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Applied Microbiology of Foods 2.0

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A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: 31 December 2024 | Viewed by 8769

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Prof. Dr. Peter M. Muriana

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1. Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078-6055, USA
2. Robert M. Kerr Food and Agricultural Product Center, Oklahoma State University, Stillwater, OK 74078-6055, USA
Interests: food microbiology of raw and processed meats and produce; foodborne pathogens: Listeria monocytogenes, Salmonella spp., STEC E. coli; vegetable nitrite (‘natural nitrite’) vs sodium nitrite, Clostridium spp.; surrogate organisms to mimic pathogens; antimicrobial interventions (chemical, biological, physical; bacteriocins as biopreservatives); microbiology and processing of dried beef (biltong); biofilms; sanitizers; shelf-life studies/microbial validation
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Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous special issue "Applied Microbiology of Foods ".

I am pleased to announce a Applied Microbiology Special Issue within the field of food microbiology: “Applied Microbiology of Foods 2.0”. This Special Issue will consider a wide scope of applied microbiology as it relates to foodborne microorganisms and their interactions with foods and processes meant to inhibit bacteria or safeguard foods involving foodborne pathogens, spoilage, or beneficial microorganisms. Topics may include antimicrobial interventions, whether chemical, biological, or physical to reduce or eliminate foodborne pathogens or spoilage microorganisms from raw/processed foods. The Special Issue may also include analysis of microbial outcomes or wholesale microbiome analyses of the result of interventions. The use of ‘natural’ antimicrobials (i.e., bacteriocins, bacteriophage, microbial fermentates, vegetable nitrite) has gained favor in applications such as food preservatives. In recent years, natural, microbial-derived ingredients have made gains in their acceptance as natural food ingredients. These include ‘microbial fermentates’ produced by lactic acid bacteria that are generally regarded as safe (GRAS) that include bacteriocins or other natural antimicrobials. Biological modifications using ‘safe’ bacteria have changed the outlook on ‘natural’ vs ‘chemical’ food preservatives and have made an impact on commercial applications in food. Natural sources of antimicrobials may result in a ‘clean/green label’ additive. Such changes have revitalized many commercial processes. Antimicrobial interventions are not limited to chemical/biological treatments; there are also physical processes (drying, blanching, sous vide, hot water shower, submersed water pasteurization, radiant heat oven, microwave processing, high-pressure processing, cold atmospheric plasma) that can provide effective food safety measures to inhibit pathogens and spoilage organisms. As Guest Editor of this Special Issue, I look forward to receiving and reviewing your contributions to this topic.

Prof. Dr. Peter M. Muriana
Guest Editor

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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. Applied Microbiology is an international peer-reviewed open access quarterly journal published by MDPI.

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Published Papers (8 papers)

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Research

27 pages, 1238 KiB

Open AccessArticle

Biogenic Amine Formation in Artisan Galotyri PDO Acid-Curd Cheeses Fermented with Greek Indigenous Starter and Adjunct Lactic Acid Bacteria Strain Combinations: Effects of Cold (4 °C) Ripening and Biotic Factors Compromising Cheese Safety

by Charikleia Tsanasidou, Loulouda Bosnea, Athanasia Kakouri and John Samelis

Appl. Microbiol. 2024, 4(1), 536-562; https://doi.org/10.3390/applmicrobiol4010038 - 18 Mar 2024

