Beneficial and Detrimental Microorganisms Occurring in Fermented Foods

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

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 21062

Special Issue Editors

National Research Council of Italy, Institute of Sciences of Food Production, CNR-ISPA, Bari, Italy
Interests: microbial food safety; probiotics; foodborne pathogenic bacteria; fermented foods; microbial food quality
Special Issues, Collections and Topics in MDPI journals
Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, 23071 Jaén, Spain
Interests: foodborne bacteria; food fermentations; lactic acid bacteria; antibiotic resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Numerous and heterogeneous populations of beneficial microorganisms originating from raw materials, equipment, and production and processing environments can by their metabolic activities affect the fermentation process, allowing for the enhancement of the nutritional value, organoleptic characteristics, overall quality, safety, and shelf-life of final food products. In addition to the beneficial pro-technological microorganisms, probiotic microorganisms or living microorganisms genetically similar to strains used as probiotics may occur in fermented foods, which may provide health benefits well beyond those of the starting food materials.

On the other hand, multiple sources of contamination of raw materials, equipment, and environments involved in the manufacturing of fermented foods may allow for the rooting and proliferation of spoilage and pathogenic microorganisms, which can cause alterations in final products and threaten consumer health.

For this Special Issue of Microorganisms, dedicated to “Beneficial and Detrimental Microorganisms Occurring in Fermented Foods”, we invite you to submit contributions concerning any aspect of pro-technological, probiotic, spoilage, and/or pathogenic microorganisms occurring in fermented foods, as well as on the characterization, evolution, and metabolism of microbiota that occur during the production, storage, and distribution of these products.

Dr. Vincenzina Fusco
Prof. Hikmate Abriouel
Dr. Evandro Leite de Souza
Guest Editors

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Keywords

  • fermented foods
  • (probiotic) lactic acid bacteria
  • pathogenic microorganisms
  • spoilage microorganisms
  • microbiota
  • omics

Published Papers (7 papers)

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Editorial

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2 pages, 188 KiB  
Editorial
Special Issue “Beneficial and Detrimental Microorganisms Occurring in Fermented Foods”: Editorial
Microorganisms 2023, 11(3), 565; https://doi.org/10.3390/microorganisms11030565 - 24 Feb 2023
Viewed by 738
Abstract
Numerous and heterogeneous populations of beneficial microorganisms originating from raw materials, equipment, and production and processing environments can affect the fermentation process by their metabolic activities, allowing for the enhancement of the nutritional value, sensory characteristics, overall quality, safety, and shelf-life of final [...] Read more.
Numerous and heterogeneous populations of beneficial microorganisms originating from raw materials, equipment, and production and processing environments can affect the fermentation process by their metabolic activities, allowing for the enhancement of the nutritional value, sensory characteristics, overall quality, safety, and shelf-life of final food products [...] Full article

