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Lutter L, Kuzina A, Andreson H. Genotypic Stability of Lactic Acid Bacteria in Industrial Rye Bread Sourdoughs Assessed by ITS-PCR Analysis. Microorganisms 2024; 12:1872. [PMID: 39338546 PMCID: PMC11434513 DOI: 10.3390/microorganisms12091872] [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: 08/29/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Sourdough bread production relies on metabolically active starters refreshed daily with flour and water. The stability of sourdough microbial strains is crucial for consistent bread quality. However, many bakeries lack information on the persistence of starter cultures in ongoing sourdough production. Consequently, there is growing interest in identifying microbial strains from regularly used sourdoughs that possess good functional properties and resist changes in the complex growth environment. This study aimed to evaluate the composition and stability of lactic acid bacteria (LAB) in industrial wheat (WS) and rye (RS) sourdoughs propagated over a long period. LAB isolates (n = 66) from both sourdoughs, sampled over four seasons, were identified using phenotypic methods and genotyped via ITS-PCR and ITS-PCR/TaqI restriction analysis. Eight LAB species were detected, with Lactiplantibacillus plantarum being the most dominant and stable. Nineteen distinct LAB genotypes were observed, highlighting significant diversity. The presence of identical LAB genotypes in both sourdoughs suggests microbial transfer through the environment and bakery workers. LAB in RS were found to be more stable than those in WS. These findings underscore the importance of monitoring microbial stability and diversity in industrial sourdough production to maintain consistent bread quality.
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Affiliation(s)
| | | | - Helena Andreson
- Chair of Food Science and Technology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 56/5, 51006 Tartu, Estonia; (L.L.)
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Lahmamsi H, Ananou S, Lahlali R, Tahiri A. Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects. Folia Microbiol (Praha) 2024; 69:465-489. [PMID: 38393576 DOI: 10.1007/s12223-024-01146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.
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Affiliation(s)
- Haitam Lahmamsi
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco
| | - Samir Ananou
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
| | - Rachid Lahlali
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
| | - Abdessalem Tahiri
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
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3
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Calabrese FM, Ameur H, Nikoloudaki O, Celano G, Vacca M, Junior WJFL, Manzari C, Vertè F, Di Cagno R, Pesole G, De Angelis M, Gobbetti M. Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance. MICROBIOME 2022; 10:148. [PMID: 36104726 PMCID: PMC9472446 DOI: 10.1186/s40168-022-01301-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND In nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which players are subjected to continuous environmental and spatiotemporal stimuli. RESULTS The inspection of spontaneous sourdough metagenomes and transcriptomes revealed dominant, subdominant and satellite players that are engaged in different functional pathways. The highest microbial richness was associated with the highest number of gene copies per pathway. Based on meta-omics data collected from 8 spontaneous sourdoughs and their identified microbiota, we de novo reconstructed a synthetic microbial community SDG. We also reconstructed SMC-SD43 from scratch using the microbial composition of its spontaneous sourdough equivalent for comparison. The KEGG number of dominant players in the SDG was not affected by depletion of a single player, whereas the subdominant and satellite species fluctuated, revealing unique contributions. Compared to SMC-SD43, SDG exhibited broader transcriptome redundancy. The invariant volatilome profile of SDG after in situ long-term back slopping revealed its stability. In contrast, SMC-SD43 lost many taxon members. Dominant, subdominant and satellite players together ensured gene and transcript redundancy. CONCLUSIONS Our study demonstrates how, by starting from spontaneous sourdoughs and reconstructing these communities synthetically, it was possible to unravel the metabolic contributions of individual players. For resilience and good performance, the sourdough metacommunity must include dominant, subdominant and satellite players, which together ensure gene and transcript redundancy. Overall, our study changes the paradigm and introduces theoretical foundations for directing food fermentations. Video Abstract.
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Affiliation(s)
| | - Hana Ameur
- Faculty of Science and Technology, Libera Università Di Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Olga Nikoloudaki
- Faculty of Science and Technology, Libera Università Di Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Giuseppe Celano
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Mirco Vacca
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Wilson JFLemos Junior
- Faculty of Science and Technology, Libera Università Di Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy
| | - Fabienne Vertè
- Puratos NV, Industrialaan 25, 1702, Groot-Bijgaarden, Belgium
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università Di Bolzano, Piazza Università 5, 39100, Bolzano, Italy.
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Università Di Bolzano, Piazza Università 5, 39100, Bolzano, Italy
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4
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De Vuyst L, Comasio A, Kerrebroeck SV. Sourdough production: fermentation strategies, microbial ecology, and use of non-flour ingredients. Crit Rev Food Sci Nutr 2021; 63:2447-2479. [PMID: 34523363 DOI: 10.1080/10408398.2021.1976100] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sourdough production is an ancient method to ferment flour from cereals for the manufacturing of baked goods. This review deals with the state-of-the-art of current fermentation strategies for sourdough production and the microbial ecology of mature sourdoughs, with a particular focus on the use of non-flour ingredients. Flour fermentation processes for sourdough production are typically carried out by heterogeneous communities of lactic acid bacteria and yeasts. Acetic acid bacteria may also occur, although their presence and role in sourdough production can be criticized. Based on the inoculum used, sourdough productions can be distinguished in fermentation processes using backslopping procedures, originating from a spontaneously fermented flour-water mixture (Type 1), starter culture-initiated fermentation processes (Type 2), and starter culture-initiated fermentation processes that are followed by backslopping (Type 3). In traditional recipes for the initiation and/or propagation of Type 1 sourdough productions, non-flour ingredients are often added to the flour-water mixture. These ingredients may be the source of an additional microbial inoculum and/or serve as (co-)substrates for fermentation. An example of the former is the addition of yoghurt; an example of the latter is the use of fruit juices. The survival of microorganisms transferred from the ingredients to the fermenting flour-water mixture depends on the competitiveness toward particular strains of the microbial species present under the harsh conditions of the sourdough ecosystem. Their survival and growth is also determined by the presence of the appropriate substrates, whether or not carried over by the ingredients added.
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Affiliation(s)
- Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Andrea Comasio
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Simon Van Kerrebroeck
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Calvert MD, Madden AA, Nichols LM, Haddad NM, Lahne J, Dunn RR, McKenney EA. A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research. PeerJ 2021; 9:e11389. [PMID: 34026358 PMCID: PMC8117929 DOI: 10.7717/peerj.11389] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/12/2021] [Indexed: 01/13/2023] Open
Abstract
The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community.
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Affiliation(s)
- Martha D Calvert
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University (Virginia Tech), Blackburg, VA, United States of America.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Anne A Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Lauren M Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
| | - Nick M Haddad
- Kellogg Biological Station and Department of Integrative Biology, Michigan State University, Hickory Corners, MI, United States of America
| | - Jacob Lahne
- Department of Food Science and Technology, Virginia Polytechnic Institute and State University (Virginia Tech), Blackburg, VA, United States of America
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Erin A McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States of America
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6
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Jiang S, Cai L, Lv L, Li L. Pediococcus pentosaceus, a future additive or probiotic candidate. Microb Cell Fact 2021; 20:45. [PMID: 33593360 PMCID: PMC7885583 DOI: 10.1186/s12934-021-01537-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Background Pediococcus pentosaceus, a promising strain of lactic acid bacteria (LAB), is gradually attracting attention, leading to a rapid increase in experimental research. Due to increased demand for practical applications of microbes, the functional and harmless P. pentosaceus might be a worthwhile LAB strain for both the food industry and biological applications. Results As an additive, P. pentosaceus improves the taste and nutrition of food, as well as the storage of animal products. Moreover, the antimicrobial abilities of Pediococcus strains are being highlighted. Evidence suggests that bacteriocins or bacteriocin-like substances (BLISs) produced by P. pentosaceus play effective antibacterial roles in the microbial ecosystem. In addition, various strains of P. pentosaceus have been highlighted for probiotic use due to their anti-inflammation, anticancer, antioxidant, detoxification, and lipid-lowering abilities. Conclusions Therefore, it is necessary to continue studying P. pentosaceus for further use. Thorough study of several P. pentosaceus strains should clarify the benefits and drawbacks in the future.