Viewed by 626

Abstract

The formation of biogenic amines (BAs) in artisan Galotyri PDO cheeses fermented with Sterptococcus thermophilus ST1 and the Greek indigenous nisin A-producing Lactococcus lactis spp. cremoris M78 (A1cheese), or with the A1 starter supplemented with either the enterocin A-B-P-producing Enterococcus faecium KE82 (A2cheese) or the multi-functional Lactiplantibacillus plantarum H25 (A4cheese) adjunct strains was evaluated. Three pilot-scale cheese trials, GL1, GL2, and GL3, made from boiled ewes’ milk, were analyzed for their BA contents before and after cold ripening at 4 °C for 30 days. Total BAs of the fresh GL1 and GL3 cheeses (pH 4.3–4.5) were below 50 mg/kg, except for the A1/GL1 and A1/GL3 cheeses, which contained ca. 300 mg/kg (81.2% histamine) and 1250 mg/kg (45.6% putrescine) BAs, respectively. Whereas due to an outgrowth (>7 log cfu/g) of post-thermal Gram-negative bacteria contaminants during fermentation, most fresh GL2 cheeses (pH 4.7–5.0) accumulated more than 1500 mg/kg of total BAs, which exceeded 3800 mg/kg in all GL2 cold-ripened cheeses due to major increases in cadaverine and putrescine. Tyramine and histamine exceeded 500 mg/kg in the fresh A1/GL2cheeses. Conversely, total BAs remained or declined below 50 mg/kg in all cold-ripened GL3 cheeses. None of the starter or adjunct cultures could be correlated with a specific BA increase, despite E. faecium KE82, which increased at 7.6–9.2 log cfu/g in the A2 cheeses is a strong tyramine producer in culture BA broth with 1% tyrosine in vitro. The adoption of strict hygienic measures during artisan Galotyri PDO cheese production (trial GL3) enabled the best performance of all starter LAB strain combinations and reduced BA formation, whereas the high presence of Gram-negative decarboxylating bacteria contaminants compromised cheese (trial GL2) safety. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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17 pages, 951 KiB

Open AccessArticle

Auxotrophy-Independent Plasmid Shuttle Vectors for Applications in Diverse Yeasts

by Jeremy R. Smith, Christine D. Sislak, Pedro Fernandez Mendoza, Laurin Carmichael, Alisha G. Lewis, Anqi Chen, Glycine Z. Jiang and Patrick A. Gibney

Appl. Microbiol. 2024, 4(1), 453-469; https://doi.org/10.3390/applmicrobiol4010031 - 28 Feb 2024

Viewed by 677

Abstract

Plasmid shuttle vectors are a common tool used to study yeast physiology. The majority of yeast plasmids have been optimized for Saccharomyces cerevisiae lab strain compatibility, relying on auxotrophic complementation as their selective property. We sought to construct a series of plasmid shuttle vectors to extend functionality beyond strains with auxotrophic requirements, and test compatibility across a diverse panel of yeasts. We constructed 18 plasmids which were successfully maintained by yeasts from several genera. From a panel of 24 yeast strains, these plasmids were maintained by 18 yeasts, spanning 11 species within the genera Lachancea, Metschnikowia, Pichia, Saccharomyces, and Torulaspora. Additionally, an integrated gene expression reporter was assayed for functional compatibility with the 18 strains. Plasmid-derived gene expression was observed for 13 strains, spanning five species within the Saccharomyces genus, in addition to Torulaspora delbrueckii. These results indicate that this plasmid series is broadly useful for advancements and applications within academia, biotechnology, and the food and fermentation industries for research utilizing diverse Saccharomyces and non-Saccharomyces yeasts. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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14 pages, 3735 KiB

Open AccessArticle

Transfer and Inactivation of Listeria monocytogenes during Pilot-Scale Dicing and Flume Washing of Onions

by Andrew M. Scollon, Haiqiang Wang and Elliot T. Ryser

Appl. Microbiol. 2024, 4(1), 439-452; https://doi.org/10.3390/applmicrobiol4010030 - 27 Feb 2024

Viewed by 470

Abstract

This study assessed the extent of L. monocytogenes transfer from onions to the surface of a commercial dicer, from inoculated onions to uninoculated onions, and the efficacy of various sanitizers during the subsequent flume washing of diced onions. Spanish yellow onions (Allium cepa L.) were dip-inoculated in a 3-strain avirulent L. monocytogenes cocktail (5.9 or 4.2 log CFU/50 g) and air-dried. After dicing one 2.2 kg batch of onions inoculated at ~5.9 log CFU/50 g followed by ten uninoculated batches of 2.2 kg each, L. monocytogenes progressively decreased from 4.6 to 2.6 log CFU/50 g in baches 1 through 10, respectively. After onions inoculated at ~4.0 log CFU/g were diced and flume washed for 2 min in tap water, electrolyzed water containing 55 ppm free chlorine, 80 ppm free chlorine from a commercial sanitizer, or 80 ppm peroxyacetic acid and dewatered on a mechanical shaker table, L. monocytogenes populations decreased 0.4, 0.3, 1.4, and 1.0 log, respectively, with populations of ~1.2 log CFU/mL in water for all three sanitizers. These findings should be useful in future risk assessments and aid in the development of improved industry guidelines to better enhance the safety of diced onions. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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25 pages, 1116 KiB

