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Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 35240

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Prof. Dr. Rosanna Tofalo

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Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
Interests: wine yeast; Saccharomyces cerevisiae; Kluyveromyces marxianus; non-Saccharomyces; yeast physiology; yeast flocculation; biofilm; biogenic amines
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Prof. Dr. Lisa Solieri

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Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, Besta Building - 42122 Reggio, Emilia, Italy
Interests: model and non-model yeast genomics and genetic manipulation; outcrossing as a genetic improvement strategy; adaptive evolution of yeasts and lactic acid bacteria; bioactive peptide release by lactic acid bacteria; whey valorization; beer innovation; dairy lactic acid bacteria functional characterization
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Dr. Alessandra Pino

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Department of Agricultural, Food and Environment, University of Catania, Santa Sofia Street, 100, 95123 Catania, Italy
Interests: lactic acid bacteria; fermented food; functional food; probiotics; omics approach
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Yeasts and lactic acid bacteria are the two foremost workhouses used for the production of many fermented foods from ancient times, and recently, they have moved into the scientific arena as promising cell factories for producing bioproducts, healthy molecules, and many other commodities in the biorefinery framework. High-throughput sequencing approaches and CRIPR-Cas gene editing technologies have boosted our understanding of food ecosystems and helped to draw precise maps on genotype–phenotype relationships for many industrially relevant species other than the model systems Saccharomyces cerevisiae and Lactococcus lactis. This body of knowledge can help us to develop innovative solutions that support healthy food development and sustainable management of agri-food byproducts, making it possible to move from a fossil to a bio-based economy. However, achieving this transition is hindered by a large pool of gene and metabolic functions that remain unknown, the many uncharacterized interactions between yeasts and lactic acid bacteria, inadequate tools to accurately measure and simulate relevant phenotypes across time and space, and the limited availability of approaches to precisely manipulate microbial cells. This Special Issue aims to collect scientific efforts to overcome these challenges, and, therefore, covers the following topics:

Yeasts and lactic acid bacteria consortia: from metagenomics to metatranscriptomics and metabolomics studies; ecological interactions and quorum sensing molecules;
Yeast and lactic acid bacteria as microbial platforms for producing added-value bio-commodities from agri-food wastes: from biodiversity bioprospecting to metabolic engineering;
Food innovation driven by non-conventional yeasts and human health-promoting lactic acid bacteria.

Dr. Rosanna Tofalo
Prof. Dr. Lisa Solieri
Dr. Alessandra Pino
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Keywords

sustainable circular economy
healthy food and beverages
added-value bioproducts
agri-food waste
synthetic biology
metagenomics
mixed consortia
alcoholic fermentation
lactic fermentation
biorefinery

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Published Papers (9 papers)

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Research

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24 pages, 7837 KiB

Open AccessArticle

Sour Beer as Bioreservoir of Novel Craft Ale Yeast Cultures

by Chiara Nasuti, Jennifer Ruffini, Laura Sola, Mario Di Bacco, Stefano Raimondi, Francesco Candeliere and Lisa Solieri

Microorganisms 2023, 11(9), 2138; https://doi.org/10.3390/microorganisms11092138 - 23 Aug 2023