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Affiliation(s)
- Shiman Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lingzhi Cai
- The Infectious Diseases Department, The First People's Hospital of Wenling, The Affiliated Wenling Hospital of Wenzhou Medical University, Taizhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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7
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Oshiro M, Zendo T, Nakayama J. Diversity and dynamics of sourdough lactic acid bacteriota created by a slow food fermentation system. J Biosci Bioeng 2021; 131:333-340. [PMID: 33358094 DOI: 10.1016/j.jbiosc.2020.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 12/21/2022]
Abstract
Sourdough is a naturally fermented dough that is used worldwide to produce a variety of baked foods. Various lactic acid bacteria (LAB), which can determine the quality of sourdough baked foods by producing metabolites, have been found in the sourdough ecosystem. However, spontaneous fermentation of sourdough leads to unpredictable growth of various micro-organisms, which result in unstable product quality. From an ecological perspective, many researchers have recently studied sourdough LAB diversity, particularly the elucidation of LAB community interactions and the dynamic mechanisms during the fermentation process, in response to requests for the control and design of a desired sourdough microbial community. This article reviews recent advances in the study of sourdough LAB diversity and its dynamics in association with unique characteristics of the fermentation system; it also discusses future perspectives for better understanding of the complex sourdough microbial ecosystem, which can be attained efficiently by both in vitro and in situ experimental approaches.
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Affiliation(s)
- Mugihito Oshiro
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Central Laboratory of Yamazaki Baking Company Limited, 3-23-27 Ichikawa, Ichikawa-shi, Chiba 272-8581, Japan.
| | - Takeshi Zendo
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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8
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Comasio A, Van Kerrebroeck S, Harth H, Verté F, De Vuyst L. Potential of Bacteria from Alternative Fermented Foods as Starter Cultures for the Production of Wheat Sourdoughs. Microorganisms 2020; 8:E1534. [PMID: 33036188 PMCID: PMC7599913 DOI: 10.3390/microorganisms8101534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 01/31/2023] Open
Abstract
Microbial strains for starter culture-initiated sourdough productions are commonly isolated from a fermenting flour-water mixture. Yet, starter culture strains isolated from matrices other than sourdoughs could provide the dough with interesting metabolic properties and hence change the organoleptic properties of the concomitant breads. Furthermore, the selection of sourdough starter cultures does not need to be limited to lactic acid bacteria (LAB), as other food-grade microorganisms are sometimes found in sourdoughs. Therefore, different strains belonging to LAB, acetic acid bacteria (AAB), and coagulase-negative staphylococci (CNS) that originated from different fermented food matrices (fermenting cocoa pulp-bean mass, fermented sausage, and water kefir), were examined as to their prevalence in a wheat sourdough ecosystem during 72-h fermentations. Limosilactobacillus fermentum IMDO 222 (fermented cocoa pulp-bean mass isolate) and Latilactobacillus sakei CTC 494 (fermented sausage isolate) seemed to be promising candidates as sourdough starter culture strains, as were the AAB strains Acetobacter pasteurianus IMDO 386B and Gluconobacter oxydans IMDO A845 (both isolated from fermented cocoa pulp-bean mass), due to their competitiveness in the wheat flour-water mixtures. Wheat breads made with G. oxydans IMDO A845 sourdoughs were significantly darker than reference wheat breads.
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Affiliation(s)
- Andrea Comasio
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium; (A.C.); (S.V.K.); (H.H.)
| | - Simon Van Kerrebroeck
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium; (A.C.); (S.V.K.); (H.H.)
| | - Henning Harth
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium; (A.C.); (S.V.K.); (H.H.)
| | - Fabienne Verté
- Puratos NV, Industrialaan 25, 1702 Groot-Bijgaarden, Belgium;
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium; (A.C.); (S.V.K.); (H.H.)
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9
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Adepehin J. Microbial diversity and pasting properties of finger millet (Eleusine coracana), pearl millet (Pennisetum glaucum) and sorghum (Sorghum bicolor) sourdoughs. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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10
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Perri G, Calabrese FM, Rizzello CG, De Angelis M, Gobbetti M, Calasso M. Sprouting process affects the lactic acid bacteria and yeasts of cereal, pseudocereal and legume flours. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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11
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Xing X, Ma J, Fu Z, Zhao Y, Ai Z, Suo B. Diversity of bacterial communities in traditional sourdough derived from three terrain conditions (mountain, plain and basin) in Henan Province, China. Food Res Int 2020; 133:109139. [PMID: 32466894 DOI: 10.1016/j.foodres.2020.109139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/29/2020] [Accepted: 02/29/2020] [Indexed: 12/23/2022]
Abstract
To elucidate the bacterial community composition of sourdoughs from different terrain conditions, thirty-two Chinese traditional sourdough samples were collected from three terrain conditions (mountain, plain and basin) in Henan Province. High-throughput sequencing and culture-dependent approaches were employed to identify the bacterial diversity of the sourdough samples. A total of two hundred and six isolates were characterized via 16S rRNA gene sequencing. Pediococcus pentosaceus was isolated from every sample and was the predominant species in the sourdough samples, accounting for 58% of the relative abundance. High-throughput sequencing revealed that the predominant genera (mainly Pediococcus) in the basin group were significantly different from those in the mountain and plain groups. The genus Lactobacillus was predominant in the plain and mountain sourdough samples. Pediococcus pentosaceus was the absolute dominant strain in the basin sourdough samples. Acetobacter, which was widely distributed only in mountain samples, was recognized as the representative genus of the mountain samples. Moreover, we first reported Gluconobacter oxydans in sourdough. This study provided insight into the bacterial diversity of sourdough from three terrain conditions (mountain, plain and basin) in Henan Province and could serve as a reference for the isolation of desired bacterial strains.
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Affiliation(s)
- Xiaolong Xing
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou 450002, China; Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingyi Ma
- College of Information and Management Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhongjun Fu
- Maize Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China
| | - Yirui Zhao
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Zhilu Ai
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou 450002, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou 450002, China; Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China.
| | - Biao Suo
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; National R&D Center For Frozen Rice&Wheat Products Processing Technology, Zhengzhou 450002, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou 450002, China.