Open AccessArticle

Assessment of the Spoilage Microbiota and the Growth Potential of Listeria monocytogenes in Minced Free-Range Chicken Meat Stored at 4 °C in Vacuum: Comparison with the Spoilage Community of Resultant Retail Modified Atmosphere Packaged Products

by Panagiota Tsafrakidou, Nikoletta Sameli, Athanasia Kakouri, Loulouda Bosnea and John Samelis

Appl. Microbiol. 2023, 3(4), 1277-1301; https://doi.org/10.3390/applmicrobiol3040088 - 28 Nov 2023

Cited by 1 | Viewed by 795

Abstract

Although current diet and nutrition trends in developed countries led the poultry industry to shift to alternative breeding/production methods, such as organic and free-range, limited data on the microbiology of alternative compared to conventional poultry meat products exist. Therefore, this study assessed the evolution and composition of the spoilage microbiota and the growth potential of inoculated (3 log cfu/g) Listeria monocytogenes in freshly minced free-range chicken meat stored at 4 °C in vacuum packages (VP; four batches) for 0, 3, 5, 7, and 10 days. Additionally, two VP batches were compared with their resultant retail products stored in modified atmosphere packages (MAP 30:70 CO₂/N₂) at 4 °C to detect potential differences with the MAP spoilage community described previously. The initial pH of the VP minces was 6.0–6.1, except for one mince, designated VP + AA, which had initial pH 5.8 and was found to contain ‘external’ 1.26% L-lactate and 0.24% acetate associated with a vinegar smell during storage. The rest of the VP batches contained on average 0.75% L-lactate and 0.02% acetate on day 0. After 7 days at 4 °C, L-lactate decreased by at least 3-fold in VP and over 5-fold in VP + AA vs. minor decreases in MAP. Acetate increased 2-fold in all batches. D-lactate (ca. 0.02% on day 0) increased by 4-fold in VP batches only. Lactic acid bacteria (LAB) became the dominant spoilers in all samples. Only VP allowed a delayed 10-fold growth (>5.0 to 6.2 log cfu/g) of pseudomonads from day 7 to day 10 at 4 °C. Compared to VP, VP + AA and MAP retarded growth of LAB, pseudomonads, and enterobacteria by 1–2 log units, at final levels below 6.5, 4.5, and 3.0 log cfu/g, respectively. Enterococci, staphylococci, yeasts, and L. monocytogenes did not grow. Latilactobacillus sakei predominated in all spoiled VP batches (65.8% of 80 meat isolates) followed by Latilactobacillus fuchuensis (9.2%), Leuconostoc carnosum (6.6%), Carnobacterium divergens (6.6%), Latilactobacillus curvatus (5.3%), and Weissella koreensis (2.6%). VP + AA favored Latilactobacillus. Brochothrix thermosphacta was frequent in one VP batch. In conclusion, cold-stored (4 °C), minced, free-range chicken meat spoils more rapidly and offensively under VP than MAP or VP combined with acetate-containing (VP + AA) antimicrobial blends. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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17 pages, 10340 KiB

Open AccessArticle

Bacillus coagulant HYI (BC-HYI) Alleviates LPS-Elicited Oxidative Stress by Engaging the Nrf2/HO-1 Signaling Pathway and Regulates Gut Macrobiotics in Laying Chickens

by Tianhang Lu, Le Wang, Qiong Wu, Hua Zhang, Defeng Cui, Bowen Liu, Jinjin Tong and Yonghong Zhang

Appl. Microbiol. 2023, 3(4), 1178-1194; https://doi.org/10.3390/applmicrobiol3040081 - 09 Oct 2023

