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New Insight in Microbial Diversity and Genomic in Foods

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A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (10 September 2023) | Viewed by 19909

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Special Issue Editors

Dr. Francisco Noe Arroyo-Lopez

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Guest Editor

Food Biotechnology Department, Spanish Research Council. Instituto de la Grasa (IG-CSIC), Sevilla, Spain
Interests: table olives; biofilms; metagenomics; probiotics; predictive microbiology; food safety; food quality; lactic acid bacteria; yeasts

Dr. Verónica Romero-Gil

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Guest Editor

Department of Food Science and Technology, University of Córdoba, Córdoba, Spain
Interests: table olives; biofilms; fish; metagenomics; probiotics; predictive microbiology; food safety; food quality; lactic acid; yeasts

Dr. Antonio Benítez-Cabello

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Guest Editor

Food Biotechnology Department, Spanish Research Council. Instituto de la Grasa (IG-CSIC), Sevilla, Spain
Interests: table olives; biofilms; metagenomics; probiotics; bioinformatic; food safety; food quality; lactic acid bacteria; yeasts

Special Issue Information

This Special Issue of Foods, entitled “New Insights in Microbial Diversity and Genomics in Foods”, aims to highlight the most recent reports on all aspects related to the study of bacterial, fungal, and phage biodiversity in diverse food matrixes, as well as the use of bioinformatic and molecular methods for the analysis, annotation, and study of their genomes. Experts from the fields of food microbiology, food ecology, food technology, bioinformatic, and molecular biology are invited to contribute their findings in the form of full research articles, short communications, or focused reviews to increase existing knowledge on this important topic.

The use of next-generation sequencing (NGS) techniques and bioinformatic analysis has opened new alternatives to the study of microbial diversity in foods compared to classical methods. Moreover, the sequencing, annotation, and study of bacterial, fungal, or phase genomes are of interest to reveal the importance and potential use of these biological agents in foods.

Dr. Francisco Arroyo-Lopez
Dr. Verónica Romero-Gil
Dr. Antonio Benítez-Cabello
Guest Editors

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Keywords

metagenomic
genomic sequencing
genomic annotation
molecular biology
fermented foods
yeasts
molds
phages
bacteria

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Published Papers (9 papers)

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Research

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20 pages, 2104 KiB

Open AccessArticle

Tracking Microbial Diversity and Hygienic-Sanitary Status during Processing of Farmed Rainbow Trout (Oncorhynchus mykiss)

by Salud María Serrano Heredia, Javier Sánchez-Martín, Verónica Romero Gil, Francisco Noé Arroyo-López, Antonio Benítez-Cabello, Elena Carrasco Jiménez and Antonio Valero Díaz

Foods 2023, 12(20), 3718; https://doi.org/10.3390/foods12203718 - 10 Oct 2023

Cited by 1 | Viewed by 1829

Abstract

Aquaculture is becoming a strategic sector for many national economies to supply the increasing demand for fish from consumers. Fish culture conditions and processing operations can lead to an increase in microbial contamination of farmed fish that may shorten the shelf-life of fish products and byproducts, and ready-to-eat fishery products. The objective of this study was to evaluate the hygienic-sanitary status of water, environment, and processing of fresh-farmed rainbow trout (Oncorhynchus mykiss) fillets produced in a local fish farm in Andalusia, Spain. To achieve this, a longitudinal study was carried out by collecting environmental (air and food-contact surfaces), water from fish ponds, and rainbow trout samples. Thereby, seven sampling visits were performed between February 2021 and July 2022, where foodborne pathogens and spoilage microorganisms, together with physicochemical parameters, were analysed in the collected samples. Further, microbial identification of microbiota was achieved through a culture-dependent technique using blast analysis of 16S RNA gene sequencing. The results showed that Listeria monocytogenes and Salmonella were not detected in the analysed samples. Regarding the hygienic-sanitary status of the fish farm, the slaughtering bath, the eviscerating machine and the outlet water from fish ponds presented the highest counts of coliforms, Enterobacteriaceae, and Aerobic Mesophilic Bacteria. Staphylococcus aureus and sulphite-reducing Clostridium were identified in the conveyor belts, fish flesh, and viscera. The 16S RNA identification confirmed the presence of viable spoilage bacteria such as Citrobacter gillenii, Macrococcus caseolyticus, Hafnia paralvei, Lactococcus lactis, Lactococcus cremoris, Klebsiella, Escherichia coli, Morganella morganii, and Shewanella. Three of these genera (Citrobacter, Hafnia, and Pseudomonas) were present in all types of samples analysed. The results evidenced potential transmission of microbial contamination from contaminated packaging belts and boxes, evisceration and filleting machines to flesh and viscera samples, thus the establishment of control measures should be implemented in fish farm facilities to extend the shelf-life of farmed fishery products. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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17 pages, 4485 KiB

