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Tsoungos A, Pemaj V, Slavko A, Kapolos J, Papadelli M, Papadimitriou K. The Rising Role of Omics and Meta-Omics in Table Olive Research. Foods 2023; 12:3783. [PMID: 37893676 PMCID: PMC10606081 DOI: 10.3390/foods12203783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.
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Affiliation(s)
- Anastasios Tsoungos
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Violeta Pemaj
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Aleksandra Slavko
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - John Kapolos
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Marina Papadelli
- Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece; (A.T.); (V.P.); (A.S.); (J.K.); (M.P.)
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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Ruiz-Barba JL, Sánchez AH, López-López A, Cortés-Delgado A, Montaño A. Microbial community and volatilome changes in brines along the spontaneous fermentation of Spanish-style and natural-style green table olives (Manzanilla cultivar). Food Microbiol 2023; 113:104286. [PMID: 37098427 DOI: 10.1016/j.fm.2023.104286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/27/2023]
Abstract
Microbial community and volatilome of brines were monitored during the spontaneous fermentations of Spanish-style and Natural-style green table olives from Manzanilla cultivar. Fermentation of olives in the Spanish style was carried out by lactic acid bacteria (LAB) and yeasts, whereas halophilic Gram-negative bacteria and archaea, along with yeasts, drove the fermentation in the Natural style. Clear differences between the two olive fermentations regarding physicochemical and biochemical features were found. Lactobacillus, Pichia, and Saccharomyces were the dominant microbial communities in the Spanish style, whereas Allidiomarina, Halomonas, Saccharomyces, Pichia, and Nakazawaea predominated in the Natural style. Numerous qualitative and quantitative differences in individual volatiles between both fermentations were found. The final products mainly differed in total amounts of volatile acids and carbonyl compounds. In addition, in each olive style, strong positive correlations were found between the dominant microbial communities and various volatile compounds, some of them previously reported as aroma-active compounds in table olives. The findings from this study provide a better understanding of each fermentation process and may help the development of controlled fermentations using starter cultures of bacteria and/or yeasts for the production of high-quality green table olives from Manzanilla cultivar.
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Affiliation(s)
- José Luis Ruiz-Barba
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Utrera Road, km 1, 41013, Seville, Spain.
| | - Antonio Higinio Sánchez
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Utrera Road, km 1, 41013, Seville, Spain.
| | - Antonio López-López
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Utrera Road, km 1, 41013, Seville, Spain.
| | - Amparo Cortés-Delgado
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Utrera Road, km 1, 41013, Seville, Spain.
| | - Alfredo Montaño
- Food Biotechnology Department, Instituto de la Grasa (CSIC), Utrera Road, km 1, 41013, Seville, Spain.
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3
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Kamilari E, Anagnostopoulos DA, Tsaltas D. Fermented table olives from Cyprus: Microbiota profile of three varieties from different regions through metabarcoding sequencing. Front Microbiol 2023; 13:1101515. [PMID: 36733778 PMCID: PMC9886855 DOI: 10.3389/fmicb.2022.1101515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The knowledge about the microbial diversity of different olives varieties from diverse regions in the Mediterranean basin is limited. This work aimed to determine the microbial diversity of three different fermented olive varieties, collected from different regions in Cyprus, via Next Generation Sequencing (NGS) analysis. Olives were spontaneously fermented for 120 days, microbial DNA was extracted from the final products, and subjected to 16S rRNA gene and ITS1 loci metabarcoding analysis for the determination of bacterial and fungal communities, respectively. Results revealed that the bacterial profile of the studied varieties was similar, while no noteworthy differences were observed in olives from different regions. The bacterial profile was dominated by the co-existence of Lactobacillus and Streptococcus, while the genera Lactococcus and Salinivibrio and the family Leuconostocaceae were also present in increased relative abundances. Regarding fungal communities, the analysis indicated discrimination among the different varieties, especially in Kalamata ones. The most abundant fungi were mainly the genera Aspergillus, Botryosphaeria, Meyerozyma, and Zygosaccharomyces for Cypriot olives, the genera Botryosphaeria, Saccharomyces, Geosmithia, and Wickeromyces for Kalamata variety, while the dominant fungi in the Picual variety were mainly members of the genera Candida, Penicillium, Saccharomyces, Hanseniospora and Botryosphaeria. Potential microbial biomarkers that distinguish the three varieties are also proposed. Moreover, interaction networks analysis identified interactions among the key taxa of the communities. Overall, the present work provides useful information and sheds light on an understudied field, such as the comparison of microbiota profiles of different varieties from several regions in Cyprus. The study enriches our knowledge and highlights the similarities and the main differences between those aspects, booming in parallel the need for further works on this frontier, in the attempt to determine potentially olives' microbial terroir in Cyprus. Our work should be used as a benchmark for future works in this direction.