Viewed by 895

Abstract

In the current study, Bacillus coagulants had a role in combating oxidative stress by inhibiting the growth of intestinal pathogens. However, there are few studies on reducing the mechanisms of oxidative stress. Therefore, this study aimed to explore the effects and underlying mechanisms of B. coagulant HYI (BC-HYI) treatment on growth and intestinal functions in laying chickens under LPS-induced oxidative stress. The in vivo experimental group included five groups of laying chicks: normal control, LPS group, B6 group, B7 group and B8 group. The test consisted of six repetitions in each group, with six animals in each repetition. In the in vitro experiment, an LPS-induced oxidative stress model of chicken fibroblast DF-1 cells was established, and the DF-1 cells were divided into control group, LPS-treated group, B5 group, B6 group and B7 group. On the one hand, we found that BC-HYI can inhibit pathological changes in some intestinal tissues. On the other hand, BC-HYI supplementation has a dual effect on the gut microbiota, promoting the proliferation of beneficial microbes such as Barbarella, Lactobacillus, and Antibacterial while maintaining symbiotic balance. The abundance of Barbarella, Bactericide, and Cloistral was significantly different between the LPS group and the BC-HYI group (p < 0.01). Moreover, compared with the LPS group, BC-HYI significantly decreased reactive oxygen species levels and prevented cell apoptosis (p < 0.01). It used to prevent oxidative stress by activating the Nrf2-ARE/HO-1 signaling pathway, enhancing the scavenging of free radicals, and reducing oxidative damage. BC-HYI alleviated oxidative stress in laying chickens by modulating the gut microbiota and activating the Nrf2-ARE/HO-1 signaling pathway. In summary, laying chickens and cell experiments indicate that BC-HYI supplementation can improve the enzyme function of antioxidants, regulate intestinal barrier function and activate the Nrf2-ARE/HO-1 signaling pathway to regulate intestinal barrier function. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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14 pages, 3308 KiB

Open AccessArticle

Recombinant Expression in Bacillus megaterium and Biochemical Characterization of Exo-Mannered Glycosyl Hydrolase Family 43 α-L-Arabinofuranosidase from the Korean Black Goat Rumen Metagenome

by Sazzad Hossen Toushik and Md. Ashrafudoulla

Appl. Microbiol. 2023, 3(4), 1164-1177; https://doi.org/10.3390/applmicrobiol3040080 - 06 Oct 2023

Viewed by 894

Abstract

There is no doubt that ruminants have the capability to digest lignocellulosic compounds and to utilize them as an absorbable form of energy by tapping into enzymes produced by the microbial population in their rumens. Among the rumens of various ruminants, this study focused on Korean goat rumens because of their unique digestibility of lignocellulosic biomasses. Therefore, a novel Gene12 gene was screened and unmasked from the constructed rumen metagenomic library of a Korean black goat and expressed in a Bacillus megaterium system. The recombinant protein was distinguished as a novel α-L-arabinofuranosidase enzyme from glycosyl hydrolase family 43 (GH43) for its capability to hydrolyze the non-reducing end of α-1,5-L-arabinofuranose linkages in α-L-arabinofuranosyl groups. The enzyme can also break apart α-L-arabinofuranosidic linkages and act synergistically with other hemicellulolytic enzymes to release α-1,2- and α-1,3-L-arabinofuranosyl groups from L-arabinose-comprising polysaccharides. In silico, phylogenetic, and computational analyses proclaimed that the Gene12 gene encodes a novel carbohydrate-active enzyme possessing a V-shaped indentation of the GH43 catalytic and functional domain (carbohydrate-binding module 6). The recombinant Gene12 protein has shared 81% sequence homology with other members of the GH43 family. Enzymic synopses (optimal pH, temperatures, and stability studies) of the recombinant Gene12 enzyme and its substrate specificity (synthetic and natural substrates) profiling were considered. The recombinant Gene12 α-L-arabinofuranosidase works best at pH 6.0 and 40 °C, and it is stable at pH 4.0 to 7.0 at temperatures of 20 to 50 °C. Additionally, 5-blended β-sheets were identified through a tertiary (3D) structure analysis along with the high substrate specificity against p-nitrophenyl-D-arabinofuranoside (pNPA). The highest substrate specificity of pNPA for Gene12 α-L-arabinofuranosidase indicated its confirmation as an exo-type arabinofuronidase. The results thus propose using the Gene12 protein as an exo-mannered GH43 α-L-arabinofuranosidase (EC 3.2.1.55) enzyme. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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20 pages, 3187 KiB

