokulich and Charles W. Bamforth
Center for Microbial Genetics and Genomics, Northern Arizona University, USA and Department of Food Science and Technology, University of California, Davis, USA; respectively
Pages: vi + 332
Publication date: June 2017Buy book
ISBN: 978-1-910190-61-6
Price: GB £159 or US $319
Publication date: June 2017Buy ebook
ISBN: 978-1-910190-62-3
Price: GB £159 or US $319

Research into brewing yeast and other organisms associated with beer and brewing has experienced many important advances in the past decade, propelled by technological advances in tools fundamental to the investigation of microbes and their metabolism.

This volume surveys the most recent discoveries in brewing microbiology, with an emphasis on omics techniques and other modern technologies. Discoveries in these areas have furthered our knowledge of brewing processes, with practical applications from barley growth and malting to yeast management, strain selection, fermentation control, and quality assurance. The chapters, written by experts in the field, aim not only to illuminate recent progress, but also to discuss its impact on brewing practices. Topics covered include the physiology, fermentation, taxonomy, diversity, typing, genetic manipulation, genomics and evolution of brewing yeasts. Further areas covered include the fungal contamination of barley and malt, spoilage by lactic acid bacteria and gram-negative bacteria, and beer-spoiling yeasts.

This volume is highly recommended for anyone involved in the microbiology of brewing.