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12
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Menezes L, Sardaro MS, Duarte R, Mazzon R, Neviani E, Gatti M, De Dea Lindner J. Sourdough bacterial dynamics revealed by metagenomic analysis in Brazil. Food Microbiol 2020; 85:103302. [DOI: 10.1016/j.fm.2019.103302] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 12/12/2022]
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13
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Naghmouchi K, Belguesmia Y, Bendali F, Spano G, Seal BS, Drider D. Lactobacillus fermentum: a bacterial species with potential for food preservation and biomedical applications. Crit Rev Food Sci Nutr 2019; 60:3387-3399. [PMID: 31729242 DOI: 10.1080/10408398.2019.1688250] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Lactic acid-producing bacteria are the most commonly used probiotics that play an important role in protecting the host against harmful microorganisms, strengthening the host immune system, improving feed digestibility, and reducing metabolic disorders. Lactobacillus fermentum (Lb. fermentum) is a Gram-positive bacterium belonging to Lactobacillus genus, and many reportedly to enhance the immunologic response as well as prevent community-acquired gastrointestinal and upper respiratory infections. Additionally, Lb. fermentum strains produce diverse and potent antimicrobial peptides, which can be applied as food preservative agents or as alternatives to antibiotics. Further functions attributed to probiotic Lb. fermentum strains are their abilities to decrease the level of blood stream cholesterol (as cholesterol-lowering agents) and to potentially help prevent alcoholic liver disease and colorectal cancer among humans. Finally, Lb. fermentum is a key microorganism in sourdough technology, contributing to flavor, texture, or health-promoting dough ingredients, and has recently been used to develop new foods stuffs such as fortified and functional foods with beneficial attributes for human health. Development of such new foodstuffs are currently taking important proportions of the food industry market. Furthermore, an increasing awareness of the consumers prompts the food-makers to implement alternative environmental friendly solutions in the production processes and/or suitable biological alternative to limit the use of antibiotics in feed and food. Here, we give an account on the application of Lb. fermentum strains in the biomedical and food preservation fields, with a focus on probiotic features such as bacteriocin production. We also summarize the use of Lb. fermentum as cell factories with the aim to improve the efficacy and health value of functional food.
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Affiliation(s)
- Karim Naghmouchi
- Department of Pharmaceutical Chemistry, College of Clinical Pharmacy, Al Baha University, Saudi Arabia.,Faculté des Sciences de Tunis, Université de Tunis El Manar, LR01ES05 Biochimie et Biotechnologie, Tunis, Tunisie
| | - Yanath Belguesmia
- Université Lille, INRA, ISA, Université d'Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, Lille, France
| | - Farida Bendali
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Giuseppe Spano
- Dipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente, Università di Foggia, Foggia, Italy
| | - Bruce S Seal
- Biology Program, Oregon State University Cascades, Bend, Oregon, USA
| | - Djamel Drider
- Université Lille, INRA, ISA, Université d'Artois, Université Littoral Côte d'Opale, EA 7394-ICV Institut Charles Viollette, Lille, France
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Dense tracking of the dynamics of the microbial community and chemicals constituents in spontaneous wheat sourdough during two months of backslopping. J Biosci Bioeng 2019; 128:170-176. [DOI: 10.1016/j.jbiosc.2019.02.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/22/2019] [Accepted: 02/12/2019] [Indexed: 12/20/2022]
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15
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Weckx S, Van Kerrebroeck S, De Vuyst L. Omics approaches to understand sourdough fermentation processes. Int J Food Microbiol 2019; 302:90-102. [DOI: 10.1016/j.ijfoodmicro.2018.05.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/12/2018] [Accepted: 05/28/2018] [Indexed: 12/31/2022]
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Reale A, Di Renzo T, Boscaino F, Nazzaro F, Fratianni F, Aponte M. Lactic Acid Bacteria Biota and Aroma Profile of Italian Traditional Sourdoughs From the Irpinian Area in Italy. Front Microbiol 2019; 10:1621. [PMID: 31396170 PMCID: PMC6667676 DOI: 10.3389/fmicb.2019.01621] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/01/2019] [Indexed: 11/13/2022] Open
Abstract
This study identified the lactic acid bacteria (LAB) biota and the volatilome profile of 28 typical sourdoughs of Irpinia—a large area of the Campania region of Southern Italy where numerous breads are produced, even today, following the ancient procedures of sourdough fermentation and for which information on the microbiological and sensory profile is lacking in literature. For this purpose, microbial quality, LAB biodiversity, chemical, and technological characteristics, as well as aroma profile by solid-phase microextraction technique (SPME)–gas chromatography/mass spectrometry (GC/MS) of Irpinian sourdoughs were investigated. The dominant LAB microbiota was examined by both culture-dependent and culture-independent methods Polymerase Chain Reaction/Denaturing Gradient Gel Electrophoresis (PCR-DGGE). Results showed a high biodiversity in LAB community whereas the most frequent lactobacilli species recognized were Lactobacillus plantarum (ca. 22% of total LAB isolates), Lactobacillus sanfranciscensis (11%), Lactobacillus paralimentarius (8%), and Lactobacillus rossiae (6.5%), whereas LAB cocci could be mainly referred to Pediococcus pentosaceus (9.5% of total LAB isolates), Leuconostoc spp. (7.8%), and Weissella cibaria (7.7%). Sourdoughs were characterized by the dominance of one or two LAB species, thus proving that the environment influences the selection and the establishment of few key LAB species and that no specific correlation can be traced between microbial composition and geographical origin of the samples. Furthermore, although sourdoughs were characterized by different qualitative and quantitative volatile organic compound (VOC) compositions, no noticeable correlation between volatilome profile and geographical origin was found. However, it emerged that for more isolated locations, it was possible to find the existence of microbial biotypes and sensory profiles with a strong identity, thus revealing the existence of highly traditional and evocative bread recipes in those geographical contexts.
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Affiliation(s)
- Anna Reale
- Institute of Food Science, National Research Council, ISA-CNR, Avellino, Italy
| | - Tiziana Di Renzo
- Institute of Food Science, National Research Council, ISA-CNR, Avellino, Italy
| | - Floriana Boscaino
- Institute of Food Science, National Research Council, ISA-CNR, Avellino, Italy
| | - Filomena Nazzaro
- Institute of Food Science, National Research Council, ISA-CNR, Avellino, Italy
| | - Florinda Fratianni
- Institute of Food Science, National Research Council, ISA-CNR, Avellino, Italy
| | - Maria Aponte
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
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Lactococci dominate the bacterial communities of fermented maize, sorghum and millet slurries in Zimbabwe. Int J Food Microbiol 2019; 289:77-87. [DOI: 10.1016/j.ijfoodmicro.2018.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 08/13/2018] [Accepted: 09/01/2018] [Indexed: 11/18/2022]
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Harth H, Van Kerrebroeck S, De Vuyst L. Impact of process conditions on the microbial community dynamics and metabolite production kinetics of teff sourdough fermentations under bakery and laboratory conditions. Food Sci Nutr 2018; 6:1438-1455. [PMID: 30258586 PMCID: PMC6145266 DOI: 10.1002/fsn3.690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 12/14/2022] Open
Abstract
Teff and teff sourdoughs are promising ingredients for bread production. Therefore, this study aimed at the characterization of spontaneous and flour-native starter culture-initiated teff sourdough productions under bakery and laboratory conditions. Backslopped laboratory and bakery teff sourdough productions were characterized by different lactic acid bacteria (LAB) and yeast species, but were both characterized by a pH below 4.0 after five backslopping steps. The sourdough-associated Lactobacillus sanfranciscensis was isolated for the first time from backslopped spontaneous teff sourdoughs. The autochthonous strain L. sanfranciscensis IMDO 150101 was tested as starter culture during laboratory teff sourdough fermentations. Its prevalence could be related to the process conditions applied, in particular the ambient temperature (below 30°C). Breads made with 20% teff sourdough (on flour basis) displayed interesting features compared with all-wheat-based reference breads. Teff sourdoughs were characterized as to their pH evolution, microbial community dynamics, and microbial species composition. Representative strains of the LAB species isolated from these sourdoughs, in particular L. sanfranciscensis, may be selected as starter cultures for the production of stable teff sourdoughs and flavorful breads, provided they are adapted to the environmental conditions applied.