Open AccessArticle

Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry

by Clinton A. Page, Ilenys M. Pérez-Díaz, Meichen Pan and Rodolphe Barrangou

Foods 2023, 12(13), 2455; https://doi.org/10.3390/foods12132455 - 23 Jun 2023

Cited by 2 | Viewed by 2023

Abstract

Lactiplantibacillus pentosus, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 L. pentosus and 3 Lactiplantibacillus plantarum isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)₅, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the L. pentosus autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The L. pentosus autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the L. pentosus subclades identified in the phylogenetic trees constructed. While L. plantarum autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous L. pentosus clade B codes for Type I-E and L. pentosus clade A hosts both types of arrays. L. pentosus 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial Lactiplantibacillus species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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18 pages, 943 KiB

Open AccessArticle

Microbial and Chemical Characterization of Natural-Style Green Table Olives from the Gordal, Hojiblanca and Manzanilla Cultivars

by José Luis Ruiz-Barba, Antonio Higinio Sánchez, Antonio López-López, Amparo Cortés-Delgado and Alfredo Montaño

Foods 2023, 12(12), 2386; https://doi.org/10.3390/foods12122386 - 15 Jun 2023

Cited by 6 | Viewed by 1440

Abstract

Microbial and biochemical changes in the brine during the spontaneous fermentation of Gordal, Hojiblanca and Manzanilla olive cultivars processed according to the natural style were monitored. The microbial composition was assessed through a metagenomic study. Sugars, ethanol, glycerol, organic acids and phenolic compounds were quantified by standard methods. In addition, the volatile profiles, contents of phenolic compounds in the olives and quality parameters of the final products were compared. Fermentation in Gordal brines was conducted by lactic acid bacteria (mainly Lactobacillus and Pediococcus) and yeasts (mainly Candida boidinii, Candida tropicalis and Wickerhamomyces anomalus). In Hojiblanca and Manzanilla brines, halophilic Gram-negative bacteria (e.g., Halomonas, Allidiomarina and Marinobacter) along with yeasts (mainly, Saccharomyces) were responsible for the fermentation. Higher acidity and lower pH values were reached in Gordal brines compared to Hojiblanca and Manzanilla. After 30 days of fermentation, no sugars were detected in Gordal brine, but residual amounts were found in the brines from Hojiblanca (<0.2 g/L glucose) and Manzanilla (2.9 g/L glucose and 0.2 g/L fructose). Lactic acid was the main acid product in Gordal fermentation, whereas citric acid was the predominant organic acid in the Hojiblanca and Manzanilla brines. Manzanilla brine samples showed a greater concentration of phenolic compounds than Hojiblanca and Gordal brines. After a 6-month fermentation, Gordal olives were superior compared to the Hojiblanca and Manzanilla varieties regarding product safety (lower final pH and absence of Enterobacteriaceae), content of volatile compounds (richer aroma), content of bitter phenolics (lower content of oleuropein, which resulted in less perceived bitterness) and color parameters (more yellow and lighter color, indicating a higher visual appraisal). The results of the present study will contribute to a better understanding of each fermentation process and could help to promote natural-style elaborations using the above-mentioned olive cultivars. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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20 pages, 3560 KiB

Open AccessEditor’s ChoiceArticle

Microbial and Biochemical Profile of Different Types of Greek Table Olives

by Niki Mougiou, Antiopi Tsoureki, Spyros Didos, Ioanna Bouzouka, Sofia Michailidou and Anagnostis Argiriou

Foods 2023, 12(7), 1527; https://doi.org/10.3390/foods12071527 - 4 Apr 2023

Cited by 10 | Viewed by 2595

Abstract

Analysis of table olives microbiome using next-generation sequencing has enriched the available information about the microbial community composition of this popular fermented food. In this study, 16S and 18S rRNA sequencing was performed on table olives of five Greek popular cultivars, Halkidikis, Thassou, Kalamon, Amfissis, and Konservolia, fermented either by Greek style (in brine or salt-drying) or by Spanish style, in order to evaluate their microbial communities. Moreover, analytical methods were used to evaluate their biochemical properties. The prevailing bacterial species of all olives belonged to Lactobacillaceae, Leuconostocaceae, and Erwiniaceae families, while the most abundant yeasts were of the Pichiaceae family. Principal coordinates analysis showed a clustering of samples cured by salt-drying and of samples stored in brine, regardless of their cultivar. The biochemical evaluation of total phenol content, antioxidant activity, hydroxytyrosol, oleuropein, oleocanthal, and oleacein showed that salt-dried olives had low amounts of hydroxytyrosol, while Spanish-style green olives had the highest amounts of oleocanthal. All the other values exhibited various patterns, implying that more than one factor affects the biochemical identity of the final product. The protocols applied in this study can provide useful insights for the final product, both for the producers and the consumers. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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19 pages, 3075 KiB

