Contamination of Fermentation Systems and Methods of Control

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Fermentation Process Design".

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 10120

Special Issue Editor

Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
Interests: industrial fermentation; industrial microbiology; biofuels; beverage alcohols; distilled spirits; beer; life cycle assessment; efficiencies; technoeconomic analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Throughout human history, carbohydrates have been fermented into alcohols for human consumption, especially for beer, wine, whiskey, and other alcoholic beverages. In recent years, we have also witnessed tremendous growth in the research, development, and commercialization of many biorenewable resources. Starches, lipids, proteins, and fibers can now be utilized to produce a variety of bio-based energy, fuels, products, chemicals, and other renewable materials. Many countries have experienced exponential growth in biofuel production, such as maize- and sugarcane-based ethanol, as well as soy, canola, palm, and other oilseed-based biodiesel. Biochemicals such as succinic acid, muconic acid, triacetic acid lactone, bioplastics such as polylactic acid, glycerol-based bioadhesives, and other bio-based products are increasingly being commercialized as well. Although the science, engineering, and technology of conversion and utilization are progressing, there is a critical need for more detailed studies on fermentation processes, the conditions used, and impacts on final products.

This Special Issue is particularly interested in studies that focus on microbial contamination of industrial fermentation systems, including plant design and operations, preventing microbial contamination, detecting contamination events, methods for identification of microbial contaminants, antibiotic and antimicrobial control of contaminated systems, understanding the competing and inhibitory effects of microbial contaminants vis-à-vis yeast on alcohol production and yield, antimicrobial residues post-fermentation, and the modeling and simulation of contaminated systems.

Contamination control for fermentations is critical whether the system is used for human beverages, biofuels, or other bio-based products.

Prof. Dr. Kurt A. Rosentrater
Guest Editor

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • batch fermentation
  • beer
  • biochemicals
  • bioenergy
  • biofuels
  • bioproducts
  • biorenewables
  • contamination
  • continuous fermentation
  • enzyme kinetics
  • fermentation
  • inhibitors
  • modeling
  • monod kinetics
  • simulation
  • whiskey/whisky
  • wine

Published Papers (3 papers)

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Research

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15 pages, 319 KiB  
Article
Development of a Taxon-Specific Real-Time PCR Method Targeting the Bacillus subtilis Group to Strengthen the Control of Genetically Modified Bacteria in Fermentation Products
Fermentation 2022, 8(2), 78; https://doi.org/10.3390/fermentation8020078 - 12 Feb 2022
Cited by 3 | Viewed by 2430
Abstract
Most of the bacteria that are used to produce fermentation products, such as enzymes, additives and flavorings, belong to the Bacillus subtilis group. Recently, unexpected contaminations with unauthorized genetically modified (GM) bacteria (viable cells and associated DNA) that were carrying antimicrobial resistance (AMR) [...] Read more.
Most of the bacteria that are used to produce fermentation products, such as enzymes, additives and flavorings, belong to the Bacillus subtilis group. Recently, unexpected contaminations with unauthorized genetically modified (GM) bacteria (viable cells and associated DNA) that were carrying antimicrobial resistance (AMR) genes was noticed in several microbial fermentation products that have been commercialized on the food and feed market. These contaminations consisted of GM Bacillus species belonging to the B. subtilis group. In order to screen for the potential presence of such contaminations, in this study we have developed a new real-time PCR method targeting the B. subtilis group, including B. subtilis, B. licheniformis, B. amyloliquefaciens and B. velezensis. The method’s performance was successfully assessed as specific and sensitive, complying with the Minimum Performance Requirements for Analytical Methods of GMO Testing that is used as a standard by the GMO enforcement laboratories. The method’s applicability was also tested on 25 commercial microbial fermentation products. In addition, this method was developed to be compatible with the PCR-based strategy that was recently developed for the detection of unauthorized GM bacteria. This taxon-specific method allows the strengthening of the set of screening markers that are targeting key sequences that are frequently found in GM bacteria (AMR genes and shuttle vector), reinforcing control over the food and feed chain in order to guarantee its safety and traceability. Full article
(This article belongs to the Special Issue Contamination of Fermentation Systems and Methods of Control)
16 pages, 1594 KiB  
Article
Differentiation of Penicillium roqueforti from Closely Related Species Contaminating Cheeses and Dairy Environment
Fermentation 2021, 7(4), 222; https://doi.org/10.3390/fermentation7040222 - 09 Oct 2021
Cited by 1 | Viewed by 2101
Abstract
Currently, Penicillium roqueforti and the closely related P. carneum and P. paneum are identified based on their macromorphology, micromorphology, and molecular properties, the determination of which involves time-consuming procedures. Culture collections focused on dairy isolates of P. roqueforti require quick and efficient tools [...] Read more.
Currently, Penicillium roqueforti and the closely related P. carneum and P. paneum are identified based on their macromorphology, micromorphology, and molecular properties, the determination of which involves time-consuming procedures. Culture collections focused on dairy isolates of P. roqueforti require quick and efficient tools for routine applications to identify the (a) taxonomy affiliation and (b) morphological properties of strains that influence the sensory properties of blue-veined cheeses. Here, we assessed the morphological variability of P. roqueforti, P. carneum, P. paneum, and P.crustosum on artificial, Edam-like, and Roquefort-like media. Molecular tools were used to test P. roqueforti strains and clones effectively. A novel primer, PrsF, was tested for specificity within strains and isolates of P. roqueforti compared to P. carneum, P. paneum, and P. crustosum. The results reveal that PrsF was specific to the P. roqueforti samples and did not amplify the other tested Penicillium species. Identification based simultaneously on the specificity of the PrsF primer pair and cultivation of P. roqueforti strains on Roquefort-like medium represents an effective method for expanding the collections and practical use of P. roqueforti in the dairy industry. Full article
(This article belongs to the Special Issue Contamination of Fermentation Systems and Methods of Control)
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Review

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12 pages, 312 KiB  
Review
The Technological Perspectives of Kombucha and Its Implications for Production
Fermentation 2022, 8(4), 185; https://doi.org/10.3390/fermentation8040185 - 13 Apr 2022
Cited by 15 | Viewed by 4519
Abstract
Fermentation is one of the oldest biotechnological tools employed by mankind. Fermenting food gives them better sensory and nutritional qualities, the latter including vitamins, phenolic compounds, antioxidants, and antimicrobials. Kombucha is the result of the fermentation of a sweetened Camellia sinensis infusion by [...] Read more.
Fermentation is one of the oldest biotechnological tools employed by mankind. Fermenting food gives them better sensory and nutritional qualities, the latter including vitamins, phenolic compounds, antioxidants, and antimicrobials. Kombucha is the result of the fermentation of a sweetened Camellia sinensis infusion by the action of a symbiotic community of yeasts and bacteria organized in a cellulosic biofilm called SCOBY and has gained great prominence among fermented foods and beverages, with a considerable increase in its popularity in the last decade, both among consumers and within the scientific community. This is explained by the particular functional and microbial characteristics of this beverage, such as its antioxidant and antimicrobial potential, long-term stable microbial communities, its suitability for fermentation under different conditions of time and temperature, and amenability to other carbon sources besides sucrose. Thus, this review aims to present and discuss the functional, microbial, and physicochemical aspects of kombucha fermentation, covering the many challenges that arise in its production, in domestic, commercial, and legislation contexts, and the next steps that need to be taken in order to understand this drink and its complex fermentation process. Full article
(This article belongs to the Special Issue Contamination of Fermentation Systems and Methods of Control)
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