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Affiliation(s)
- Henning Harth
- Research Group of Industrial Microbiology and Food BiotechnologyFaculty of Sciences and Bioengineering SciencesVrije Universiteit BrusselBrusselsBelgium
| | - Simon Van Kerrebroeck
- Research Group of Industrial Microbiology and Food BiotechnologyFaculty of Sciences and Bioengineering SciencesVrije Universiteit BrusselBrusselsBelgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food BiotechnologyFaculty of Sciences and Bioengineering SciencesVrije Universiteit BrusselBrusselsBelgium
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Minervini F, Lattanzi A, Dinardo FR, De Angelis M, Gobbetti M. Wheat endophytic lactobacilli drive the microbial and biochemical features of sourdoughs. Food Microbiol 2018; 70:162-171. [DOI: 10.1016/j.fm.2017.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/08/2017] [Accepted: 09/10/2017] [Indexed: 11/27/2022]
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21
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Fujimoto A, Ito K, Itou M, Narushima N, Ito T, Yamamoto A, Hirayama S, Furukawa S, Morinaga Y, Miyamoto T. Microbial behavior and changes in food constituents during fermentation of Japanese sourdoughs with different rye and wheat starting materials. J Biosci Bioeng 2018; 125:97-104. [DOI: 10.1016/j.jbiosc.2017.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/15/2017] [Accepted: 08/17/2017] [Indexed: 11/28/2022]
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22
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Sourdoughs as a function of their species diversity and process conditions, a meta-analysis. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.08.016] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation. Sci Rep 2017; 7:11504. [PMID: 28912444 PMCID: PMC5599536 DOI: 10.1038/s41598-017-12016-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/30/2017] [Indexed: 12/28/2022] Open
Abstract
The genomic and metabolic features of Leuconostoc (Leu) mesenteroides were investigated through pan-genomic and transcriptomic analyses. Relatedness analysis of 17 Leu. mesenteroides strains available in GenBank based on 16S rRNA gene sequence, average nucleotide identity, in silico DNA-DNA hybridization, molecular phenotype, and core-genome indicated that Leu. mesenteroides has been separated into different phylogenetic lineages. Pan-genome of Leu. mesenteroides strains, consisting of 999 genes in core-genome, 1,432 genes in accessory-genome, and 754 genes in unique genome, and their COG and KEGG analyses showed that Leu. mesenteroides harbors strain-specifically diverse metabolisms, probably representing high evolutionary genome changes. The reconstruction of fermentative metabolic pathways for Leu. mesenteroides strains showed that Leu. mesenteroides produces various metabolites such as lactate, ethanol, acetate, CO2, mannitol, diacetyl, acetoin, and 2,3-butanediol through an obligate heterolactic fermentation from various carbohydrates. Fermentative metabolic features of Leu. mesenteroides during kimchi fermentation were investigated through transcriptional analyses for the KEGG pathways and reconstructed metabolic pathways of Leu. mesenteroides using kimchi metatranscriptomic data. This was the first study to investigate the genomic and metabolic features of Leu. mesenteroides through pan-genomic and metatranscriptomic analyses, and may provide insights into its genomic and metabolic features and a better understanding of kimchi fermentations by Leu. mesenteroides.
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He GQ, Liu TJ, Sadiq FA, Gu JS, Zhang GH. Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches. J Zhejiang Univ Sci B 2017; 18:289-302. [PMID: 28378567 DOI: 10.1631/jzus.b1600148] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches.
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Affiliation(s)
- Guo-Qing He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Tong-Jie Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Faizan A Sadiq
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Jing-Si Gu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
| | - Guo-Hua Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Food Microbiology, Zhejiang University, Hangzhou 310058, China
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Coda R, Kianjam M, Pontonio E, Verni M, Di Cagno R, Katina K, Rizzello CG, Gobbetti M. Sourdough-type propagation of faba bean flour: Dynamics of microbial consortia and biochemical implications. Int J Food Microbiol 2017; 248:10-21. [PMID: 28242419 DOI: 10.1016/j.ijfoodmicro.2017.02.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/28/2016] [Accepted: 02/18/2017] [Indexed: 10/20/2022]
Abstract
The microbial ecology of faba bean sourdoughs obtained from an Italian (Ita) and a Finnish (Fi) cultivar, belonging respectively to Vicia faba major and V. faba minor groups, was described by 16S rRNA gene pyrosequencing and culture-dependent analysis. The sourdoughs were propagated with traditional backslopping procedure throughout 14days. Higher microbial diversity was found in the sourdough deriving from V. faba minor (Fi), still containing residual hulls after the milling procedure. After 2days of propagation, the microbial profile of Ita sourdough was characterized by the dominance of the genera Pediococcus, Leuconostoc and Weissella, while the genera Lactococcus, Lactobacillus and Escherichia, as well as Enterobacteriaceae were present in Fi sourdoughs. Yeasts were in very low cell density until the second backslopping and were not anymore found after this time by plate count or pyrosequencing analysis. Among the lactic acid bacteria isolates, Pediococcus pentosaceus, Leuconostoc mesenteroides and Weissella koreensis had the highest frequency of occurrence in both the sourdoughs. Lactobacillus sakei was the only lactobacillus isolated from the first to the last propagation day in Fi sourdough. According to microbiological and acidification properties, the maturity of the sourdoughs was reached after 5days. The presence of hulls and the different microbial composition reflected on biochemical characteristics of Fi sourdoughs, including acidification and phenolic compounds. Moreover, proteolysis in Fi sourdough was more intense compared to Ita. The microbial dynamic of the faba bean sourdoughs showed some differences with the most studied cereal sourdoughs.
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Affiliation(s)
- Rossana Coda
- University of Helsinki, Department of Food and Environmental Sciences, Agnes Sjioberginkatu 2, Helsinki, Finland
| | - Maryam Kianjam
- University of Helsinki, Department of Food and Environmental Sciences, Agnes Sjioberginkatu 2, Helsinki, Finland
| | - Erica Pontonio
- University of Bari "Aldo Moro", Department of Soil, Plant, and Food Science, Via Amendola 165/a, 70125 Bari, Italy
| | - Michela Verni
- University of Bari "Aldo Moro", Department of Soil, Plant, and Food Science, Via Amendola 165/a, 70125 Bari, Italy
| | - Raffaella Di Cagno
- Faculty of Food Science and Technology, University of Bozen, 39100 Bolzano, Italy
| | - Kati Katina
- University of Helsinki, Department of Food and Environmental Sciences, Agnes Sjioberginkatu 2, Helsinki, Finland
| | - Carlo Giuseppe Rizzello
- University of Bari "Aldo Moro", Department of Soil, Plant, and Food Science, Via Amendola 165/a, 70125 Bari, Italy.
| | - Marco Gobbetti
- Faculty of Food Science and Technology, University of Bozen, 39100 Bolzano, Italy
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Microbial Ecology and Process Technology of Sourdough Fermentation. ADVANCES IN APPLIED MICROBIOLOGY 2017; 100:49-160. [PMID: 28732554 DOI: 10.1016/bs.aambs.2017.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From a microbiological perspective, sourdough is to be considered as a specific and stressful ecosystem, harboring yeasts and lactic acid bacteria (LAB), that is used for the production of baked goods. With respect to the metabolic impact of the sourdough microbiota, acidification (LAB), flavor formation (LAB and yeasts), and leavening (yeasts and heterofermentative LAB species) are most noticeable. Three distinct types of sourdough fermentation processes can be discerned based on the inocula applied, namely backslopped ones (type 1), those initiated with starter cultures (type 2), and those initiated with a starter culture followed by backslopping (type 3). A sourdough-characteristic LAB species is Lactobacillus sanfranciscensis. A sourdough-characteristic yeast species is Candida humilis. Although it has been suggested that the microbiota of a specific sourdough may be influenced by its geographical origin, region specificity often seems to be an artefact resulting from interpretation of the research data, as those are dependent on sampling, isolation, and identification procedures. It is however clear that sourdough-adapted microorganisms are able to withstand stress conditions encountered during their growth. Based on the technological setup, type 0 (predoughs), type I (artisan bakery firm sourdoughs), type II (industrial liquid sourdoughs), and type III sourdoughs (industrial dried sourdoughs) can be distinguished. The production of all sourdoughs, independent of their classification, depends on several intrinsic and extrinsic factors. Both the flour (type, quality status, etc.) and the process parameters (fermentation temperature, pH and pH evolution, dough yield, water activity, oxygen tension, backslopping procedure and fermentation duration, etc.) determine the dynamics and outcome of (backslopped) sourdough fermentation processes.