Table of contents
1. Brewing Yeast Physiology
Chris Boulton
Pages: 1-28.
Characterisation of the genomes of yeast belonging to the genus, Saccharomyces, including those used in brewing has been the subject of intense investigation. Fundamental differences between ale and lager strains have been demonstrated. The linkage of many genes with cellular function has been made. Although essential, this has also highlighted a fundamental lack of knowledge as to how expression of the genome is made manifest in terms of phenotype, in particular how the phenotype is regulated at the level of the metabolome. The intention of this chapter is to review current research that has been directed towards these ends. The chapter addresses how yeast physiology is influenced by the conditions it is exposed to in current modern brewing practice, what are the potential pitfalls, and how can processes be managed to increase the likelihood of a controlled and consistent outcome. Of particular note are the factors that influence passage of cells into and out of quiescence, coincident with fermentation initiation and eventual removal of cropped yeast to storage. Since the majority of published studies have used haploid laboratory strains grown aerobically on semi-defined media, attempts have been made to extrapolate results to encompass brewing strains serially re-pitched in semi-aerobic fermentations using wort as the feedstock.
2. Yeast Stress and Brewing Fermentations
Katherine A. Smart
Pages: 29-52.
A key performance indicator of brewing fermentations is the capacity of the yeast to convert wort into the desired fermentate in an appropriate timescale. Balancing the needs of the brewer and the yeast is more complex than is always appreciated. Brewery fermentations can impose a variety of stresses on the yeast cell, particularly when conducted at scale, and this is exacerbated by the use of serial repitching, in which the yeast is recycled to complete a number of successive fermentations. Brewing yeast strains are routinely exposed to fluctuations in oxygen concentration and the accumulation of carbon dioxide, hyperosmotic stresses which are wort gravity-dependent; pH downshifts during fermentation, which can be extreme if acid washing is applied between successive fermentations; accumulation of acetaldehyde, ethanol, and organic acids; nutrient abundance, imbalance, and scarcity; and temperature shifts from around 21°C to 2°C. This chapter will focus on some of the stresses that may be encountered during lager, ale, and where appropriate wheat beer fermentations conducted at scale.
3. Yeast Supply, Fermentation, and Handling Insights, Best Practice and Consequences of Failure
David E. Quain
Pages: 53-84.
The bottom line in brewery fermentation is that consistency is paramount. Whatever the scale of the operation, excellent yeast quality is a fundamental process requirement to ensure good and sustainable beer quality. The recycling of yeast across numerous fermentations adds complexity and biological stress. It is recommended that this be compensated by application of best practice in yeast supply/propagation, pitching, fermentation and storage. Craft brewers operating at a small scale and without recycling should be conscious of best practice for the rehydration of active dried yeast.
4. Taxonomy, Diversity, and Typing of Brewing Yeasts
José Paulo Sampaio, Ana Pontes, Diego Libkind and Mathias Hutzler
Pages: 85-118.
The taxonomy and systematics of brewing yeasts have been a matter of debate and controversy since the early days of microbiology in the 1800´s, when Saccharomyces cerevisiae and Saccharomyces carlsbergensis were first cultivated. The turbulent history of beer yeast systematics epitomizes the endeavours of yeast taxonomy since its origins when researchers used morphological characters and physiological traits to distinguish and classify species. The molecular revolution initiated in the 1980's exposed limitations of phenotypic methods, revealing numerous species synonyms and misclassifications. Today, DNA sequence data provide the means for accurate species identifications, strain typing, and phylogenetic classifications. Progress in the scientific knowledge of beer yeasts was also delayed by another level of complexity, which included inter-species hybridizations occurring in the brewing environment. Inter-species hybridizations created a plethora of chimeric genomes that could only be completely resolved when genomics entered the scene in the last two decades. Indeed, many key beer genotypes like S. pastorianus, the lager yeast, and S. bayanus, a beer contaminant, are complex multi-Saccharomyces species hybrids whose life history and ancestry are only now being revealed. Recently, a combination of novel genome sequencing approaches and microbial ecology studies solved decades-long disputes and revealed the wild genetic stocks of domesticated beer lineages. Here, we give an historical perspective of brewer's yeast taxonomy including also non-Saccharomyces yeast species and review available phenotypic and genetic-based typing methods for species and strain discrimination.
5. Genetic Manipulation of Brewing Yeasts: Challenges and Opportunities
Barbara Dunn, Daniel J. Kvitek and Gavin Sherlock
Pages: 119-144.
Brewing yeasts are notoriously difficult to work with genetically, due to their complex genomes, which are often polyploid, aneuploid, and/or derived from interspecific hybridization events. We discuss the possibilities for both traditional and non-traditional genetic manipulations of brewing yeasts as a way to combine or enhance beneficial traits already present in such yeasts, or to possibly identify and introduce novel traits from non-brewing yeasts. For genetically tractable yeast strains, classic genetic breeding via meiosis and direct mating of spores can increase genetic variability and combine desired traits. For intractable strains, non-traditional breeding methods such as rare-mating, mating by transient HO-induction, cytoduction, and protoplast fusion can be utilized. These various techniques can also be performed using mixed populations in a "mass-mating" manner and/or to create interspecific hybrids. Once cells or populations with increased genetic variability are obtained, genome shuffling can create novel combinations of traits; adaptive evolution of shuffled populations allows the eventual selection of strains that exhibit desired fermentation or other selectable characteristics, while high-throughput quantitative trait loci (QTL) analysis can lead to insights about the actual genes that contribute to the traits of interest. The above techniques yield non-genetically-modified (non-GM) yeasts. However, recent advances in "minimally invasive" GM techniques that result in precise genome modifications with no remaining foreign DNA may eventually be deemed as acceptable by consumers and the brewing industry as a way to obtain brewing yeasts with desired traits. Overall, there is a wide variety of tools available for the genetic manipulation of brewing yeasts to alter or enhance any of a number of characteristics, from fermentation behavior to sensory profile.
6. Genomics and Evolution of Beer Yeasts
Brigida Gallone, Stijn Mertens, Sam Crauwelse, Bart Lievense, Kevin J. Verstrepen and Jan Steensels
Pages: 145-178.