Cited by 2 | Viewed by 2580

Abstract

The increasing demand for craft beer is driving the search for novel ale yeast cultures from brewing-related wild environments. The focus of bioprospecting for craft cultures is to identify feral yeasts suitable to imprint unique sensorial attributes onto the final product. Here, we integrated phylogenetic, genotypic, genetic, and metabolomic techniques to demonstrate that sour beer during aging in wooden barrels is a source of suitable craft ale yeast candidates. In contrast to the traditional lambic beer maturation phase, during the aging of sour-matured production-style beer, different biotypes of Saccharomyces cerevisiae dominated the cultivable in-house mycobiota, which were followed by Pichia membranifaciens, Brettanomyces bruxellensis, and Brettanomyces anomalus. In addition, three putative S. cerevisiae × Saccharomyces uvarum hybrids were identified. S. cerevisiae feral strains sporulated, produced viable monosporic progenies, and had the STA1 gene downstream as a full-length promoter. During hopped wort fermentation, four S. cerevisiae strains and the S. cerevisiae × S. uvarum hybrid WY213 exceeded non-Saccharomyces strains in fermentative rate and ethanol production except for P. membranifaciens WY122. This strain consumed maltose after a long lag phase, in contrast to the phenotypic profile described for the species. According to the STA1+ genotype, S. cerevisiae partially consumed dextrin. Among the volatile organic compounds (VOCs) produced by S. cerevisiae and the S. cerevisiae × S. uvarum hybrid, phenylethyl alcohol, which has a fruit-like aroma, was the most prevalent. In conclusion, the strains characterized here have relevant brewing properties and are exploitable as indigenous craft beer starters. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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17 pages, 2860 KiB

Open AccessArticle

Effect of Fermentation with Streptococcus thermophilus Strains on In Vitro Gastro-Intestinal Digestion of Whey Protein Concentrates

by Ahmed Helal, Sara Pierri, Davide Tagliazucchi and Lisa Solieri

Microorganisms 2023, 11(7), 1742; https://doi.org/10.3390/microorganisms11071742 - 3 Jul 2023

Cited by 3 | Viewed by 1755

Abstract

Three Streptococcus thermophilus strains, namely RBC6, RBC20, and RBN16, were proven to release bioactive peptides during whey protein concentrate (WPC) fermentation, resulting in WPC hydrolysates with biological activities. However, these bioactive peptides can break down during gastro-intestinal digestion (GID), hindering the health-promoting effect of fermented WPC hydrolysates in vivo. In this work, the effect of simulated GID on three WPC hydrolysates fermented with S. thermophilus strains, as well as on unfermented WPC was studied in terms of protein hydrolysis, biological activities, and peptidomics profiles, respectively. In general, WPC fermentation enhanced protein hydrolysis compared to unfermented WPC. After in vitro GID, WPC fermented with S. thermophilus RBC20 showed the highest antioxidant activity, whereas WPC fermented with strain RBC06 displayed the highest angiotensin-converting enzyme (ACE)- and dipeptidyl peptidase IV (DPP-IV)-inhibitory activities. Peptidomics analysis revealed that all digested WPC samples were highly similar to each other in peptide profiles, and 85% of the 46 identified bioactive peptides were shared among fermented and unfermented samples. However, semi-quantitative analysis linked the observed differences in biological activities among the samples to differences in the amount of bioactive peptides. The anti-hypertensive peptides VPP and IPP, as well as the DPP-IV-inhibitory peptide APFPE, were quantified. In conclusion, WPC fermentation with S. thermophilus positively impacted protein hydrolysis and bioactive peptide release during GID. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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18 pages, 3063 KiB

Open AccessArticle

Exploring the Potential of Sustainable Acid Whey Cheese Supplemented with Apple Pomace and GABA-Producing Indigenous Lactococcus lactis Strain

by Justina Mileriene, Loreta Serniene, Beatrice Kasparaviciene, Lina Lauciene, Neringa Kasetiene, Gintare Zakariene, Milda Kersiene, Daiva Leskauskaite, Jonas Viskelis, Yiannis Kourkoutas and Mindaugas Malakauskas

Microorganisms 2023, 11(2), 436; https://doi.org/10.3390/microorganisms11020436 - 9 Feb 2023