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Van Kerrebroeck S, Bastos FCC, Harth H, De Vuyst L. A low pH does not determine the community dynamics of spontaneously developed backslopped liquid wheat sourdoughs but does influence their metabolite kinetics. Int J Food Microbiol 2016; 239:54-64. [DOI: 10.1016/j.ijfoodmicro.2016.07.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/09/2016] [Accepted: 07/11/2016] [Indexed: 11/24/2022]
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28
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Gobbetti M, Minervini F, Pontonio E, Di Cagno R, De Angelis M. Drivers for the establishment and composition of the sourdough lactic acid bacteria biota. Int J Food Microbiol 2016; 239:3-18. [DOI: 10.1016/j.ijfoodmicro.2016.05.022] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/11/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
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Mangunwardoyo W, Abinawanto, Salamah A, Sukara E, Sulistiani, Dinoto A. Diversity and distribution of culturable lactic acid bacterial species in Indonesian Sayur Asin. IRANIAN JOURNAL OF MICROBIOLOGY 2016; 8:274-281. [PMID: 28210467 PMCID: PMC5296942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND AND OBJECTIVES Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. MATERIALS AND METHODS Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3-7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia. LAB strains were isolated by using MRS agar method supplemented with 1% CaCO 3 and characterized morphologically. Identification of the strains was performed basedon 16S rDNA analysis and the phylogenetic tree was drawn to understand the phylogenetic relationship of the collected strains. RESULTS Different profiles were detected in total count of the plates, salinity and pH of fermenting liquor of Sayur Asin in TA and KDR provinces. A total of 172 LAB isolates were successfully isolated and identified based on their 16S rDNA sequences. Phylogenetic analysis of 27 representative LAB strains from Sayur Asin showed that these strains belonged to 5 distinct species namely Lactobacilus farciminis (N=32), L. fermentum (N=4), L. namurensis (N=15), L. plantarum (N=118) and L. parafarraginis (N=1). Strains D5-S-2013 and B4-S-2013 showed a close phylogenetic relationship with L. composti and L. paralimentarius, respectively where as the sequence had slightly lower similarity of lower than 99%, suggesting that they may be classified into novel species and need further investigation due to exhibition of significant differences in their nucleotide sequences. Lactobacillus plantarum was found being dominant in all sayur asin samples. CONCLUSION Lactobacilli were recognized as the major group of lactic acid bacteria in Sayur Asin including 5 known and 2 novel candidate species. The distribution of LAB species was associated with the manufactures where Sayur Asin is produced.
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Affiliation(s)
- Wibowo Mangunwardoyo
- Department of Biology, Faculty of Mathematic and Sciences, Universitas Indonesia, Depok, Indonesia,Corresponding author: Dr. Wibowo Mangunwardoyo, Department of Biology, Faculty of Mathematic and Sciences, Universitas Indonesia, Depok, Indonesia. Phone: 62-21-7270163, Fax: 62-21-78884910, E-mail:;
| | - Abinawanto
- Department of Biology, Faculty of Mathematic and Sciences, Universitas Indonesia, Depok, Indonesia
| | - Andi Salamah
- Department of Biology, Faculty of Mathematic and Sciences, Universitas Indonesia, Depok, Indonesia
| | - Endang Sukara
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia
| | - Sulistiani
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia
| | - Achmad Dinoto
- Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia
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Community dynamics and metabolite target analysis of spontaneous, backslopped barley sourdough fermentations under laboratory and bakery conditions. Int J Food Microbiol 2016; 228:22-32. [DOI: 10.1016/j.ijfoodmicro.2016.04.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 11/19/2022]
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31
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Taccari M, Aquilanti L, Polverigiani S, Osimani A, Garofalo C, Milanović V, Clementi F. Microbial Diversity of Type I Sourdoughs Prepared and Back-Slopped with Wholemeal and Refined Soft (Triticum aestivum) Wheat Flours. J Food Sci 2016; 81:M1996-2005. [PMID: 27332783 DOI: 10.1111/1750-3841.13372] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 05/18/2016] [Accepted: 05/20/2016] [Indexed: 01/10/2023]
Abstract
The fermentation of type I sourdough was studied for 20 d with daily back-slopping under laboratory and artisan bakery conditions using 1 wholemeal and 2 refined soft wheat (Triticum aestivum) flours. The sourdough bacterial and yeast diversity and dynamics were investigated by plate counting and a combination of culture-dependent and culture-independent PCR-DGGE approach. The pH, total titrable acidity, and concentration of key organic acids (phytic, lactic, and acetic) were measured. Three flours differed for both chemical and rheological properties. A microbial succession was observed, with the atypical sourdough species detected at day 0 (i.e. Lactococcus lactis and Leuconostoc holzapfelii/citreum group for bacteria and Candida silvae and Wickerhamomyces anomalus for yeasts) being progressively replaced by taxa more adapted to the sourdough ecosystem (Lactobacillus brevis, Lactobacillus alimentarius/paralimentarius, Saccharomyces cerevisiae). In mature sourdoughs, a notably different species composition was observed. As sourdoughs propagated with the same flour at laboratory and artisan bakery level were compared, the influence of both the substrate and the propagation environment on microbial diversity was assumed.
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Affiliation(s)
- Manuela Taccari
- Dipt. di Scienze Agrarie Alimentari ed Ambientali (D3A), Univ. Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Lucia Aquilanti
- Dipt. di Scienze Agrarie Alimentari ed Ambientali (D3A), Univ. Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Serena Polverigiani
- Dipt. di Scienze Agrarie Alimentari ed Ambientali (D3A), Univ. Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Andrea Osimani
- Dipt. di Scienze Agrarie Alimentari ed Ambientali (D3A), Univ. Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Cristiana Garofalo
- Dipt. di Scienze Agrarie Alimentari ed Ambientali (D3A), Univ. Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Vesna Milanović
- Dipt. di Scienze Agrarie Alimentari ed Ambientali (D3A), Univ. Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Francesca Clementi
- Dipt. di Scienze Agrarie Alimentari ed Ambientali (D3A), Univ. Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
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32
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Liu T, Li Y, Chen J, Sadiq FA, Zhang G, Li Y, He G. Prevalence and diversity of lactic acid bacteria in Chinese traditional sourdough revealed by culture dependent and pyrosequencing approaches. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.12.025] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Bokulich NA, Lewis ZT, Boundy-Mills K, Mills DA. A new perspective on microbial landscapes within food production. Curr Opin Biotechnol 2016; 37:182-189. [PMID: 26773388 PMCID: PMC4913695 DOI: 10.1016/j.copbio.2015.12.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/10/2015] [Accepted: 12/15/2015] [Indexed: 01/01/2023]
Abstract
High-throughput, 'next-generation' sequencing tools offer many exciting new possibilities for food research. From investigating microbial dynamics within food fermentations to the ecosystem of the food-processing built environment, amplicon sequencing, metagenomics, and transcriptomics present novel applications for exploring microbial communities in, on, and around our foods. This review discusses the many uses of these tools for food-related and food facility-related research and highlights where they may yield nuanced insight into the microbial world of food production systems.