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Benítez-Cabello A, Ramiro-García J, Romero-Gil V, Medina E, Arroyo-López FN. Fungal biodiversity in commercial table olive packages. Food Microbiol 2022; 107:104082. [DOI: 10.1016/j.fm.2022.104082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022]
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5
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García-Serrano P, Brenes M, Romero C, García-García P. Reuse of KOH Solutions during Black Ripe Olive Processing, Effect on the Quality of the Final Product and Valorization of Wastewaters as Possible Fertilizer Product. Foods 2022; 11:foods11121749. [PMID: 35741949 PMCID: PMC9222265 DOI: 10.3390/foods11121749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023] Open
Abstract
A high volume of water is needed to produce black ripe olives, which also entails a significant volume of wastewater with a high organic and inorganic contaminant charge. To reduce this problem, the reuse of KOH solutions (lyes) in a new process was studied. Once the lyes were removed from the tanks, KOH was then added for a new darkening process. Reusing the lyes up to four times gave rise to a product with similar physico–chemical and organoleptic characteristics as obtained with fresh solutions. The application of this process reduced coadjutant consumption by 32% and water by 20%, while global wastewater presented a high K content whose concentration could be valorized as a fertilizer by replacing commercial potassium nitrate.
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de Castro A, Ruiz-Barba JL, Romero C, Sánchez AH, García P, Brenes M. Formation of gas pocket defect in Spanish-style green olives by the halophile Celerinatantimonas sp. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Revealing the bacterial abundance and diversity in brines from started Spanish-style green table olives. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Anagnostopoulos DA, Tsaltas D. Current Status, Recent Advances, and Main Challenges on Table Olive Fermentation: The Present Meets the Future. Front Microbiol 2022; 12:797295. [PMID: 35095807 PMCID: PMC8793684 DOI: 10.3389/fmicb.2021.797295] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/01/2021] [Indexed: 01/18/2023] Open
Abstract
Table olives are among the most well-known fermented foods, being a vital part of the Mediterranean pyramid diet. They constitute a noteworthy economic factor for the producing countries since both their production and consumption are exponentially increasing year by year, worldwide. Despite its significance, olive’s processing is still craft based, not changed since antiquity, leading to the production of an unstable final product with potential risk concerns, especially related to deterioration. However, based on industrial needs and market demands for reproducible, safe, and healthy products, the modernization of olive fermentation processing is the most important challenge of the current decade. In this sense, the reduction of sodium content and more importantly the use of suitable starter cultures, exhibiting both technological and potential probiotic features, to drive the process may extremely contribute to this need. Prior, to achieve in this effort, the full understanding of table olive microbial ecology during fermentation, including an in-depth determination of microbiota presence and/or dominance and its functionality (genes responsible for metabolite production) that shape the sensorial characteristics of the final product, is a pre-requisite. The advent of meta-omics technology could provide a thorough study of this complex ecosystem, opening in parallel new insights in the field, such as the concept of microbial terroir. Herein, we provide an updated overview in the field of olive fermentation, pointing out some important challenges/perspectives that could be the key to the olive sector’s advancement and modernization.
