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Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation. Foods 2023; 12:foods12030673. [PMID: 36766201 PMCID: PMC9914028 DOI: 10.3390/foods12030673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.
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De Roos J, Verce M, Weckx S, De Vuyst L. Temporal Shotgun Metagenomics Revealed the Potential Metabolic Capabilities of Specific Microorganisms During Lambic Beer Production. Front Microbiol 2020; 11:1692. [PMID: 32765478 PMCID: PMC7380088 DOI: 10.3389/fmicb.2020.01692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/29/2020] [Indexed: 01/03/2023] Open
Abstract
Lambic beer production processes are characterized by a temporal succession of well-adapted microbial species. Temporal metagenomic analysis of a Belgian, traditional, lambic beer production process, which was examined microbiologically and metabolomically before, confirmed that the microbial diversity is limited. Moreover, it allowed to link the consumption and production of certain compounds to specific microbial groups or species. Fermentation characteristics, such as the conversion of malic acid into lactic acid and acetoin production, were retrieved and could be attributed to specific microorganisms, namely Pediococcus damnosus and Acetobacter species, respectively. Traits previously ascribed to brewery-specific Dekkera bruxellensis strains were confirmed during the lambic beer production process examined multiphasically; in particular, the higher production of 4-ethylguaiacol compared to 4-ethylphenol was further shown by mass spectrometric analysis. Moreover, the absence of phenolic acid decarboxylase in Brettanomyces custersianus was shown culture-independently and could explain its late occurrence during the maturation phase. Furthermore, the potential of maltooligosaccharide degradation could be ascribed metagenomically to not only Brettanomyces species but also Saccharomyces kudriavzevii, possibly explaining their degradation early in the lambic beer production process. Also, acetic acid bacteria (AAB) seemed to be able to consume maltooligosaccharides via their conversion into trehalose. Furthermore, these AAB possessed esterase genes, potentially capable of forming ethyl acetate, which may contribute to the flavor of lambic beer. Improved knowledge on the reasons behind certain community dynamics and the role of the different microorganisms in terms of potential functionality could improve brewery practices to assure to produce more quality-stable end-products.
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Affiliation(s)
- Jonas De Roos
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Mehra R, Kumar H, Kumar N, Kaushik R. Red rice conjugated with barley and rhododendron extracts for new variant of beer. Journal of Food Science and Technology 2020; 57:4152-4159. [PMID: 33071336 DOI: 10.1007/s13197-020-04452-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/03/2020] [Accepted: 04/15/2020] [Indexed: 11/25/2022]
Abstract
This study aimed to determine the effect and potential of red rice in conjunction with barley and rhododendron extracts to develop a new variant of beer. In this study red rice, barley, and rhododendron extracts were used in different combinations and the best combination was selected based on quality and sensory characteristics. The results showed that the developed beer was rich in antioxidant activity (47.68 ± 0.96) and contained a good amount of anthocyanin (35.12 ± 0.79), flavonoids (0.119 ± 0.002), and polyphenols (0.410 ± 0.002). The red rice has more dietary significance than that of polished or milled rice, further, the use of rhododendron provides a large number of secondary metabolites such as tannins, saponins, alkaloids, tannins, and flavonoids. Besides, the sensory profile of the developed beer was quite distinct in terms of aroma, taste, and color from other alternatives available in the market.
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Affiliation(s)
- Rahul Mehra
- Amity Institute of Food Technology, Amity University, Jaipur, Rajasthan India
- School of Bioengineering and Food Technology, Shoolini University, Solan, HP India
| | - Harish Kumar
- Amity Institute of Food Technology, Amity University, Jaipur, Rajasthan India
| | - Naveen Kumar
- Amity Institute of Food Technology, Amity University, Jaipur, Rajasthan India
| | - Ravinder Kaushik
- Amity Institute of Food Technology, Amity University, Noida, Uttar Pradesh 201313 India
- School of Bioengineering and Food Technology, Shoolini University, Solan, HP India
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De Roos J, Vandamme P, De Vuyst L. Wort Substrate Consumption and Metabolite Production During Lambic Beer Fermentation and Maturation Explain the Successive Growth of Specific Bacterial and Yeast Species. Front Microbiol 2018; 9:2763. [PMID: 30510547 PMCID: PMC6252343 DOI: 10.3389/fmicb.2018.02763] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
The present study combined high-throughput culture-dependent plating and culture-independent amplicon sequencing with a metabolite target analysis to systematically dissect the identity, evolution, and role of the microorganisms, substrates, and metabolites during the four-phase fermentation and maturation process of lambic beer production. This led to the following new insights. The changing physicochemical parameters and substrate and metabolite compositions of the fermenting wort and maturing lambic beer provoked several transitions between microbial species and explained the four-step production process. Manual wort acidification with lactic acid shortened the enterobacterial phase and thus kept biogenic amine formation by enterobacteria present during the early stages of fermentation at a minimum. Growth advantages during the alcoholic fermentation phase caused a transition from the prevalence by Hanseniaspora uvarum and Kazachstania species to that by Saccharomyces cerevisiae and later on Saccharomyces kudriavzevii, due to changing environmental parameters. During the acidification phase, Pediococcus damnosus was prevalent and performed a malolactic fermentation. Acetobacter pasteurianus produced acetic acid and acetoin. Upon maturation, Dekkera species appeared, together with P. damnosus and Pichia membranifaciens, thereby contributing to acetic acid production, depending on the oxygen availability. Moreover, the Dekkera species consumed the acetoin produced by the acetic acid bacteria for redox balancing. The breakdown of maltooligosaccharides seemed to be independent of the occurrence of Dekkera species and started already early in the fermentation process.