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Affiliation(s)
- Nicholas A Bokulich
- Department of Viticulture and Enology, University of California, Davis, CA 95616,United States; Department of Food Science and Technology, University of California, Davis, CA 95616,United States; Foods for Health Institute, University of California, Davis, CA 95616, United States
| | - Zachery T Lewis
- Department of Food Science and Technology, University of California, Davis, CA 95616,United States; Foods for Health Institute, University of California, Davis, CA 95616, United States
| | - Kyria Boundy-Mills
- Department of Food Science and Technology, University of California, Davis, CA 95616,United States
| | - David A Mills
- Department of Viticulture and Enology, University of California, Davis, CA 95616,United States; Department of Food Science and Technology, University of California, Davis, CA 95616,United States; Foods for Health Institute, University of California, Davis, CA 95616, United States.
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Minervini F, Celano G, Lattanzi A, Tedone L, De Mastro G, Gobbetti M, De Angelis M. Lactic Acid Bacteria in Durum Wheat Flour Are Endophytic Components of the Plant during Its Entire Life Cycle. Appl Environ Microbiol 2015; 81:6736-48. [PMID: 26187970 PMCID: PMC4561690 DOI: 10.1128/aem.01852-15] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/14/2015] [Indexed: 11/20/2022] Open
Abstract
This study aimed at assessing the dynamics of lactic acid bacteria and other Firmicutes associated with durum wheat organs and processed products. 16S rRNA gene-based high-throughput sequencing showed that Lactobacillus, Streptococcus, Enterococcus, and Lactococcus were the main epiphytic and endophytic genera among lactic acid bacteria. Bacillus, Exiguobacterium, Paenibacillus, and Staphylococcus completed the picture of the core genus microbiome. The relative abundance of each lactic acid bacterium genus was affected by cultivars, phenological stages, other Firmicutes genera, environmental temperature, and water activity (aw) of plant organs. Lactobacilli, showing the highest sensitivity to aw, markedly decreased during milk development (Odisseo) and physiological maturity (Saragolla). At these stages, Lactobacillus was mainly replaced by Streptococcus, Lactococcus, and Enterococcus. However, a key sourdough species, Lactobacillus plantarum, was associated with plant organs during the life cycle of Odisseo and Saragolla wheat. The composition of the sourdough microbiota and the overall quality of leavened baked goods are also determined throughout the phenological stages of wheat cultivation, with variations depending on environmental and agronomic factors.
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Affiliation(s)
- Fabio Minervini
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Giuseppe Celano
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Anna Lattanzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Tedone
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Giuseppe De Mastro
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Gobbetti
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
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Abstract
Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been "in culture" for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the "parts list" (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.
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Ufarté L, Potocki-Veronese G, Laville É. Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. Front Microbiol 2015; 6:563. [PMID: 26097471 PMCID: PMC4456863 DOI: 10.3389/fmicb.2015.00563] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/21/2015] [Indexed: 12/30/2022] Open
Abstract
The rapid expansion of new sequencing technologies has enabled large-scale functional exploration of numerous microbial ecosystems, by establishing catalogs of functional genes and by comparing their prevalence in various microbiota. However, sequence similarity does not necessarily reflect functional conservation, since just a few modifications in a gene sequence can have a strong impact on the activity and the specificity of the corresponding enzyme or the recognition for a sensor. Similarly, some microorganisms harbor certain identified functions yet do not have the expected related genes in their genome. Finally, there are simply too many protein families whose function is not yet known, even though they are highly abundant in certain ecosystems. In this context, the discovery of new protein functions, using either sequence-based or activity-based approaches, is of crucial importance for the discovery of new enzymes and for improving the quality of annotation in public databases. This paper lists and explores the latest advances in this field, along with the challenges to be addressed, particularly where microfluidic technologies are concerned.
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Affiliation(s)
- Lisa Ufarté
- Université de Toulouse, Institut National des Sciences Appliquées (INSA), Université Paul Sabatier (UPS), Institut National Polytechnique (INP), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) , Toulouse, France ; INRA - UMR792 Ingénierie des Systèmes Biologiques et des Procédés , Toulouse, France ; CNRS, UMR5504 , Toulouse, France
| | - Gabrielle Potocki-Veronese
- Université de Toulouse, Institut National des Sciences Appliquées (INSA), Université Paul Sabatier (UPS), Institut National Polytechnique (INP), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) , Toulouse, France ; INRA - UMR792 Ingénierie des Systèmes Biologiques et des Procédés , Toulouse, France ; CNRS, UMR5504 , Toulouse, France
| | - Élisabeth Laville
- Université de Toulouse, Institut National des Sciences Appliquées (INSA), Université Paul Sabatier (UPS), Institut National Polytechnique (INP), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP) , Toulouse, France ; INRA - UMR792 Ingénierie des Systèmes Biologiques et des Procédés , Toulouse, France ; CNRS, UMR5504 , Toulouse, France
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Organic cultivation of Triticum turgidum subsp. durum is reflected in the flour-sourdough fermentation-bread axis. Appl Environ Microbiol 2015; 81:3192-204. [PMID: 25724957 DOI: 10.1128/aem.04161-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Triticum turgidum subsp. durum was grown according to four farming systems: conventional (CONV), organic with cow manure (OMAN) or green manure (OLEG), and without inputs (NOINPUT). Some chemical and technological characteristics differed between CONV and organic flours. As shown by two-dimensional electrophoresis (2-DE) analysis, OMAN and OLEG flours showed the highest number of gliadins, and OMAN flour also had the highest number of high-molecular-mass glutenins. Type I sourdoughs were prepared at the laboratory level through a back-slopping procedure, and the bacterial ecology during sourdough preparation was described by 16S rRNA gene pyrosequencing. Before fermentation, the dough made with CONV flour showed the highest bacterial diversity. Flours were variously contaminated by genera belonging to the Proteobacteria, Firmicutes, and Actinobacteria. Mature sourdoughs were completely and stably dominated by lactic acid bacteria. The diversity of Firmicutes was the highest for mature sourdoughs made with organic and, especially, NOINPUT flours. Beta diversity analysis based on the weighted UniFrac distance showed differences between doughs and sourdoughs. Those made with CONV flour were separated from the other with organic flours. Lactic acid bacterium microbiota structure was qualitatively confirmed through the culturing method. As shown by PCR-denaturing gradient gel electrophoresis (DGGE) analysis, yeasts belonging to the genera Saccharomyces, Candida, Kazachstania, and Rhodotorula occurred in all sourdoughs. Levels of bound phenolic acids and phytase and antioxidant activities differed depending on the farming system. Mature sourdoughs were used for bread making. Technological characteristics were superior in the breads made with organic sourdoughs. The farming system is another determinant affecting the sourdough microbiota. The organic cultivation of durum wheat was reflected along the flour-sourdough fermentation-bread axis.