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Affiliation(s)
- Dimitrios A Anagnostopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
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9
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Arroyo-López FN, Benítez-Cabello A, Romero-Gil V, Rodríguez-Gómez F, Garrido-Fernández A. Delving into the bacterial diversity of spoiled green Manzanilla Spanish-style table olive fermentations. Int J Food Microbiol 2021; 359:109415. [PMID: 34607034 DOI: 10.1016/j.ijfoodmicro.2021.109415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/13/2021] [Accepted: 09/19/2021] [Indexed: 11/28/2022]
Abstract
This work applies metataxonomic, standard statistics, and compositional data (CoDa) techniques to study the bacterial diversity of spoiled and normal Spanish-style table olive fermentations, analysing a total of 10-tons of industrial fermentation containers from two processing yards. Forty percent were affected by butyric, sulfidic, or putrid spoilage, while 60% followed the ordinary fermentation course. The samples were obtained at 30 days of fermentation, determining their 16S rRNA gene Amplicon Sequence Variant compositions (ASVs). The butyric containers showed a bacterial profile strongly associated with the genera Enterococcus, Leuconostoc, and Atlantibacter, but also with Lactiplantibacillus and Melissococcus, and less confident to Raoultella, Enterobacter, Serratia, and Celerinatantimonas. The sulfidic fermentation was linked to Alkalibacterium and, to a lesser extent, Marinilactibacillus and the absence of Lactiplantibacillus. Putrid spoilage was mainly related to Halolactibacillus and Alkalibacterium. Sulfidic/putrid (together) differed from butyric spoilage by the presence of Alkalibacterium/Marinilactibacillus as well as by Halomonas/Halanaerobium. Lactiplantibacillus dominated normal fermentations, but Vibrio was also frequently found (0-46%), apparently not causing any alteration. These results contribute to a better microbial characterisation of non-zapatera spoiled table olive fermentations. They also suggest using several statistical techniques to discriminate normal vs spoiled fermentations adequately.
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Affiliation(s)
- Francisco Noé Arroyo-López
- Instituto de la Grasa (CSIC), Food Biotechnology Department, Campus Universitario Pablo de Olavide, Building 46, Ctra. Sevilla-Utrera, km 1, 41013 Seville, Spain
| | - Antonio Benítez-Cabello
- Instituto de la Grasa (CSIC), Food Biotechnology Department, Campus Universitario Pablo de Olavide, Building 46, Ctra. Sevilla-Utrera, km 1, 41013 Seville, Spain.
| | - Verónica Romero-Gil
- Technological Applications for Improvements of the Quality and Safety in Foods, Avda. Diego Martínez Barrio 10, 2ª Planta, 41013 Seville, Spain
| | - Francisco Rodríguez-Gómez
- Instituto de la Grasa (CSIC), Food Biotechnology Department, Campus Universitario Pablo de Olavide, Building 46, Ctra. Sevilla-Utrera, km 1, 41013 Seville, Spain
| | - Antonio Garrido-Fernández
- Instituto de la Grasa (CSIC), Food Biotechnology Department, Campus Universitario Pablo de Olavide, Building 46, Ctra. Sevilla-Utrera, km 1, 41013 Seville, Spain
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Michailidou S, Trikka F, Pasentsis K, Petrovits GE, Kyritsi M, Argiriou A. Insights into the evolution of Greek style table olives microbiome stored under modified atmosphere: Biochemical implications on the product quality. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Sab C, Romero C, Brenes M, Montaño A, Ouelhadj A, Medina E. Industrial Processing of Algerian Table Olive Cultivars Elaborated as Spanish Style. Front Microbiol 2021; 12:729436. [PMID: 34803946 PMCID: PMC8600317 DOI: 10.3389/fmicb.2021.729436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/07/2021] [Indexed: 12/01/2022] Open
Abstract
Olives from the Sigoise, Verdale, and Sevillana cultivars were elaborated as Spanish-style table olives by four Algerian factories, and the quality and food safety of the industrial table olives have been studied by the analysis of physicochemical and microbiological parameters. Differences were observed between the treatments carried out by the different factories throughout the manufacturing process, especially during the washing stage, but no significant differences were found between the analyzed samples for the concentration of sugars and polyphenols. The final pH values reached at the end of fermentation ranged between 5.04 and 4.27, and the titratable acidity was above 0.4% for all samples. Lactic and acetic acids were produced in mean concentrations of 0.68% and 0.21% as a result of lactic acid bacteria (LAB) and yeast metabolism, respectively. However, the presence of butyric, isobutyric, and propionic acids was also detected, and was related to the growth of undesirable spoilage microorganisms, responsible for secondary fermentations. The high-throughput sequencing of bacterial DNA suggested the dominance of LAB species belonging to genera Lactiplantibacillus, Leuconostoc, Pediococcus, Oenococcus, or Enterococcus. The Enterobacteriaceae family was detected during the first days of brining and in only one sample after 120 days of fermentation. Other spoilage microorganisms were found, such as Lentilactobacillus buchneri or the Pectinatus and Acetobacter genera, capable of consuming lactic acid and these played an essential role in the onset of spoilage. The Clostridium and Enterobacter genera, producers of butyric and propionic acids, were responsible for the malodorous fermentation present in the industrial samples that were analyzed. The study concluded that the safety of the table olives analyzed was compromised by the presence of undesirable microorganisms and microbial stability was not guaranteed. The elaboration process can be improved by reducing the washing steps and the time should be reduced to avoid the loss of fermentable matter, with the goal of reaching a pH < 4.0 after the fermentation and preventing the possibility of the growth of spoilage microorganisms and foodborne pathogens.