Open AccessArticle

Screening of Rhizobacterial Isolates from Apple Rhizosphere for Their Biocontrol and Plant Growth Promotion Activity

by Salma Jabiri, Ikram Legrifi, Majda Benhammou, Salah-Eddine Laasli, Fouad Mokrini, Mohammed Bendriss Amraoui and Rachid Lahlali

Appl. Microbiol. 2023, 3(3), 948-967; https://doi.org/10.3390/applmicrobiol3030065 - 22 Aug 2023

Cited by 2 | Viewed by 1197

Abstract

Apple crops are prone to several diseases that limit their production—in particular, root rot caused by a new genus of oomycetes, mainly Phytopythium vexans. This study aims to screen antagonistic bacteria that can play an important role in the biological control of this pathogenic oomycete and to evaluate their capacity to promote plant growth. The dual culture test revealed that, out of 200 bacterial isolates, 16 have been able to inhibit the mycelial growth of P. vexans with inhibition rates greater than 50%. The selected isolates were identified based on the 16S rDNA genes: 14 bacteria belonging to the genus Bacillus, Stenotrophomonas, and the family Enterobacteriaceae. Notably, two isolates, B1 and M2-6 (identified as Bacillus velezensis), demonstrated the highest inhibition rates of 70% and 68%, respectively. These selected isolates were examined for their ability to produce different compounds related to biocontrol and plant growth promotion. Furthermore, the 16 selected isolates were evaluated for their ability to produce compounds associated with biocontrol and plant growth promotion, including hydrolytic enzymes (cellulases, proteases, and amylases), HCN (hydrogen cyanide) production, phosphate solubilization, IAA (indole-3-acetic acid) production, pectinase production, and stimulation of sorghum bicolor growth in vivo. Variations were observed among the bacterial isolates in terms of their compound production and phytostimulation capabilities. However, the secretion of proteases was consistently detected in all antagonistic isolates. The presence of genes responsible for the production of antifungal lipopeptides (bacillomycin, fengycin, and iturin) in the selected bacterial isolates was determined using polymerase chain reaction (PCR) techniques, while the absence of genes involved in surfactin biosynthesis was also confirmed through PCR studies. These isolates demonstrated inhibitory activity through the production of proteases and antifungal lipopeptides. Further research is needed to explore their potential use in biological control strategies and to improve apple crop productivity. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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16 pages, 2960 KiB

Open AccessArticle

Phosphorus Recycling, Biocontrol, and Growth Promotion Capabilities of Soil Bacterial Isolates from Mexican Oak Forests: An Alternative to Reduce the Use of Agrochemicals in Maize Cultivation

by Rocío Hernández-León, Antonio González-Rodríguez and Yunuen Tapia-Torres

Appl. Microbiol. 2022, 2(4), 965-980; https://doi.org/10.3390/applmicrobiol2040074 - 16 Nov 2022

Cited by 1 | Viewed by 1986

Abstract

Six bacteria (Bacillus velezensis 13, Bacillus subtillis 42, Pseudomonas fluorescens E221, Pseudomonas Poae EE12, Rahnella sp. EM1, and Serratia sp. EM2) isolated from the soil and litter of Mexican oak forests were characterized by identifying their ability to acquire phosphorus from different sources, analyzed for their biocontrol capabilities against two different phytopathogenic fungi, and finally tested for their ability to stimulate the germination of maize seeds and promotion of maize seedling growth. The greatest capacity to biocontrol the mycelial growth of phytopathogenic fungi Botrytis cinerea and Fusarium oxysporum was found in B. velezensis 13 and B. subtillis 42. P. poae EE12 and P. fluorescens E221 significantly promoted germination and the length of the primary root in Zea mays. Rahnella sp. EM1 and Serratia sp. EM2 could produce indole compounds related to auxin synthesis and increased the fresh weight of the maize seedlings. Together, these isolates represent an alternative to reduce the use of agrochemicals in maize cultivation. In general, soil microorganisms from Mexican oak forests represent a source of genetic resources for the sustainable management and conservation of soils for agricultural use. Full article

(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)

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