Open AccessEditor’s ChoiceArticle

In Silico Evidence of the Multifunctional Features of Lactiplantibacillus pentosus LPG1, a Natural Fermenting Agent Isolated from Table Olive Biofilms

by Elio López-García, Antonio Benítez-Cabello, Javier Ramiro-García, Victor Ladero and Francisco Noé Arroyo-López

Foods 2023, 12(5), 938; https://doi.org/10.3390/foods12050938 - 22 Feb 2023

Cited by 8 | Viewed by 2190

Abstract

In recent years, there has been a growing interest in obtaining probiotic bacteria from plant origins. This is the case of Lactiplantibacillus pentosus LPG1, a lactic acid bacterial strain isolated from table olive biofilms with proven multifunctional features. In this work, we have sequenced and closed the complete genome of L. pentosus LPG1 using both Illumina and PacBio technologies. Our intention is to carry out a comprehensive bioinformatics analysis and whole-genome annotation for a further complete evaluation of the safety and functionality of this microorganism. The chromosomic genome had a size of 3,619,252 bp, with a GC (Guanine-Citosine) content of 46.34%. L. pentosus LPG1 also had two plasmids, designated as pl1LPG1 and pl2LPG1, with lengths of 72,578 and 8713 bp (base pair), respectively. Genome annotation revealed that the sequenced genome consisted of 3345 coding genes and 89 non-coding sequences (73 tRNA and 16 rRNA genes). Taxonomy was confirmed by Average Nucleotide Identity analysis, which grouped L. pentosus LPG1 with other sequenced L. pentosus genomes. Moreover, the pan-genome analysis showed that L. pentosus LPG1 was closely related to the L. pentosus strains IG8, IG9, IG11, and IG12, all of which were isolated from table olive biofilms. Resistome analysis reported the absence of antibiotic resistance genes, whilst PathogenFinder tool classified the strain as a non-human pathogen. Finally, in silico analysis of L. pentosus LPG1 showed that many of its previously reported technological and probiotic phenotypes corresponded with the presence of functional genes. In light of these results, we can conclude that L. pentosus LPG1 is a safe microorganism and a potential human probiotic with a plant origin and application as a starter culture for vegetable fermentations. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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17 pages, 3314 KiB

Open AccessArticle

Effect of Alkali on the Microbial Community and Aroma Profile of Chinese Steamed Bread Prepared with Chinese Traditional Starter

by Ning Tang, Xiaolong Xing, Huipin Li, Honggang Jiao, Shengxin Ji and Zhilu Ai

Foods 2023, 12(3), 617; https://doi.org/10.3390/foods12030617 - 1 Feb 2023

Cited by 4 | Viewed by 2086

Abstract

Alkali is an indispensable additive in Chinese steamed bread (CSB) production. This work aimed to evaluate the key roles of alkali in the microbial community of dough fermented using Chinese traditional starter (CTS) and the aroma profiles of CSB. The dominant fungi in CTS and fermented dough were members of the phylum Ascomycota and the genus Saccharomyces. Pediococcus, Companilactobacillus, and Weissella were the dominant bacterial genera in CTS and fermented dough. Adding alkali could retain the types of dominant yeasts and LAB derived from CTS, decrease the relative abundance of Companilactobacillus crustorum and Weissella cibaria, and increase that of Pediococcus pentosaceus, in fermented dough. Principal component analysis (PCA) indicated that adding alkali decreased the content of sourness-related volatiles in CSB fermented by CTS. Correlation analysis showed that Pediococcus and Weissella in fermented dough were positively correlated with the lipid oxidation flavor-related compounds in CSB, and Lactobacillus was positively correlated with sourness-related aroma compounds. Synthetic microbial community experiments indicated that CSB fermented by the starter containing P. pentosaceus possessed a strong aroma, and adding alkali weakened the flavor intensity. Alkali addition could promote the formation of ethyl acetate and methyl acetate with a pleasant fruity aroma in W. cibaria-associated CSB. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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12 pages, 913 KiB

Open AccessArticle

Study of Lactic Acid Bacteria Biodiversity in Fermented Cobrançosa Table Olives to Determine Their Probiotic Potential

by Joana Coimbra-Gomes, Patrícia J. M. Reis, Tânia G. Tavares, Francisco Xavier Malcata and Angela C. Macedo