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Affiliation(s)
- Chafiaa Sab
- Laboratory of Food Quality and Food Safety, Faculty of Biological and Agricultural Sciences, Mouloud Mammeri University, Tizi Ouzou, Algeria
| | - Concepción Romero
- Food Biotechnology Department, Instituto de la Grasa, IG-CSIC, Seville, Spain
| | - Manuel Brenes
- Food Biotechnology Department, Instituto de la Grasa, IG-CSIC, Seville, Spain
| | - Alfredo Montaño
- Food Biotechnology Department, Instituto de la Grasa, IG-CSIC, Seville, Spain
| | - Akli Ouelhadj
- Laboratory of Food Quality and Food Safety, Faculty of Biological and Agricultural Sciences, Mouloud Mammeri University, Tizi Ouzou, Algeria
| | - Eduardo Medina
- Food Biotechnology Department, Instituto de la Grasa, IG-CSIC, Seville, Spain
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New Insights into Microbial Diversity of the Traditional Packed Table Olives Aloreña de Málaga through Metataxonomic Analysis. Microorganisms 2021; 9:microorganisms9030561. [PMID: 33803149 PMCID: PMC8000080 DOI: 10.3390/microorganisms9030561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/25/2022] Open
Abstract
Aloreña de Málaga is a table olive especially characterised by its natural freshness and short shelf-life. In this work, we applied a metataxonomic approach to unravel the microbial diversity of bacterial and fungi populations through the shelf-life of traditionally packed Aloreña de Málaga. A significant increase in lactic acid bacteria and mesophilic aerobic populations was observed during shelf-life, reaching the maximum population levels (4-5 log10 CFU) at the end of the study (260 days). On the contrary, a rapid reduction in yeast and mould populations was reported. The use of a metataxonomic analysis based on the amplification of 16S (bacteria) and internal transcribed spacer (ITS) region (fungi) regions revealed a low diversity for both microbial groups. Lactiplantibacillus (65.05 ± 8.65% in brine vs. 58.70 ± 15.70% in fruit), Pediococcus (28.17 ± 7.36% in brine vs. 27.20 ± 15.95% in fruit), and Celerinatantimonas (4.64 ± 1.08% in brine vs. 11.82 ± 18.17% in fruit) were the main genera found among bacteria, and an increase in Lactiplantibacillus and a reduction in Celerinatantimonas populations during the shelf-life were observed. On the other hand, Citeromyces was the dominant fungi genus (54.11 ± 2.00% in brine vs. 50.91 ± 16.14% in fruit), followed by Candida (8.80 ± 2.57% in brine vs. 12.32 ± 8.61% in fruit) and Penicillium (6.48 ± 1.87% vs. 8.48 ± 4.43% in fruit). No food-borne pathogen genera were detected in any of the samples analysed, indicating the high level of food safety found in this ready-to-eat fermented vegetable. Data obtained in this work will help in the design of new strategies for the control of microbial populations during the shelf-life of Aloreña de Málaga.