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Affiliation(s)
- Jonas De Roos
- Research Group of Industrial Microbiology and Food Biotechnology, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Peter Vandamme
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels, Belgium
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Bokulich NA, Bamforth CW, Mills DA. A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2012-0709-01] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nicholas A. Bokulich
- Department of Viticulture and Enology and Department of Food Science and Technology
| | | | - David A. Mills
- Department of Viticulture and Enology and Department of Food Science and Technology, University of California, Davis 95616
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Liu SP, Mao J, Liu YY, Meng XY, Ji ZW, Zhou ZL, Ai-lati A. Bacterial succession and the dynamics of volatile compounds during the fermentation of Chinese rice wine from Shaoxing region. World J Microbiol Biotechnol 2015; 31:1907-21. [DOI: 10.1007/s11274-015-1931-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/23/2015] [Indexed: 01/14/2023]
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Spitaels F, Van Kerrebroeck S, Wieme AD, Snauwaert I, Aerts M, Van Landschoot A, De Vuyst L, Vandamme P. Microbiota and metabolites of aged bottled gueuze beers converge to the same composition. Food Microbiol 2015; 47:1-11. [DOI: 10.1016/j.fm.2014.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 10/02/2014] [Accepted: 10/07/2014] [Indexed: 11/28/2022]
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Indigenous bacteria and fungi drive traditional kimoto sake fermentations. Appl Environ Microbiol 2014; 80:5522-9. [PMID: 24973064 DOI: 10.1128/aem.00663-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sake (Japanese rice wine) production is a complex, multistage process in which fermentation is performed by a succession of mixed fungi and bacteria. This study employed high-throughput rRNA marker gene sequencing, quantitative PCR, and terminal restriction fragment length polymorphism to characterize the bacterial and fungal communities of spontaneous sake production from koji to product as well as brewery equipment surfaces. Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus var. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. The microbiota driving these fermentations were also prevalent in the production environment, illustrating the reservoirs and routes for microbial contact in this traditional food fermentation. Interrogating the microbial consortia of production environments in parallel with food products is a valuable approach for understanding the complete ecology of food production systems and can be applied to any food system, leading to enlightened perspectives for process control and food safety.
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Abstract
Brewing beer involves microbial activity at every stage, from raw material production and malting to stability in the package. Most of these activities are desirable, as beer is the result of a traditional food fermentation, but others represent threats to the quality of the final product and must be controlled actively through careful management, the daily task of maltsters and brewers globally. This review collates current knowledge relevant to the biology of brewing yeast, fermentation management, and the microbial ecology of beer and brewing.
