Beneficial and Detrimental Microorganisms Occurring in Fermented Foods 2.0

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

Deadline for manuscript submissions: 15 April 2024 | Viewed by 5808

Special Issue Editors

Institute of Sciences of Food Production of the National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy
Interests: food microbiology; fermented foods; probiotics; lactic acid bacteria; pathogenic bacteria; spoilage bacteria; molecular methods; genomics
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 2.0”, 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. Dr. Hikmate Abriouel
Dr. Evandro Leite de Souza
Guest Editors

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Keywords

  • fermented foods
  • probiotics
  • lactic acid bacteria
  • pathogenic microorganisms
  • spoilage microorganisms
  • microbiome
  • omics

Published Papers (4 papers)

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Research

20 pages, 2750 KiB  
Article
Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia
Microorganisms 2024, 12(1), 16; https://doi.org/10.3390/microorganisms12010016 - 21 Dec 2023
Viewed by 606
Abstract
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) [...] Read more.
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32–35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel’s milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries. Full article
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17 pages, 5732 KiB  
Article
Motility in Periweissella Species: Genomic and Phenotypic Characterization and Update on Motility in Lactobacillaceae
Microorganisms 2023, 11(12), 2923; https://doi.org/10.3390/microorganisms11122923 - 05 Dec 2023
Cited by 1 | Viewed by 617
Abstract
The genus Weissella and the recently described genus Periweissella, to which some previously named Weissella species have been reclassified as a result of a taxogenomic assessment, includes lactic acid bacteria species with high biotechnological and probiotic potential. Only one species, namely, Periweissella [...] Read more.
The genus Weissella and the recently described genus Periweissella, to which some previously named Weissella species have been reclassified as a result of a taxogenomic assessment, includes lactic acid bacteria species with high biotechnological and probiotic potential. Only one species, namely, Periweissella (P.) beninensis, whose type strain has been shown to possess probiotic features, has so far been described to be motile. However, the availability of numerous genome sequences of Weissella and Periweissella species prompted the possibility to screen for the presence of the genetic determinants encoding motility in Weissella and Periweissellas spp. other than P. beninensis. Herein, we performed a comprehensive genomic analysis to identify motility-related proteins in all Weissella and Periweissella species described so far, and extended the analysis to the recently sequenced Lactobacillaceae spp. Furthermore, we performed motility assays and transmission electron microscopy (TEM) on Periweissella type strains to confirm the genomic prediction. The homology-based analysis revealed genes coding for motility proteins only in the type strains of P. beninensis, P. fabalis, P. fabaria and P. ghanensis genomes. However, only the P. beninensis type strain was positive in the motility assay and displayed run-and-tumble behavior. Many peritrichous and long flagella on bacterial cells were visualized via TEM, as well. As for the Lactobacillaceae, in addition to the species previously described to harbor motility proteins, the genetic determinants of motility were also found in the genomes of the type strains of Lactobacillus rogosae and Ligilactobacillus salitolerans. This study, which is one of the first to analyze the genomes of Weissella, Periweissella and the recently sequenced Lactobacillaceae spp. for the presence of genes coding for motility proteins and which assesses the associated motility phenotypes, provides novel results that expand knowledge on these genera and are useful in the further characterization of lactic acid bacteria. Full article
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18 pages, 2514 KiB  
Article
Repression of Staphylococcus aureus and Escherichia coli by Lactiplantibacillus plantarum Strain AG10 in Drosophila melanogaster In Vivo Model
Microorganisms 2023, 11(5), 1297; https://doi.org/10.3390/microorganisms11051297 - 16 May 2023
Cited by 1 | Viewed by 1389
Abstract
Probiotic bacteria exhibiting antagonistic activities against pathogenic bacteria are widely considered as potential options for the prevention and treatment of various infectious diseases and represent potential substitutes of antibiotics. Here we show that the L. plantarum AG10 strain represses the growth of Staphylococcus [...] Read more.
Probiotic bacteria exhibiting antagonistic activities against pathogenic bacteria are widely considered as potential options for the prevention and treatment of various infectious diseases and represent potential substitutes of antibiotics. Here we show that the L. plantarum AG10 strain represses the growth of Staphylococcus aureus and Escherichia coli in vitro and diminishes their negative effects in vivo in a Drosophila melanogaster model of survival on embryonic (larvae) and pupa stages. In an agar drop diffusion test, L. plantarum AG10 exhibited antagonistic properties against Escherichia coli, Staphylococcus aureus, Serratia marcescens and Pseudomonas aeruginosa, and repressed the growth of E. coli and S. aureus during milk fermentation. In a Drosophila melanogaster model, L. plantarum AG10 alone did not provide any significant effect, either during the embryonic stage or during further development of the flies. Despite this, it was able to restore the viability of groups infected with either E. coli and S. aureus, almost to the level of non-treated control at all stages of development (larvae, pupa and adult). Moreover, in the presence of L. plantarum AG10, pathogens-induced mutation rates and recombination events reduced 1.5–2-fold. The genome of L. plantarum AG10 was sequenced and deposited at NCBI under the accession number PRJNA953814 and consists of annotated genome and raw sequence data. It consists of 109 contigs and is 3,479,919 bp in length with a GC content of 44.5%. The analysis of the genome has revealed considerably few putative virulence factors and three genes responsible for the biosynthesis of putative antimicrobial peptides, with one of them exhibiting a high probability of antimicrobial properties. Taken together, these data allow the suggestion that the L. plantarum AG10 strain is promising for use in both dairy production and probiotics as a preservative from foodborne infections. Full article
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14 pages, 7377 KiB  
Article
Whole Genome Sequencing of the Novel Probiotic Strain Lactiplantibacillus plantarum FCa3L
Microorganisms 2023, 11(5), 1234; https://doi.org/10.3390/microorganisms11051234 - 07 May 2023
Cited by 1 | Viewed by 2099
Abstract
Lactiplantibacillus plantarum is best known for its significant adaptive potential and ability to colonize different ecological niches. Different strains of L. plantarum are widely used as probiotics. To characterize the probiotic potential of the novel L. plantarum FCa3L strain isolated from fermented cabbage, [...] Read more.
Lactiplantibacillus plantarum is best known for its significant adaptive potential and ability to colonize different ecological niches. Different strains of L. plantarum are widely used as probiotics. To characterize the probiotic potential of the novel L. plantarum FCa3L strain isolated from fermented cabbage, we sequenced its whole genome using the Illumina MiSeq platform. This bacterial isolate had a circular chromosome of 3,365,929 bp with 44.3% GC content and a cyclic phage phiX174 of 5386 bp with 44.7% GC content. The results of in vitro studies showed that FCa3L was comparable with the reference probiotic strain L. plantarum 8PA3 in terms of acid and bile tolerance, adhesiveness, H2O2 production, and acidification rate. The strain 8PA3 possessed higher antioxidant activity, while FCa3L demonstrated superior antibacterial properties. The antibiotic resistance of FCa3L was more relevant to the probiotic strain than that of 8PA3, although a number of silent antibiotic resistance genes were identified in its genome. Genomic evidence to support adhesive and antibacterial properties, biosynthesis of bioactive metabolites, and safety of FCa3L was also presented. Thus, this study confirmed the safety and probiotic properties of L. plantarum FCa3L via complete genome and phenotype analysis, suggesting its potential as a probiotic, although further in vivo investigations are still necessary. Full article
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