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García-Serrano P, Romero C, de Castro A, García-García P, Montaño A, Medina E, Brenes M. Aerobic treatment of black ripe olive processing streams to reduce biological contamination. INNOV FOOD SCI EMERG 2020. [DOI: 10.1016/j.ifset.2020.102491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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14
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Leech J, Cabrera-Rubio R, Walsh AM, Macori G, Walsh CJ, Barton W, Finnegan L, Crispie F, O'Sullivan O, Claesson MJ, Cotter PD. Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants. mSystems 2020; 5:e00522-20. [PMID: 33172966 PMCID: PMC7657593 DOI: 10.1128/msystems.00522-20] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of "industrialization" of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.
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Affiliation(s)
- John Leech
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Guerrino Macori
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Wiley Barton
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
| | - Laura Finnegan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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15
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Molecular identification and antibiotic resistance of bacteriocinogenic lactic acid bacteria isolated from table olives. Arch Microbiol 2020; 203:597-607. [PMID: 32995979 DOI: 10.1007/s00203-020-02053-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/21/2020] [Accepted: 09/15/2020] [Indexed: 01/18/2023]
Abstract
In the present study, lactic acid bacteria were isolated from table olive in Morocco. Random Amplified Polymorphic DNA fingerprinting with (GTG)'(5) primer revealed a remarquable variability within isolates. According to the molecular identification, Enterococcus faecium was the most dominant species isolated with 32 strains (84.21%), followed by 4 strains of Weissella paramesenteroides (10.52%), 1 strain of Leuconostoc mesenteroides (2.63%) and Lactobacillus plantarum (2.63%). All of the strains that were identified showed occurrence of more than one bacteriocin-encoding gene. Based on the results obtained, L. plantarum 11 showed a mosaic of loci coding for nine bacteriocins (pln A, pln D, pln K, pln G, pln B, pln C, pln N, pln J, ent P). A phenotypic and genotypic antibiotic resistance was also examined. L. plantarum 11, L. mesenteroides 62, W. paramesenteroides 9 and W. paramesenteroides 36 as well as all the strains of E. faecium were susceptible to ampicillin, clindamycin and teicoplanin; however, isolates showed a resistance profile against tetracycline and erythromycin. Except E. faecium 114, E. faecium 130 and L. plantarum 11, no antibiotic resistance genes were detected in all of the strains, which might be due to resistances resulting from non-transferable or non-acquired resistance determinants (intrinsic mechanism).
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García-Béjar B, Árevalo-Villena M, Briones A. Characterization of yeast population from unstudied natural sources in La Mancha region. J Appl Microbiol 2020; 130:650-664. [PMID: 32726883 DOI: 10.1111/jam.14795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/26/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023]
Abstract
AIMS This study aims to identify the yeast species and strains which entitled an unstudied area of Spain and evaluate the yeast species diversity richness and the genetic variety. METHODS AND RESULTS A total of 702 yeasts were isolated from different environments in a central Spanish region (La Mancha) with diverse sources of origin (food, animals, flowers and environmental sources) during spring season. Thanks to the analysis carried out by the PCR-RFLP technique and sequencing, 35 species were identified. A neighbour-joining phylogenetic tree was created based on D1/D2 sequences. Moreover 330 strains were determined by PCR-RAPD and their profiles were analysed using the bioinformatics programme BioNumerics 7·6. The Simpson's index (D) and the genetic diversity percentage were calculated with the aim of studying the richness of the species in each environment and the genetic variety in each species. CONCLUSIONS This study has permitted to know that the majority of the species found was Diutina rugosa while the most ubiquitous was Rhodotorula mucilaginosa which expose the dispersion capability of this species. The diversity parameters has revealed that the highest species richness was associated to environmental samples and the highest genetic variety was presented in those species with better dispersion capability or a smaller number of isolates. SIGNIFICANCE AND IMPACT OF THE STUDY This study permits to better understand the yeast communities in La Mancha region which gives a value the microbial potential of this region.