Research

Jump to: Editorial

18 pages, 3826 KiB  
Article
Characterization of Bacterial Cellulose Produced by Komagataeibacter maltaceti P285 Isolated from Contaminated Honey Wine
Microorganisms 2022, 10(3), 528; https://doi.org/10.3390/microorganisms10030528 - 28 Feb 2022
Cited by 15 | Viewed by 3815
Abstract
Bacterial cellulose (BC), a biopolymer, is synthesized by BC-producing bacteria. Almost all producing strains are classified in the family Acetobacteraceae. In this study, bacterial strain P285 was isolated from contaminated honey wine in a honey factory in northern Thailand. Based on 16S [...] Read more.
Bacterial cellulose (BC), a biopolymer, is synthesized by BC-producing bacteria. Almost all producing strains are classified in the family Acetobacteraceae. In this study, bacterial strain P285 was isolated from contaminated honey wine in a honey factory in northern Thailand. Based on 16S rRNA gene sequence identification, the strain P285 revealed 99.8% identity with Komagataeibacter maltaceti LMG 1529 T. K. maltaceti P285 produced the maximum BC production at 20–30 °C and an initial media pH of 9.0. The highest BC production in modified mineral salt medium (MSM) was exhibited when glucose (16%, w/v) and yeast extract (3.2%, w/v) were applied as carbon and nitrogen sources, respectively. When sugarcane (8–16%, w/v) or honey (ratio of honey to water = 1: 4) supplemented with yeast extract was used, the BC production was greater. The characterization of BC synthesized by K. maltaceti P285 was undertaken using scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectrometry. Meanwhile, X-ray diffraction results confirmed the presence of crystalline cellulose (2θ = 18.330, 21.390 and 22.640°). The maximum temperature of BC degradation was observed at 314 °C. Tensile properties analysis of hydrated and dried BC showed breaking strength of 1.49 and 0.66 MPa, respectively. These results demonstrated that K. maltaceti P285 has a high potential for BC production especially when grown in high initial media pH. Therefore, the strain would be suitable as an agent to make BC, the value-added product in the related factories. Full article
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20 pages, 6697 KiB  
Article
Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing
Microorganisms 2021, 9(8), 1574; https://doi.org/10.3390/microorganisms9081574 - 23 Jul 2021
Cited by 17 | Viewed by 3552
Abstract
Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products [...] Read more.
Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination. Full article
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17 pages, 2001 KiB  
Article
Evaluation of Probiotic Properties of Pediococcus acidilactici M76 Producing Functional Exopolysaccharides and Its Lactic Acid Fermentation of Black Raspberry Extract
Microorganisms 2021, 9(7), 1364; https://doi.org/10.3390/microorganisms9071364 - 23 Jun 2021
Cited by 15 | Viewed by 2814
Abstract
This study aimed to determine the probiotic potential of Pediococcus acidilactici M76 (PA-M76) for lactic acid fermentation of black raspberry extract (BRE). PA-M76 showed outstanding probiotic properties with high tolerance in acidic GIT environments, broad antimicrobial activity, and high adhesion capability in the [...] Read more.
This study aimed to determine the probiotic potential of Pediococcus acidilactici M76 (PA-M76) for lactic acid fermentation of black raspberry extract (BRE). PA-M76 showed outstanding probiotic properties with high tolerance in acidic GIT environments, broad antimicrobial activity, and high adhesion capability in the intestinal tract of Caenorhabditis elegans. PA-M76 treatment resulted in significant increases of pro-inflammatory cytokine mRNA expression in macrophages, indicating that PA-M76 elicits an effective immune response. When PA-M76 was used for lactic acid fermentation of BRE, an EPS yield of 1.62 g/L was obtained under optimal conditions. Lactic acid fermentation of BRE by PA-M76 did not significantly affect the total anthocyanin and flavonoid content, except for a significant increase in total polyphenol content compared to non-fermented BRE (NfBRE). However, fBRE exhibited increased DPPH radical scavenging activity, linoleic acid peroxidation inhibition rate, and ABTS scavenging activity of fBRE compared to NfBRE. Among the 28 compounds identified in the GC-MS analysis, esters were present as the major groups. The total concentration of volatile compounds was higher in fBRE than that in NfBRE. However, the undesirable flavor of terpenes decreased. PA-M76 might be useful for preparing functionally enhanced fermented beverages with a higher antioxidant activity of EPS and enhanced flavors. Full article
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17 pages, 2925 KiB  
Article
Bacterial Distribution, Biogenic Amine Contents, and Functionalities of Traditionally Made Doenjang, a Long-Term Fermented Soybean Food, from Different Areas of Korea
Microorganisms 2021, 9(7), 1348; https://doi.org/10.3390/microorganisms9071348 - 22 Jun 2021
Cited by 14 | Viewed by 2082
Abstract
Since doenjang quality depends on the bacterial composition, which ambient bacteria in the environment and production conditions influence, a complete understanding of the bacteria community in traditionally madetraditionally made doenjang (TMD) from different regions is needed. We aimed to investigate the bacteria composition [...] Read more.