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Affiliation(s)
- Nicholas A. Bokulich
- Department of Food Science and Technology, University of California, Davis, California, USA
- Department of Viticulture and Enology, University of California, Davis, California, USA
| | - Charles W. Bamforth
- Department of Food Science and Technology, University of California, Davis, California, USA
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Vriesekoop F, Krahl M, Hucker B, Menz G. 125thAnniversary Review: Bacteria in brewing: The good, the bad and the ugly. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/jib.49] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Frank Vriesekoop
- Department of Food Science and Agri-Food Supply Chain Management; Harper Adams University; Newport TF10 8NB UK
- School of Health Sciences; University of Ballarat; Ballarat Victoria Australia
| | | | - Barry Hucker
- School of Health Sciences; University of Ballarat; Ballarat Victoria Australia
| | - Garry Menz
- School of Health Sciences; University of Ballarat; Ballarat Victoria Australia
- Carlton and United Breweries; Yatala Brewery; Yatala Queensland Australia
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Martens H, Iserentant D, Verachtert H. MICROBIOLOGICAL ASPECTS OF A MIXED YEAST-BACTERIAL FERMENTATION IN THE PRODUCTION OF A SPECIAL BELGIAN ACIDIC ALE. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1997.tb00939.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Bokulich NA, Bamforth CW, Mills DA. Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale. PLoS One 2012; 7:e35507. [PMID: 22530036 PMCID: PMC3329477 DOI: 10.1371/journal.pone.0035507] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/16/2012] [Indexed: 01/22/2023] Open
Abstract
American coolship ale (ACA) is a type of spontaneously fermented beer that employs production methods similar to traditional Belgian lambic. In spite of its growing popularity in the American craft-brewing sector, the fermentation microbiology of ACA has not been previously described, and thus the interface between production methodology and microbial community structure is unexplored. Using terminal restriction fragment length polymorphism (TRFLP), barcoded amplicon sequencing (BAS), quantitative PCR (qPCR) and culture-dependent analysis, ACA fermentations were shown to follow a consistent fermentation progression, initially dominated by Enterobacteriaceae and a range of oxidative yeasts in the first month, then ceding to Saccharomyces spp. and Lactobacillales for the following year. After one year of fermentation, Brettanomyces bruxellensis was the dominant yeast population (occasionally accompanied by minor populations of Candida spp., Pichia spp., and other yeasts) and Lactobacillales remained dominant, though various aerobic bacteria became more prevalent. This work demonstrates that ACA exhibits a conserved core microbial succession in absence of inoculation, supporting the role of a resident brewhouse microbiota. These findings establish this core microbial profile of spontaneous beer fermentations as a target for production control points and quality standards for these beers.
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Affiliation(s)
- Nicholas A. Bokulich
- Department of Viticulture and Enology, Robert Mondavi Institute of Wine and Food Science, University of California Davis, Davis, California, United States of America
- Department of Food Science and Technology, Robert Mondavi Institute of Wine and Food Science, University of California Davis, Davis, California, United States of America
| | - Charles W. Bamforth
- Department of Food Science and Technology, Robert Mondavi Institute of Wine and Food Science, University of California Davis, Davis, California, United States of America
| | - David A. Mills
- Department of Viticulture and Enology, Robert Mondavi Institute of Wine and Food Science, University of California Davis, Davis, California, United States of America
- Department of Food Science and Technology, Robert Mondavi Institute of Wine and Food Science, University of California Davis, Davis, California, United States of America
- * E-mail:
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Farkas G, Rezessy-Szabó J, Zákány F, Hoschke Á. Interaction ofSaccharomycesand non-Saccharomycesyeast strains in an alcoholic fermentation process. ACTA ALIMENTARIA 2005. [DOI: 10.1556/aalim.34.2005.1.11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Hasona A, York SW, Yomano LP, Ingram LO, Shanmugam KT. Decreasing the level of ethyl acetate in ethanolic fermentation broths of Escherichia coli KO11 by expression of Pseudomonas putida estZ esterase. Appl Environ Microbiol 2002; 68:2651-9. [PMID: 12039716 PMCID: PMC123972 DOI: 10.1128/aem.68.6.2651-2659.2002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the fermentation of sugars to ethanol relatively high levels of an undesirable coproduct, ethyl acetate, are also produced. With ethanologenic Escherichia coli strain KO11 as the biocatalyst, the level of ethyl acetate in beer containing 4.8% ethanol was 192 mg liter(-1). Although the E. coli genome encodes several proteins with esterase activity, neither wild-type strains nor KO11 contained significant ethyl acetate esterase activity. A simple method was developed to rapidly screen bacterial colonies for the presence of esterases which hydrolyze ethyl acetate based on pH change. This method allowed identification of Pseudomonas putida NRRL B-18435 as a source of this activity and the cloning of a new esterase gene, estZ. Recombinant EstZ esterase was purified to near homogeneity and characterized. It belongs to family IV of lipolytic enzymes and contains the conserved catalytic triad of serine, aspartic acid, and histidine. As expected, this serine esterase was inhibited by phenylmethylsulfonyl fluoride and the histidine reagent diethylpyrocarbonate. The native and subunit molecular weights of the recombinant protein were 36,000, indicating that the enzyme exists as a monomer. By using alpha-naphthyl acetate as a model substrate, optimal activity was observed at pH 7.5 and 40 degrees C. The Km and Vmax for alpha-naphthyl acetate were 18 microM and 48.1 micromol. min(-1). mg of protein(-1), respectively. Among the aliphatic esters tested, the highest activity was obtained with propyl acetate (96 micromol. min(-1). mg of protein(-1)), followed by ethyl acetate (66 micromol. min(-1). mg of protein(-1)). Expression of estZ in E. coli KO11 reduced the concentration of ethyl acetate in fermentation broth (4.8% ethanol) to less than 20 mg liter(-1).
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Affiliation(s)
- Adnan Hasona
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, USA
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