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Affiliation(s)
- B García-Béjar
- Department of Analytical Chemistry and Food Technology, University of Castilla-La Mancha, Ciudad Real, Spain
| | - M Árevalo-Villena
- Department of Analytical Chemistry and Food Technology, University of Castilla-La Mancha, Ciudad Real, Spain
| | - A Briones
- Department of Analytical Chemistry and Food Technology, University of Castilla-La Mancha, Ciudad Real, Spain
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FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation. Food Microbiol 2020; 92:103606. [PMID: 32950142 DOI: 10.1016/j.fm.2020.103606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/18/2023]
Abstract
Table olives are considered the most widespread fermented food in the Mediterranean area and their consumption is expanding all over the world. This fermented vegetable can be considered as a natural functional food thanks to their high nutritional value and high content of bioactive compounds that contribute to the health and well-being of consumers. The presence of bioactive compounds is strongly influenced by a complex microbial consortium, traditionally exploited through culture-dependent approaches. Recently, the rapid spread of omics technologies has represented an important challenge to better understand the function, the adaptation and the exploitation of microbial diversity in different complex ecosystems, such as table olives. This review provides an overview of the potentiality of omics technologies to in depth investigate the microbial composition and the metabolic processes that drive the table olives fermentation, affecting both sensorial profile and safety properties of the final product. Finally, the review points out the role of omics approaches to raise at higher sophisticated level the investigations on microbial, gene, protein, and metabolite, with huge potential for the integration of table olives composition with functional assessments.
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18
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Benítez-Cabello A, Romero-Gil V, Medina-Pradas E, Garrido-Fernández A, Arroyo-López FN. Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis. Sci Rep 2020; 10:11381. [PMID: 32647238 PMCID: PMC7347591 DOI: 10.1038/s41598-020-68305-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/23/2020] [Indexed: 11/12/2022] Open
Abstract
In this work, a total of 72 samples of non-thermally treated commercial table olives were obtained from different markets of the world. Then, prokaryotic diversity in olive biofilms was investigated by metataxonomic analysis. A total of 660 different OTUs were obtained, belonging to Archaea (2.12%) and Bacteria domains (97.88%). From these, 41 OTUs with a proportion of sequences ≥ 0.01% were studied by compositional data analysis. Only two genera were found in all samples, Lactobacillus, which was the predominant bacteria in the biofilm consortium (median 54.99%), and Pediococcus (26.09%). Celerinatantimonas, Leuconostoc, Alkalibacterium, Pseudomonas, Marinilactibacillus, Weissella, and the family Enterobacteriaceae were also present in at least 80% of samples. Regarding foodborne pathogens, only Enterobacteriaceae, Vibrio, and Staphylococcus were detected in at least 91.66%, 75.00%, and 54.10% of samples, respectively, but their median values were always below 0.15%. Compositional data analysis allowed discriminating between lye treated and natural olive samples, as well as between olives packaged in glass, PET and plastic bags. Leuconostoc, Celerinatantimonas, and Alkalibacterium were the bacteria genera with a higher discriminant power among samples. These results expand our knowledge of the bacteria diversity in olive biofilms, providing information about the sanitary and hygienic status of this ready-to-eat fermented vegetable.
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Affiliation(s)
- Antonio Benítez-Cabello
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain
| | - Verónica Romero-Gil
- Technological Applications for Improvement of Quality and Safety in Foods, Carretera de Marbella nº22. Planta-1, 29108, Guaro, Málaga, Spain
| | - Eduardo Medina-Pradas
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain
| | - Antonio Garrido-Fernández
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain
| | - Francisco Noé Arroyo-López
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain.