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Gordún E, del Valle LJ, Ginovart M, Carbó R. Comparison of the microbial dynamics and biochemistry of laboratory sourdoughs prepared with grape, apple and yogurt. FOOD SCI TECHNOL INT 2014; 21:428-39. [DOI: 10.1177/1082013214543033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/13/2014] [Indexed: 11/17/2022]
Abstract
The microbiological culture-dependent characterization and physicochemical characteristics of laboratory sourdough prepared with grape (GS) were evaluated and compared with apple (AS) and yogurt (YS), which are the usual Spanish sourdough ingredients. Ripe GS took longer than AS and YS to reach the appropriate acidity and achieved lower values of lactic acid. In all sourdoughs, the lactic acid bacteria (LAB) increased during processing and were the dominant microorganisms (>1E + 8 CFU/g). GS, as well as AS, had high diversity of LAB species. In ripe YS, Pediococcus pentosaceus was the only species identified; in GS and AS, several Lactobacilli were also found, Lb. plantarum, Lb. brevis, and Lb. sakei; in addition, in GS Weisella cibaria also appeared. Regarding the yeast population, non- Saccharomyces yeasts from GS and AS showed a very high specific population (>1E + 7 CFU/g), but this was reduced in ripe sourdough (<1E + 4 CFU/g). Finally, the Saccharomyces group dominated in all sourdoughs. Starting ingredients or raw material provided microbiological specificity to sourdoughs, and grape could be considered one of them.
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Affiliation(s)
- Elena Gordún
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Spain
| | - Luis J del Valle
- Centre d'Enginyeria Biotecnològica i Molecular (CEBIM), Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Spain
| | - Marta Ginovart
- Department of Applied Mathematics III, Universitat Politècnica de Catalunya, Spain
| | - Rosa Carbó
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Spain
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Minervini F, De Angelis M, Di Cagno R, Gobbetti M. Ecological parameters influencing microbial diversity and stability of traditional sourdough. Int J Food Microbiol 2014; 171:136-46. [DOI: 10.1016/j.ijfoodmicro.2013.11.021] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/20/2013] [Accepted: 11/22/2013] [Indexed: 11/30/2022]
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Russo P, Capozzi V, Arena MP, Spadaccino G, Dueñas MT, López P, Fiocco D, Spano G. Riboflavin-overproducing strains of Lactobacillus fermentum for riboflavin-enriched bread. Appl Microbiol Biotechnol 2014; 98:3691-700. [PMID: 24413973 DOI: 10.1007/s00253-013-5484-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/17/2013] [Accepted: 12/18/2013] [Indexed: 12/15/2022]
Abstract
Lactobacillus fermentum isolated from sourdough was able to produce riboflavin. Spontaneous roseoflavin-resistant mutants were obtained by exposing the wild strain (named L. fermentum PBCC11) to increasing concentrations of roseoflavin. Fifteen spontaneous roseoflavin-resistant mutants were isolated, and the level of vitamin B₂ was quantified by HPLC. Seven mutant strains produced concentrations of vitamin B₂ higher than 1 mg L⁻¹. Interestingly, three mutants were unable to overproduce riboflavin even though they were able to withstand the selective pressure of roseoflavin. Alignment of the rib leader region of PBCC11 and its derivatives showed only point mutations at two neighboring locations of the RFN element. In particular, the highest riboflavin-producing isolates possess an A to G mutation at position 240, while the lowest riboflavin producer carries a T to A substitution at position 236. No mutations were detected in the derivative strains that did not have an overproducing phenotype. The best riboflavin overproducing strain, named L. fermentum PBCC11.5, and its parental strain were used to fortify bread. The effect of two different periods of fermentation on the riboflavin level was compared. Bread produced using the coinoculum yeast and L. fermentum PBCC11.5 led to an approximately twofold increase of final vitamin B₂ content.
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Affiliation(s)
- Pasquale Russo
- Department of Agriculture, Food and Environment Sciences, University of Foggia, via Napoli 25, 71122, Foggia, Italy
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Valdés A, Ibáñez C, Simó C, García-Cañas V. Recent transcriptomics advances and emerging applications in food science. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.06.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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The carbohydrate metabolism signature of lactococcus lactis strain A12 reveals its sourdough ecosystem origin. Appl Environ Microbiol 2013; 79:5844-52. [PMID: 23872564 DOI: 10.1128/aem.01560-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Lactococcus lactis subsp. lactis strain A12 was isolated from sourdough. Combined genomic, transcriptomic, and phenotypic analyses were performed to understand its survival capacity in the complex sourdough ecosystem and its role in the microbial community. The genome sequence comparison of strain A12 with strain IL1403 (a derivative of an industrial dairy strain) revealed 78 strain-specific regions representing 23% of the total genome size. Most of the strain-specific genes were involved in carbohydrate metabolism and are potentially required for its persistence in sourdough. Phenotype microarray, growth tests, and analysis of glycoside hydrolase content showed that strain A12 fermented plant-derived carbohydrates, such as arabinose and α-galactosides. Strain A12 exhibited specific growth rates on raffinose that were as high as they were on glucose and was able to release sucrose and galactose outside the cell, providing soluble carbohydrates for sourdough microflora. Transcriptomic analysis identified genes specifically induced during growth on raffinose and arabinose and reveals an alternative pathway for raffinose assimilation to that used by other lactococci.
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43
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Microbial ecology of sourdough fermentations: diverse or uniform? Food Microbiol 2013; 37:11-29. [PMID: 24230469 DOI: 10.1016/j.fm.2013.06.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/14/2013] [Accepted: 06/03/2013] [Indexed: 01/16/2023]
Abstract
Sourdough is a specific and stressful ecosystem inhabited by yeasts and lactic acid bacteria (LAB), mainly heterofermentative lactobacilli. On the basis of their inocula, three types of sourdough fermentation processes can be distinguished, namely backslopped ones, those initiated with starter cultures, and those initiated with a starter culture followed by backslopping. Typical sourdough LAB species are Lactobacillus fermentum, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus sanfranciscensis. Typical sourdough yeast species are Candida humilis, Kazachstania exigua, and Saccharomyces cerevisiae. Whereas region specificity is claimed in the case of artisan backslopped sourdoughs, no clear-cut relationship between a typical sourdough and its associated microbiota can be found, as this is dependent on the sampling, isolation, and identification procedures. Both simple and very complex consortia may occur. Moreover, a series of intrinsic and extrinsic factors may influence the composition of the sourdough microbiota. For instance, an influence of the flour (type, quality status, etc.) and the process parameters (temperature, pH, dough yield, backslopping practices, etc.) occurs. In this way, the presence of Lb. sanfranciscensis during sourdough fermentation depends on specific environmental and technological factors. Also, Triticum durum seems to select for obligately heterofermentative LAB species. Finally, there are indications that the sourdough LAB are of intestinal origin.