Cited by 8 | Viewed by 2478

Abstract

This study aimed to utilize two by-products, acid whey and apple pomace, as well as an indigenous Lactococcus lactis LL16 strain with the probiotic potential to produce a sustainable cheese with functional properties. Acid whey protein cheese was made by thermocoagulation of fresh acid whey and enhancing the final product by adding apple pomace, L. lactis LL16 strain, or a mixture of both. The sensory, the physicochemical, the proteolytic, and the microbiological parameters were evaluated during 14 days of refrigerated storage. The supplementation of the cheese with apple pomace affected (p ≤ 0.05) the cheese composition (moisture, protein, fat, carbohydrate, and fiber), the texture, the color (lightness, redness, and yellowness), and the overall sensory acceptability. The addition of the presumptive probiotic L. lactis LL16 strain decreased (p ≤ 0.05) the concentration of glutamic acid, thus increasing γ-aminobutyric acid (GABA) significantly in the acid whey cheese. The supplementation with apple pomace resulted in slightly (p < 0.05) higher counts of L. lactis LL16 on day seven, suggesting a positive effect of apple pomace components on strain survival. The symbiotic effect of apple pomace and LL16 was noted on proteolysis (pH 4.6-soluble nitrogen and free amino acids) in the cheese on day one, which may have positively influenced the overall sensory acceptance. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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11 pages, 1158 KiB

Open AccessArticle

Effect of Trehalose and Lactose Treatments on the Freeze-Drying Resistance of Lactic Acid Bacteria in High-Density Culture

by Shumao Cui, Mengyu Hu, Yuanyuan Sun, Bingyong Mao, Qiuxiang Zhang, Jianxin Zhao, Xin Tang and Hao Zhang

Microorganisms 2023, 11(1), 48; https://doi.org/10.3390/microorganisms11010048 - 23 Dec 2022

Cited by 12 | Viewed by 4102

Abstract

Freeze-drying is a commonly used method in commercial preparations of lactic acid bacteria. However, some bacteria are killed during the freeze-drying process. To overcome this, trehalose and lactose are often used as protective agents. Moreover, high-density culture is an efficient way to grow bacterial strains but creates a hypertonic growth environment. We evaluated the effects of trehalose and lactose, as a primary carbon source or as an additive in fermentation, on the freeze-drying survival of Lactobacillus fermentum FXJCJ6-1, Lactobacillus brevis 173-1-2, and Lactobacillus reuteri CCFM1040. Our results showed that L. fermentum FXJCJ6-1 accumulated but did not use intracellular trehalose in a hypertonic environment, which enhanced its freeze-drying resistance. Furthermore, genes that could transport trehalose were identified in this bacterium. In addition, both the lactose addition and lactose culture improved the freeze-drying survival of the bacterium. Further studies revealed that the added lactose might exert its protective effect by attaching to the cell surface, whereas lactose culture acted by reducing extracellular polysaccharide production and promoting the binding of the protectant to the cell membrane. The different mechanisms of lactose and trehalose in enhancing the freeze-drying resistance of bacteria identified in this study will help to elucidate the anti-freeze-drying mechanisms of other sugars in subsequent investigations. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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15 pages, 2534 KiB

Open AccessArticle

Microbial Consortia Involved in Traditional Sicilian Sourdough: Characterization of Lactic Acid Bacteria and Yeast Populations

by Alessandra Pino, Nunziatina Russo, Lisa Solieri, Laura Sola, Cinzia Caggia and Cinzia Lucia Randazzo

Microorganisms 2022, 10(2), 283; https://doi.org/10.3390/microorganisms10020283 - 26 Jan 2022

Cited by 22 | Viewed by 3538

Abstract

Sourdough is one of the oldest starters traditionally used for making baked goods, offering several advantages to the sensory, rheology, and shelf life of final products. The present study investigated, for the first time, the microbiota of spontaneously fermented Maiorca dough samples collected from bakeries located in Sicily (Italy). Four sourdough samples (M1, M2, M3, and M4), were produced using Triticum vulgare Host. var. albidum Koern (Maiorca grain) were subjected to LAB and yeasts isolation and identification at the species level. The in-depth characterization of the lactobacilli population revealed that Lactiplantibacillus plantarum and Levilactobacillus brevis unquestionably dominated the Maiorca sourdough ecosystem. Concerning the yeasts community, high species diversity was found. Saccharomyces cerevisiae and Wickerhamomyces anomalus were the most frequently isolated species. In addition, Torulaspora delbrueckii, Pichia kluyveri, Candida boidinii, and Candida diddensiae were also detected. Investigations on both pro-technological and functional traits of the isolated strains could lead to the selection of starters for the production of baked goods. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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20 pages, 19104 KiB