Since doenjang quality depends on the bacterial composition, which ambient bacteria in the environment and production conditions influence, a complete understanding of the bacteria community in traditionally madetraditionally made doenjang (TMD) from different regions is needed. We aimed to investigate the bacteria composition and quality of TMD in the following areas: Chonbuk (CB), Chonnam (CN), Kyungsang (KS), Kangwon (KW), Chungchung (CC) provinces, and Jeju island (JJ) of Korea. Twenty-nine TMD samples from different regions were used to assess biogenic amine contents, bacteria composition using next-generation methods, and metabolic functions of the bacteria using Picrust2. Bacillus spp. were isolated, and their antioxidant and fibrinolytic activities were determined. Most TMD contained high amounts of beneficial bacteria (Bacillus, Lactobacillus, Pediococcus and Weissella). However, some KS samples contained harmful bacteria (Cronobacter, Proteus and Acinetobacter) and less beneficial B. velezensis bacteria. There was no similarity among the regional groups, and each TMD showed a different bacteria composition. Shannon index, α-diversity index, was lower in TMD from JJ and CB than the other areas, but there was no β-diversity among TMD from the six area groups. Picrust2 analysis revealed that the functional potential for arachidonic acid metabolism was lowest in JJ and CN, that for supporting insulin action was highest in KS and JJ, and that for carbohydrate digestion and absorption was lowest in CB and JJ among all groups (p < 0.05) according to the Kyoto Encyclopedia of Genes and Genomes Orthology. Histamine contents were lower in CN and CC, and tyramine contents did not differ significantly. B. velezensis, B. subtilis, B. licheniformis, B. siamensis, and B. amyloliquefaciens were isolated from TMD. None of the isolated Bacillus spp. contained the B. cereus gene. B. subtilis from CN had the highest fibrinolytic activity, and B. velezensis from CB had the highest antioxidant activity. In conclusion, TMD mainly contained various Bacillus spp., and the predominant one was B. velezensis, which had antioxidant and fibrinolytic activity regardless of the regional origin. Full article
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20 pages, 5340 KiB  
Article
Isolation and Characterization of Potential Starter Cultures from the Nigerian Fermented Milk Product nono
Microorganisms 2021, 9(3), 640; https://doi.org/10.3390/microorganisms9030640 - 19 Mar 2021
Cited by 9 | Viewed by 3176
Abstract
Nono, an important traditional fermented dairy food produced from cow’s milk in Nigeria, was studied for microbial diversity and for starter culture development for industrial production. On the basis of a polyphasic approach, including phenotypic and genotypic methods such as 16S rRNA [...] Read more.
Nono, an important traditional fermented dairy food produced from cow’s milk in Nigeria, was studied for microbial diversity and for starter culture development for industrial production. On the basis of a polyphasic approach, including phenotypic and genotypic methods such as 16S rRNA gene sequencing, repetitive element PCR (rep-PCR) fingerprinting metagenomics, and whole genome sequencing, we identified Lactobacillus (Lb.) helveticus, Limosilactobacillus (L.) fermentum, Lb. delbrueckii, and Streptococcus (S.) thermophilus as predominant bacterial species involved with milk fermentation during traditional nono production in Nigeria, while the predominant yeast species in nono was identified as Saccharomyces cerevisiae. Using metagenomics, Shigella and potential pathogens such as enterobacteria were detected at low levels of abundance. Strains of the predominant lactic acid bacteria (LAB) were selected for starter cultures combination on the basis of their capacities for rapid growth in milk and reduction of pH below 4.5 and their gelling characteristic, which was demonstrated noticeably only by the S. thermophilus strains. Whole genome sequence analysis of selected bacterial strains showed the largest assembled genome size to be 2,169,635 bp in Lb. helveticus 314, while the smallest genome size was 1,785,639 bp in Lb. delbrueckii 328M. Genes encoding bacteriocins were not detected in all the strains, but all the LAB possessed genes potentially involved in diacetyl production and citrate metabolism. These bacteria isolated from nono can thus be used to improve the microbial safety quality of nono in Nigeria, in addition to improving technological parameters such as gelling viscosity, palatability, and product consistency. Full article
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17 pages, 2393 KiB  
Article
Strain-Dependent Cheese Spoilage Potential of Clostridium tyrobutyricum
Microorganisms 2020, 8(11), 1836; https://doi.org/10.3390/microorganisms8111836 - 22 Nov 2020
Cited by 18 | Viewed by 3429
Abstract
Clostridium tyrobutyricum, a Gram-positive, anaerobic, spore-forming bacterium, is considered as one of the main causative agents for spoilage of hard and semihard cheeses. Growth of C. tyrobutyricum in cheese is critically influenced by ripening temperature and time, pH, salt and lactic acid [...] Read more.
Clostridium tyrobutyricum, a Gram-positive, anaerobic, spore-forming bacterium, is considered as one of the main causative agents for spoilage of hard and semihard cheeses. Growth of C. tyrobutyricum in cheese is critically influenced by ripening temperature and time, pH, salt and lactic acid concentration, moisture and fat content, and the presence of other microorganisms. Previous studies revealed high intraspecies diversity of C. tyrobutyricum strains and variable tolerance toward pH, temperatures, and salt concentrations. These findings indicate that strain-dependent characteristics may be relevant to assess the risk for cheese spoilage if clostridial contamination occurs. In this study, we aimed to compare the phenotypes of 12 C. tyrobutyricum strains which were selected from 157 strains on the basis of genotypic and proteotypic variability. The phenotypic analysis comprised the assessment of gas production and organic acid concentrations in an experimental cheese broth incubated at different temperatures (37, 20, and 14 °C). For all tested strains, delayed gas production at lower incubation temperatures and a strong correlation between gas production and the change in organic acid concentrations were observed. However, considering the time until gas production was visible at different incubation temperatures, a high degree of heterogeneity was found among the tested strains. In addition, variation among replicates of the same strain and differences due to different inoculum levels became evident. This study shows, that, among other factors, strain-specific germination and growth characteristics should be considered to evaluate the risk of cheese spoilage by C. tyrobutyricum. Full article
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