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Jung JY, Lee SH, Jin HM, Hahn Y, Madsen EL, Jeon CO. Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation. Int J Food Microbiol 2013; 163:171-9. [DOI: 10.1016/j.ijfoodmicro.2013.02.022] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 12/25/2022]
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van Hijum SAFT, Vaughan EE, Vogel RF. Application of state-of-art sequencing technologies to indigenous food fermentations. Curr Opin Biotechnol 2013; 24:178-86. [DOI: 10.1016/j.copbio.2012.08.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 12/21/2022]
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46
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Tan Q, Xu H, Aguilar ZP, Peng S, Dong S, Wang B, Li P, Chen T, Xu F, Wei H. Safety Assessment and Probiotic Evaluation ofEnterococcus FaeciumYF5 Isolated from Sourdough. J Food Sci 2013; 78:M587-93. [DOI: 10.1111/1750-3841.12079] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 01/14/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Qianglai Tan
- State Key Laboratory of Food Science and Technology; Nanchang Univ., 235 Nanjing Donglu, Nanchang 330047, P.R. China; Jiangxi-OAI Joint Research Inst., Nanchang Univ.; Nanchang; 330047, P.R.; China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Technology, Nanchang Univ.; 235 Nanjing; Donglu, Nanchang 330047, P.R.; China
| | - Zoraida P. Aguilar
- Dept. of Immunochemistry, Covance Laboratories, Inc.; Chantilly VA; 20150; U.S.A
| | - Shanshan Peng
- State Key Laboratory of Food Science and Technology, Nanchang Univ.; 235 Nanjing; Donglu, Nanchang 330047, P.R.; China
| | - Suqin Dong
- State Key Laboratory of Food Science and Technology, Nanchang Univ.; 235 Nanjing; Donglu, Nanchang 330047, P.R.; China
| | - Baogui Wang
- State Key Laboratory of Food Science and Technology, Nanchang Univ.; 235 Nanjing; Donglu, Nanchang 330047, P.R.; China
| | - Ping Li
- State Key Laboratory of Food Science and Technology, Nanchang Univ.; 235 Nanjing; Donglu, Nanchang 330047, P.R.; China
| | - Tingtao Chen
- Jiangxi-OAI Joint Research Inst.; Nanchang Univ.; Nanchang 330047, P.R.; China
| | - Feng Xu
- Jiangxi-OAI Joint Research Inst.; Nanchang Univ.; Nanchang 330047, P.R.; China
| | - Hua Wei
- State Key Laboratory of Food Science and Technology, Nanchang Univ.; 235 Nanjing; Donglu, Nanchang 330047, P.R.; China
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Bron PA, Wels M, Bongers RS, van Bokhorst-van de Veen H, Wiersma A, Overmars L, Marco ML, Kleerebezem M. Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PLoS One 2012; 7:e38720. [PMID: 22802930 PMCID: PMC3389018 DOI: 10.1371/journal.pone.0038720] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 05/14/2012] [Indexed: 01/04/2023] Open
Abstract
Lactic acid bacteria (LAB) are utilized widely for the fermentation of foods. In the current post-genomic era, tools have been developed that explore genetic diversity among LAB strains aiming to link these variations to differential phenotypes observed in the strains investigated. However, these genotype-phenotype matching approaches fail to assess the role of conserved genes in the determination of physiological characteristics of cultures by environmental conditions. This manuscript describes a complementary approach in which Lactobacillus plantarum WCFS1 was fermented under a variety of conditions that differ in temperature, pH, as well as NaCl, amino acid, and O2 levels. Samples derived from these fermentations were analyzed by full-genome transcriptomics, paralleled by the assessment of physiological characteristics, e.g., maximum growth rate, yield, and organic acid profiles. A data-storage and -mining suite designated FermDB was constructed and exploited to identify correlations between fermentation conditions and industrially relevant physiological characteristics of L. plantarum, as well as the associated transcriptome signatures. Finally, integration of the specific fermentation variables with the transcriptomes enabled the reconstruction of the gene-regulatory networks involved. The fermentation-genomics platform presented here is a valuable complementary approach to earlier described genotype-phenotype matching strategies which allows the identification of transcriptome signatures underlying physiological variations imposed by different fermentation conditions.
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Affiliation(s)
- Peter A. Bron
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
| | - Michiel Wels
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Roger S. Bongers
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Hermien van Bokhorst-van de Veen
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Anne Wiersma
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Lex Overmars
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Maria L. Marco
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Michiel Kleerebezem
- TI Food and Nutrition, Wageningen, The Netherlands
- NIZO food research, Ede, The Netherlands
- Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
- Host-Microbe Interactomics, Wageningen University and Research Centre, Wageningen, The Netherlands
- * E-mail:
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48
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Modulation of Lactobacillus plantarum gastrointestinal robustness by fermentation conditions enables identification of bacterial robustness markers. PLoS One 2012; 7:e39053. [PMID: 22802934 PMCID: PMC3389004 DOI: 10.1371/journal.pone.0039053] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/14/2012] [Indexed: 01/01/2023] Open
Abstract
Background Lactic acid bacteria (LAB) are applied worldwide in the production of a variety of fermented food products. Additionally, specific Lactobacillus species are nowadays recognized for their health-promoting effects on the consumer. To optimally exert such beneficial effects, it is considered of great importance that these probiotic bacteria reach their target sites in the gut alive. Methodology/Principal Findings In the accompanying manuscript by Bron et al. the probiotic model organism Lactobacillus plantarum WCFS1 was cultured under different fermentation conditions, which was complemented by the determination of the corresponding molecular responses by full-genome transcriptome analyses. Here, the gastrointestinal (GI) survival of the cultures produced was assessed in an in vitro assay. Variations in fermentation conditions led to dramatic differences in GI-tract survival (up to 7-log) and high robustness could be associated with low salt and low pH during the fermentations. Moreover, random forest correlation analyses allowed the identification of specific transcripts associated with robustness. Subsequently, the corresponding genes were targeted by genetic engineering, aiming to enhance robustness, which could be achieved for 3 of the genes that negatively correlated with robustness and where deletion derivatives displayed enhanced survival compared to the parental strain. Specifically, a role in GI-tract survival could be confirmed for the lp_1669-encoded AraC-family transcription regulator, involved in capsular polysaccharide remodeling, the penicillin-binding protein Pbp2A involved in peptidoglycan biosynthesis, and the Na+/H+ antiporter NapA3. Moreover, additional physiological analysis established a role for Pbp2A and NapA3 in bile salt and salt tolerance, respectively. Conclusion Transcriptome trait matching enabled the identification of biomarkers for bacterial (gut-)robustness, which is important for our molecular understanding of GI-tract survival and could facilitate the design of culture conditions aimed to enhance probiotic culture robustness.
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Siezen RJ, van Hylckama Vlieg JET. Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer. Microb Cell Fact 2011; 10 Suppl 1:S3. [PMID: 21995294 PMCID: PMC3271238 DOI: 10.1186/1475-2859-10-s1-s3] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In the past decade it has become clear that the lactic acid bacterium Lactobacillus plantarum occupies a diverse range of environmental niches and has an enormous diversity in phenotypic properties, metabolic capacity and industrial applications. In this review, we describe how genome sequencing, comparative genome hybridization and comparative genomics has provided insight into the underlying genomic diversity and versatility of L. plantarum. One of the main features appears to be genomic life-style islands consisting of numerous functional gene cassettes, in particular for carbohydrates utilization, which can be acquired, shuffled, substituted or deleted in response to niche requirements. In this sense, L. plantarum can be considered a "natural metabolic engineer".
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Affiliation(s)
- Roland J Siezen
- Kluyver Centre for Genomics of Industrial Fermentation, NIZO food research, P.O. Box 20, 6710 BA Ede, The Netherlands.
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50
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Adaptation of Lactobacillus plantarum IMDO 130201, a wheat sourdough isolate, to growth in wheat sourdough simulation medium at different pH values through differential gene expression. Appl Environ Microbiol 2011; 77:3406-12. [PMID: 21460118 DOI: 10.1128/aem.02668-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sourdough is a very competitive and challenging environment for microorganisms. Usually, a stable microbiota composed of lactic acid bacteria (LAB) and yeasts dominates this ecosystem. Although sourdough is rich in carbohydrates, thus providing an ideal environment for microorganisms to grow, its low pH presents a particular challenge. The nature of the adaptation to this low pH was investigated for Lactobacillus plantarum IMDO 130201, an isolate from a laboratory wheat sourdough fermentation. Batch fermentations were carried out in wheat sourdough simulation medium, and total RNA was isolated from mid-exponential-growth-phase cultures, followed by differential gene expression analysis using a LAB functional gene microarray. At low pH values, an increased expression of genes involved in peptide and amino acid metabolism was found as well as that of genes involved in plantaricin production and lipoteichoic acid biosynthesis. The results highlight cellular mechanisms that allow L. plantarum to function at a low environmental pH.
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