Open AccessArticle

Characterization of Yeasts Isolated from Parmigiano Reggiano Cheese Natural Whey Starter: From Spoilage Agents to Potential Cell Factories for Whey Valorization

by Serena Martini, Mattia Bonazzi, Ilaria Malorgio, Valentina Pizzamiglio, Davide Tagliazucchi and Lisa Solieri

Microorganisms 2021, 9(11), 2288; https://doi.org/10.3390/microorganisms9112288 - 3 Nov 2021

Cited by 14 | Viewed by 3072

Abstract

Whey is the main byproduct of the dairy industry and contains sugars (lactose) and proteins (especially serum proteins and, at lesser extent, residual caseins), which can be valorized by the fermentative action of yeasts. In the present study, we characterized the spoilage yeast population inhabiting natural whey starter (NWS), the undefined starter culture of thermophilic lactic acid bacteria used in Parmigiano Reggiano (PR) cheesemaking, and evaluated thermotolerance, mating type, and the aptitude to produce ethanol and bioactive peptides from whey lactose and proteins, respectively, in a selected pool of strains. PCR-RFLP assay of ribosomal ITS regions and phylogenetic analysis of 26S rDNA D1/D2 domains showed that PR NWS yeast population consists of the well-documented Kluyveromyces marxianus, as well as of other species (Saccharomyces cerevisiae, Wickerhamiella pararugosa, and Torulaspora delbrueckii), with multiple biotypes scored within each species as demonstrated by (GTG)₅-based MSP-PCR. Haploid and diploid K. marxianus strains were identified through MAT genotyping, while thermotolerance assay allowed the selection of strains suitable to grow up to 48 °C. In whey fermentation trials, one thermotolerant strain was suitable to release ethanol with a fermentation efficiency of 86.5%, while another candidate was able to produce the highest amounts of both ethanol and bioactive peptides with potentially anti-hypertensive function. The present work demonstrated that PR NWS is a reservoir of ethanol and bioactive peptides producer yeasts, which can be exploited to valorize whey, in agreement with the principles of circularity and sustainability. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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18 pages, 5124 KiB

Open AccessArticle

Exogenous Probiotics Improve Fermentation Quality, Microflora Phenotypes, and Trophic Modes of Fermented Vegetable Waste for Animal Feed

by Guilin Du, Jiping Shi, Jingxian Zhang, Zhiguo Ma, Xiangcen Liu, Chenyang Yuan, Baoguo Zhang, Zhanying Zhang and Mark D. Harrison

Microorganisms 2021, 9(3), 644; https://doi.org/10.3390/microorganisms9030644 - 19 Mar 2021

Cited by 15 | Viewed by 3495

Abstract

The fermentation of leaf vegetable waste to produce animal feed reduces the environmental impact of vegetable production and transforms leaf vegetable waste into a commodity. We investigated the effect of exogenous probiotics and lignocellulose enzymes on the quality and microbial community of fermented feed (FF) produced from cabbage waste. The addition of exogenous probiotics resulted in increased crude protein (CP) content (p < 0.05), better odor (moderate organic acid and ethanol, with low ammonia-N, p < 0.05), and a lower relative abundance (RA) of pathogens (below 0.4%, p < 0.05) in FF, compared to without. With the addition of exogenous probiotics, only Pediococcus and Saccharomyces were enriched and symbiotic in FF; these were the keystone taxa to reduce the abundance of aerobic, form-biofilms, and pathogenic microorganisms, resulting in an efficient anaerobic fermentation system characterized by facultative anaerobic and Gram-positive bacterial communities, and undefined saprotroph fungal communities. Thus, inoculation of vegetable waste fermentation with exogenous probiotics is a promising strategy to enhance the biotransformation of vegetable waste into animal feed. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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Review