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19
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Anagnostopoulos DA, Kamilari E, Tsaltas D. Evolution of Bacterial Communities, Physicochemical Changes and Sensorial Attributes of Natural Whole and Cracked Picual Table Olives During Spontaneous and Inoculated Fermentation. Front Microbiol 2020; 11:1128. [PMID: 32547528 PMCID: PMC7273852 DOI: 10.3389/fmicb.2020.01128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
Table olives are one of the most well-known traditionally fermented products, and their global consumption is exponentially increasing. In direct brining, table olives are produced spontaneously, without any debittering pre-treatment. Up to date, fermentation process remains empirical and inconstant, as it is affected by the physicochemical attributes of the fruit, tree and fruit management of pro and post-harvest. In the present study, whole and cracked Picual table olives were fermented at industrial scale for 120 days, using three distinct methods (natural fermentation, inoculation with lactic acid bacteria (LAB) at a 7 or a 10% NaCl concentration). Microbial, physicochemical and sensorial alterations monitored during the whole process, and several differences were observed between treatments. Results indicated that in all treatments, the dominant microflora were LAB. Yeasts also detected in noteworthy populations, especially in non-inoculated samples. However, LAB population was significantly higher in inoculated compared to non-inoculated samples. Microbial profiles identified by metagenomic approach showed meaningful differences between spontaneous and inoculated treatments. As a result, the profound dominance of starter culture had a severe effect on olives fermentation, resulting in lower pH and higher acidification, which was mainly caused by the higher levels of lactic acid produced. Furthermore, the elimination of Enterobacteriaceae was shortened, even at lower salt concentration. Although no effect observed concerning the quantitated organoleptic parameters such as color and texture, significantly higher levels in terms of antioxidant capacity were recorded in inoculated samples. At the same time, the degradation time of oleuropein was shortened, leading to the production of higher levels of hydroxytyrosol. Based on this evidence, the establishment of starter culture driven Picual olives fermentation is strongly recommended. It is crucial to mention that the inoculated treatment with reducing sodium content was highly appreciated by the sensory panel, enhancing the hypothesis that the production of Picual table olives at reduced NaCl levels is achievable.
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Affiliation(s)
- Dimitrios A Anagnostopoulos
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Eleni Kamilari
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
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García-Serrano P, Romero C, Medina E, García-García P, de Castro A, Brenes M. Effect of calcium on the preservation of green olives intended for black ripe olive processing under free-sodium chloride conditions. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108870] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Anagnostopoulos DA, Goulas V, Xenofontos E, Vouras C, Nikoloudakis N, Tsaltas D. Benefits of the Use of Lactic Acid Bacteria Starter in Green Cracked Cypriot Table Olives Fermentation. Foods 2019; 9:foods9010017. [PMID: 31878011 PMCID: PMC7023104 DOI: 10.3390/foods9010017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 02/02/2023] Open
Abstract
Table olives are one of the most established Mediterranean vegetables, having an exponential increase consumption year by year. In the natural-style processing, olives are produced by spontaneous fermentation, without any chemical debittering. This natural fermentation process remains empirical and variable since it is strongly influenced by physicochemical parameters and microorganism presence in olive drupes. In the present work, Cypriot green cracked table olives were processed directly in brine (natural olives), using three distinct methods: spontaneous fermentation, inoculation with lactic acid bacteria at a 7% or a 10% NaCl concentration. Sensory, physicochemical, and microbiological alterations were monitored at intervals, and major differences were detected across treatments. Results indicated that the predominant microorganisms in the inoculated treatments were lactic acid bacteria, while yeasts predominated in control. As a consequence, starter culture contributed to a crucial effect on olives fermentation, leading to faster acidification and lower pH. This was attributed to a successful lactic acid fermentation, contrasting the acetic and alcoholic fermentation observed in control. Furthermore, it was established that inhibition of enterobacteria growth was achieved in a shorter period and at a significantly lower salt concentration, compared to the spontaneous fermentation. Even though no significant variances were detected in terms of the total phenolic content and antioxidant capacity, the degradation of oleuropein was achieved faster in inoculated treatments, thus, producing higher levels of hydroxytyrosol. Notably, the reduction of salt concentration, in combination with the use of starter, accented novel organoleptic characteristics in the final product, as confirmed from a sensory panel; hence, it becomes obvious that the production of Cypriot table olives at reduced NaCl levels is feasible.