The evolutionary adaptation of organisms to a specific niche is one of the most fascinating processes in biology. Classic Darwinian theory explains how the interplay between (genetic and phenotypic) variation on one hand, and selection on the other, drives evolution. For certain traits, evolutionary adaptation is forced by man-mediated selection, which results in domestication or the adaptation of organisms to man-made niches, as is commonly observed in crops, livestock, and pet animals. Yeasts serve as a very interesting model organism for adaptive evolution, since their small and compact genomes provide a very attractive and powerful model for comparative genomics and genome-evolution studies. Moreover, several species, such as the traditional baker's or brewer's yeast Saccharomyces cerevisiae, have been subjected to natural as well as human selection, both of which shaped their genotypes and phenotypes. The emergence of whole-genome sequencing technologies resulted in an overwhelming amount of high-quality and highly detailed yeast genome sequences, allowing researchers to investigate how these yeasts interacted with (and adapted to) their environment. In this chapter, we describe how evolutionary processes shaped the genome and phenome of three intriguing yeast species associated with beer brewing: S. cerevisiae, Saccharomyces pastorianus, and Brettanomyces bruxellensis.
7. Microbial Ecology of Traditional Beer Fermentations
Freek Spitaels, Anneleen Diane Wieme, Isabel Snauwaert, Luc De Vuyst and Peter Vandamme
Pages: 179-196.
Traditional beer fermentations do not apply inoculation of pure cultures to initiate the fermentation process. In contrast, they rely on spontaneous inoculation, 'backslopping', or inoculation with an undetermined mixture of microorganisms for the production of the beer. Knowledge about the microbiota responsible for these special fermentation processes does not only enable a closer quality management, but the isolation of the microorganisms involved enables their application as starter cultures. Very commonly, the same microorganisms are involved in these processes, i.e., the yeasts Saccharomyces cerevisiae and/or Saccharomyces pastorianus plus Brettanomyces (Dekkera) bruxellensis, lactic acid bacteria and/or acetic acid bacteria. All traditional beers share a desirable tartness and their production processes take from several days to several years to complete. This chapter reviews notable types of traditional beer fermentations, their microbial ecology, and methods used to investigate their composition.
8. Fungal Contamination of Barley and Malt
Ludwig Niessen
Pages: 197-244.
Fungal contamination of barley and malt results in a high economic burden from malt yield loss, quality failure, and costs connected to the presence of toxic fungal secondary metabolites, i.e. mycotoxins. This chapter describes the routes and factors that influence fungal contamination of cereals and malt, both qualitatively and quantitatively, as well as the consequences which fungal growth may have in terms of malt and beer quality. Focus is given to the role of mycotoxins and their fate during malting and brewing as well as to recent research in the field of beer gushing. Since analysis is a strong tool to prevent fungi and their metabolites from entering the malt-beer chain, recent developments in the analytical toolbox are discussed, including chemical and molecular biology-based approaches. Finally, possible ways for the prevention of fungal growth in the field and during malting are discussed.
9. Investigation of Beer-Spoilage Lactic Acid Bacteria using Omic Approaches
Jordyn Bergsveinson and Barry Ziola
Pages: 245-274.
Consistent production of quality beer requires brewers be concerned with not only the health of fermenting yeast and optimizing brewing conditions, but also with the potential for bacterial contamination at every stage of production. This perpetual threat has driven investigation into mechanisms of bacterial beer-spoilage, with significant emphasis placed on isolates belonging to the group broadly known as lactic acid bacteria (LAB). These organisms are problematic for the global brewing industry, as they are not only able to grow in and spoil the harsh, niche environment of beer, but also frequently elude even current means of detection and control due to the lack of genetic uniformity among diverse brewing-related LAB. This chapter summarizes relevant background in beer-spoilage LAB characterization, detection, and control within the context of beer-spoilage LAB genetic variability. While traditional methods of analysis remain more accessible to brewers for quality control, the advantages of incorporating powerful omics-based methods within the industry are presented. Lastly, current omics methods are discussed in terms of their notable ability to help solve developing issues related to the use of LAB as controlled flavoring and/or fermentation agents by popular craft or specialty brewing operations.
10. Brewery- and Beer-Spoilage-Related Gram-negative Bacteria: The Unpleasant, The Malodorous and The Outright Fetid
Barry Ziola and Jordyn Bergsveinson
Pages: 275-288.
As emphasized by the chapter title, growth of selected Gram-negative bacteria in beer results in an unpalatable product, leading to consumer complaints, and loss of brewer and brand loyalty. Aerobic Gram-negative bacteria historically have been a major problem for brewers, but with improved packaging methods resulting in reduced oxygen levels in beer, these bacteria now are mostly found in improperly attended draft beer systems. Concurrently, reduced oxygen in packaged product resulted in emergence of the anaerobic Gram-negative spoilage bacteria, particularly those within the genera Megasphaera and Pectinatus. Little is known about the genetics of these anaerobic bacteria, given that minimal omics-based research has been done on them. This chapter presents the historical aspects of brewing-related Gram-negative bacteria, where the anaerobic brewing-related bacteria likely originate from and where they are found within breweries, and the evolution of molecular-based approaches for the rapid detection and identification of these bacteria for brewery quality control. Finally, application of metagenomics, genomics, and transcriptomics for improved understanding of brewing-related Gram-negative bacteria is discussed from the perspectives of bacterial persistence within breweries as well as growth in and spoilage of beer.
11. Beer-Spoiling Yeasts: Genomics, Detection, and Control
Chris D. Powell and Daniel W.M. Kerruish
Pages: 289-328.
Beer-spoiling yeasts comprise a diverse group of organisms that can have a variety of impacts on beer production. Invariably, contamination of wort or beer by these yeasts leads to inconsistencies within the process, and quality defects in packaged beer. Beer-spoiling yeasts can be broadly separated into non-fermentative (aerobic) and fermentative yeasts. The former typically exploit process steps associated with raw materials, and areas where oxygen ingress is difficult to prevent, such as unpasteurized cask beers or dispense. Fermentative yeasts are arguably more problematic due to their capacity to compete with production strains during fermentation. Major impacts include altered sugar utilisation, flocculation and ethanol production, as well as the formation of phenolic compounds, acidity, estery off-flavours, and haze or turbidity. These effects occur primarily due to differences in the genetic, metabolic and physiological characteristics of the spoilage yeast and the production strain. In this chapter, we describe the characteristics and functionality of beer-spoiling yeasts, as well as methods for their isolation and identification.

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(EAN: 9781910190616 9781910190623 Subjects: [bacteriology] [microbiology] [mycology] )