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25 pages, 1406 KiB

Open AccessReview

Lactic Acid Bacteria and Bacteriocins: Novel Biotechnological Approach for Biopreservation of Meat and Meat Products

by Dipanwita Bhattacharya, Pramod Kumar Nanda, Mirian Pateiro, José M. Lorenzo, Pubali Dhar and Arun K. Das

Microorganisms 2022, 10(10), 2058; https://doi.org/10.3390/microorganisms10102058 - 18 Oct 2022

Cited by 34 | Viewed by 7765

Abstract

Meat and meat products are perishable in nature, and easily susceptible to microbial contamination and chemical deterioration. This not only results in an increased risk to health of consumers, but also causes economic loss to the meat industry. Some microorganisms of the lactic acid bacteria (LAB) group and their ribosomal-synthesized antimicrobial peptides—especially bacteriocins—can be used as a natural preservative, and an alternative to chemical preservatives in meat industry. Purified or partially purified bacteriocins can be used as a food additive or incorporated in active packaging, while bacteriocin-producing cells could be added as starter or protective cultures for fermented meats. Large-scale applications of bacteriocins are limited, however, mainly due to the narrow antimicrobial spectrum and varying stability in different food matrixes. To overcome these limitations, bioengineering and biotechnological techniques are being employed to combine two or more classes of bacteriocins and develop novel bacteriocins with high efficacy. These approaches, in combination with hurdle concepts (active packaging), provide adequate safety by reducing the pathogenicity of spoilage microorganisms, improving sensory characteristics (e.g., desirable flavor, texture, aroma) and enhancing the shelf life of meat-based products. In this review, the biosynthesis of different classes of LAB bacteriocins, their mechanism of action and their role in the preservation of meats and meat products are reviewed. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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12 pages, 307 KiB

Open AccessReview

Olive Pomace and Pâté Olive Cake as Suitable Ingredients for Food and Feed

by Paola Foti, Alessandra Pino, Flora V. Romeo, Amanda Vaccalluzzo, Cinzia Caggia and Cinzia L. Randazzo

Microorganisms 2022, 10(2), 237; https://doi.org/10.3390/microorganisms10020237 - 21 Jan 2022

Cited by 25 | Viewed by 4408

Abstract

Olive oil extraction generates several by-products that represent an environmental issue, mainly for Mediterranean countries where olive oil is mostly produced. These by-products represent an ecological issue for their phenolic components, such as oleuropein, hydroxytyrosol, and tyrosol. However, olive oil by-products can be treated and properly exploited in different fields for their health-promoting properties, and they represent great potential for the food and beverage, cosmetic, and pharmaceutical industries. Furthermore, recovery and treatment processes can contribute to efficient waste management, which can enhance the sustainability of the olive oil industry, and in turn, lead to relevant economic benefits. The solid waste, i.e., olive pomace, could be considered to be a suitable matrix or primary resource of molecules with high added value due to their high phenolic content. Olive pomace, at different moisture contents, is the main by-product obtained from two- or three-phase extraction systems. A commonly used centrifugal extraction system, i.e., a multiphase decanter (DMF), does not require the addition of water and can generate a new by-product called pâté or olive pomace cake, consisting of moist pulp that is rich in phenols, in particular, secoiridoids, without any trace of kernel. Although several reviews have been published on olive wastes, only a few reviews have specifically focused on the solid by-products. Therefore, the aim of the present review is to provide a comprehensive overview on the current valorization of the main solid olive oil by-products, in particular, olive pomace or pâté olive cake, highlighting their use in different fields, including human nutrition. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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