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Benítez-Cabello A, Romero-Gil V, Medina E, Sánchez B, Calero-Delgado B, Bautista-Gallego J, Jiménez-Díaz R, Arroyo-López FN. Metataxonomic analysis of the bacterial diversity in table olive dressing components. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.05.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Analysis of bacterial and fungal communities by Illumina MiSeq platforms and characterization of Aspergillus cristatus in Fuzhuan brick tea. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.04.092] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Ruiz-Moyano S, Esperilla A, Hernández A, Benito MJ, Casquete R, Martín-Vertedor D, Pérez-Nevado F. Application of ISSR-PCR as a rapid method for clustering and typing of yeasts isolated from table olives. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.04.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Microbiota and Metabolite Profiling of Spoiled Spanish-Style Green Table Olives. Metabolites 2018; 8:metabo8040073. [PMID: 30384453 PMCID: PMC6316098 DOI: 10.3390/metabo8040073] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 12/25/2022] Open
Abstract
The aim of the present study was to assess the malodorous spoilages of Spanish-style green table olives through microbial and metabolite composition using current measuring techniques (e.g., high-throughput DNA sequencing, headspace solid-phase microextraction combined with gas chromatography-mass spectrometry). Under different alkaline and washing conditions, the spoilage fermentations were reproduced with Gordal and Manzanilla olive cultivars using a low salt concentration (71 g L−1 NaCl) in the initial brine. The degradation of lactic acid and significant increases in volatile fatty acids and phenols were found in all the spoiled samples in comparison with the unspoiled control samples. According to high-throughput DNA sequencing, Cardiobacteriaceae and Ruminococcus were the dominant bacteria in the spoiled samples. PLS regression and Pearson’s correlation coefficient analyses revealed positive and negative correlations among microbial communities, metabolites, and sensory spoilage descriptors. Notably, the “zapatera” descriptor was significantly associated with Propionibacterium, which was positively correlated with acetic acid, propionic acid, succinic acid, and methyl propanoate; while the “butyric” descriptor exhibited a significant positive relationship with the genus Ruminococcus, which gave an almost significant correlation with propionic and butyric acids.
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Xu X, Luo D, Bao Y, Liao X, Wu J. Characterization of Diversity and Probiotic Efficiency of the Autochthonous Lactic Acid Bacteria in the Fermentation of Selected Raw Fruit and Vegetable Juices. Front Microbiol 2018; 9:2539. [PMID: 30405588 PMCID: PMC6205992 DOI: 10.3389/fmicb.2018.02539] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
The diversity of indigenous lactic acid bacteria (LAB) in fermented broccoli, cherry, ginger, white radish, and white-fleshed pitaya juices was analyzed using culture-independent and -dependent approaches. The major properties of selected probiotic strains, including dynamic variations in pH, viable cell counts, antibiotic resistance, bacterial adhesion to hydrophobic compounds, and survivability during simulated gastrointestinal transit, were investigated using broccoli as the fermentation substrate. In broccoli and ginger juices, the genus Lactobacillus occupied the dominant position (abundances of 79.0 and 30.3%, respectively); in cherry and radish juices, Weissella occupied the dominant position (abundances of 78.3 and 83.2%, respectively); and in pitaya juice, Streptococcus and Lactococcus occupied the dominant positions (52.2 and 37.0%, respectively). Leuconostoc mesenteroides, Weissella cibaria/soli/confusa, Enterococcus gallinarum/durans/hirae, Pediococcus pentosaceus, Bacillus coagulans, and Lactococcus garvieae/lactis subspecies were identified by partial 16S rRNA gene sequencing. In general, the selected autochthonous LAB isolates displayed no significant differences in comparison with commercial strains with regard to growth rates or acidification in fermented broccoli juice. Among all the isolates, L. mesenteroides B4-25 exhibited the highest antibiotic resistance profile (equal to that of L. plantarum CICC20265), and suitable adhesion properties (adhesion of 13.4 ± 5.2% ∼ 36.4 ± 3.2% and 21.6 ± 1.4% ∼ 69.6 ± 2.3% to ethyl acetate and xylene, respectively). Furthermore, P. pentosaceus Ca-4 and L. mesenteroides B-25 featured the highest survival rates (22.4 ± 2.6 and 21.2 ± 1.4%, respectively), after simulated gastrointestinal transit. These results indicated a high level of diversity among the autochthonous bacterial community in fermented fruit and vegetable juices, and demonstrated the potential of these candidate probiotics for applications in fermentation.
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Affiliation(s)
- Xinxing Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Dongsheng Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Yejun Bao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Xiaojun Liao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
| | - Jihong Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- National Engineering Research Center for Fruit and Vegetable Processing, Beijing, China
- Key Laboratory of Fruit and Vegetable Processing, Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory for Food Non-thermal Processing, Beijing, China
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