Foods 2022, 11(19), 3050; https://doi.org/10.3390/foods11193050 - 1 Oct 2022

Cited by 7 | Viewed by 2031

Abstract

Current market trends point at increasing demand for functional foods, namely those carrying probiotics. In the case of table olives, presence of probiotics would convey a competitive advantage to Mediterranean-based diets, already established for their cultural heritage and gastronomic character. This work assessed the safety and resistance to gastrointestinal digestion of 19 native LAB strains from Cobrançosa table olives. Strains were identified via molecular sequencing (4 fingerprints/10 strains for Lactiplantibacillus pentosus, and 2 fingerprints/9 strains for L. paraplantarum), and exposed to simulated gastrointestinal fluids, as per the INFOGEST in vitro protocol with modifications. None of those strains proved dangerous for human consumption. Survivability to the gastrointestinal resistance test ranged from 29% to 70%, with strain-dependent variability. L. paraplantarum i18, i27, and i102, and L. pentosus i10 and i11 exhibited statistically lower survival rates (29–35%) than probiotic the Greek table olive reference strain L. pentosus B281 (53%). Among the other strains, L. paraplantarum i101 and L. pentosus i53 and i106 showed the highest survival rates but were not significantly different from the strain of Lacticaseibacillus casei isolated from commercial probiotic yoghurt (65–70%). In vitro results proved that strains retrieved from fermenting cultivar Cobrançosa possess the potential to be claimed as probiotics—thus deserving further attention toward the development of a specific starter culture. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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13 pages, 2079 KiB

Open AccessArticle

Investigation on the Microbial Diversity of Fresh-Cut Lettuce during Processing and Storage Using High Throughput Sequencing and Their Relationship with Quality

by Yeting Sun, Xiaoyan Zhao, Yue Ma, Zhihong Ma, Zhaoying He, Wenting Zhao, Pan Wang, Shuang Zhao and Dan Wang

Foods 2022, 11(12), 1683; https://doi.org/10.3390/foods11121683 - 8 Jun 2022

Cited by 12 | Viewed by 2563

Abstract

Microbial community distribution in vegetables can affect their quality. This study analyzed the distribution of the microbial community at various stages during processing and storage with the microbial diversity analysis, and evaluated the correlation between the dominant bacteria and sensory quality of lettuce using correspondence analysis with multiple regression analysis. Results showed that the process of washing, cutting, then disinfection and dewatering could change the community distribution and dominant bacteria in lettuce, and maintain better texture, morphology, aroma, color qualities of lettuce. The total number of colonies and relative abundance of Xanthomonas in fresh-cut lettuce decreased, while Afipia and Ralstonia increased during processing and pre-storage (storage for 6 h, 12 h and 1 d). After storage for 3 d, the total number of colonies in lettuce increased (more than 5 log CFU/g), especially the relative abundance of Pseudomonas, which led to the obvious deterioration of the sensory quality of lettuce. Throughout the process, the number of Bacillus cereus, Staphylococcus aureus, and E. coli was less than 100 CFU/g and 3 MPN/g. The number of typical pathogenic bacteria, Salmonella, Listeria monocytogenes and E. coli O157:H7, was below the detection limit. Overall, the prevention and control of psychrotrophic Pseudomonas in lettuce was still necessary. These results will provide useful information for the fresh-cut lettuce industry. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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Review

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30 pages, 2868 KiB

Open AccessReview

Main Challenges Expected from the Impact of Climate Change on Microbial Biodiversity of Table Olives: Current Status and Trends

by Antonio Benítez-Cabello, Amélia M. Delgado and Célia Quintas

Foods 2023, 12(19), 3712; https://doi.org/10.3390/foods12193712 - 9 Oct 2023

Cited by 3 | Viewed by 2042

Abstract

Climate change is a global emergency that is affecting agriculture in Mediterranean countries, notably the production and the characteristics of the final products. This is the case of olive cultivars, a source of olive oil and table olives. Table olives are the most important fermented vegetables in the Mediterranean area, whose world production exceeds 3 million tons/year. Lactic acid bacteria and yeast are the main microorganisms responsible for the fermentation of this product. The microbial diversity and population dynamics during the fermentation process are influenced by several factors, such as the content of sugars and phenols, all of which together influence the quality and safety of the table olives. The composition of fruits is in turn influenced by environmental conditions, such as rainfall, temperature, radiation, and the concentration of minerals in the soil, among others. In this review, we discuss the effect of climate change on the microbial diversity of table olives, with special emphasis on Spanish and Portuguese cultivars. The alterations expected to occur in climate change scenario(s) include changes in the microbial populations, their succession, diversity, and growth kinetics, which may impact the safety and quality of the table olives. Mitigation and adaptation measures are proposed to safeguard the authenticity and sensorial features of this valuable fermented food while ensuring food safety requirements. Full article

(This article belongs to the Special Issue New Insight in Microbial Diversity and Genomic in Foods)

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