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Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology. FERMENTATION 2022. [DOI: 10.3390/fermentation8080365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.
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2
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Bacterial metataxonomic analysis of industrial Spanish-style green table olive fermentations. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3
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Penland M, Pawtowski A, Pioli A, Maillard MB, Debaets S, Deutsch SM, Falentin H, Mounier J, Coton M. Brine salt concentration reduction and inoculation with autochthonous consortia: Impact on Protected Designation of Origin Nyons black table olive fermentations. Food Res Int 2022; 155:111069. [DOI: 10.1016/j.foodres.2022.111069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 11/04/2022]
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4
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Posada-Izquierdo GD, Valero A, Arroyo-López FN, González-Serrano M, Ramos-Benítez AM, Benítez-Cabello A, Rodríguez-Gómez F, Jimenez-Diaz R, García-Gimeno RM. Behavior of Vibrio spp. in Table Olives. Front Microbiol 2021; 12:650754. [PMID: 34149640 PMCID: PMC8211755 DOI: 10.3389/fmicb.2021.650754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022] Open
Abstract
The presence of Vibrio species in table olive fermentations has been confirmed by molecular biology techniques in recent studies. However, there has been no report of any foodborne outbreak caused by Vibrio due to the consumption of table olives, and their role as well as the environmental conditions allowing their survival in table olives has not been elucidated so far. The aims of this work were to model the behavior of an inoculated Vibrio cocktail in diverse table olive environments and study the possible behavior of an inoculated Vibrio cocktail in table olives. First, an in vitro study has been performed where the microbial behavior of a Vibrio cocktail was evaluated in a laboratory medium and in olive brines using predictive models at different NaCl concentrations (2-12%) and pH levels (4.0-9.0). Afterward, a challenge testing was done in lye-treated olives inoculated at the beginning of fermentation with the Vibrio cocktail for 22 days. The Vibrio cocktail inoculated in table olives has not been detected in olive brines during fermentation at different pH levels. However, it was observed that this microorganism in a laboratory medium could reach an optimal growth at pH 9 and 2% salt, without time of constant absorbance (t A), and the maximum absorbance value (y end) observed was at pH 8 and 2% salt conditions. The statistical analysis demonstrated that the effect of salt concentration was higher than pH for the kinetic growth parameters (μmax, t A, and y end). On the other hand, it was confirmed that no growth of the Vibrio cocktail on any sample was noticed in lye-treated olive fermentations. Thus, it was concluded that the presence of olive compounds (unknown) did not allow the development of Vibrio strains, so it is a very safety product as it has a natural antimicrobial compound, but the possibility that a native Vibrio sp. is able to acquire the capacity to adapt to this compound should be considered in further studies.
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Affiliation(s)
- Guiomar Denisse Posada-Izquierdo
- Department of Food Science and Technology, Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Córdoba, Spain
| | - Antonio Valero
- Department of Food Science and Technology, Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Córdoba, Spain
| | - Francisco Noé Arroyo-López
- Food Biotechnology Department, Instituto de la Grasa (IG-CSIC), University Campus Pablo de Olavide, Seville, Spain
| | - Miriam González-Serrano
- Department of Food Science and Technology, Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Córdoba, Spain
| | - Alfonso M Ramos-Benítez
- Department of Food Science and Technology, Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Córdoba, Spain
| | - Antonio Benítez-Cabello
- Food Biotechnology Department, Instituto de la Grasa (IG-CSIC), University Campus Pablo de Olavide, Seville, Spain
| | - Francisco Rodríguez-Gómez
- Food Biotechnology Department, Instituto de la Grasa (IG-CSIC), University Campus Pablo de Olavide, Seville, Spain
| | - Rufino Jimenez-Diaz
- Food Biotechnology Department, Instituto de la Grasa (IG-CSIC), University Campus Pablo de Olavide, Seville, Spain
| | - Rosa M García-Gimeno
- Department of Food Science and Technology, Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Córdoba, Spain
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5
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A Review on Adventitious Lactic Acid Bacteria from Table Olives. Foods 2020; 9:foods9070948. [PMID: 32709144 PMCID: PMC7404733 DOI: 10.3390/foods9070948] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 12/18/2022] Open
Abstract
Spontaneous fermentation constitutes the basis of the chief natural method of processing of table olives, where autochthonous strains of lactic acid bacteria (LAB) play a dominant role. A thorough literature search has unfolded 197 reports worldwide, published in the last two decades, that indicate an increasing interest in table olive-borne LAB, especially in Mediterranean countries. This review attempted to extract extra information from such a large body of work, namely, in terms of correlations between LAB strains isolated, manufacture processes, olive types, and geographical regions. Spain produces mostly green olives by Spanish-style treatment, whereas Italy and Greece produce mainly green and black olives, respectively, by both natural and Spanish-style. More than 40 species belonging to nine genera of LAB have been described; the genus most often cited is Lactobacillus, with L. plantarum and L. pentosus as most frequent species—irrespective of country, processing method, or olive type. Certain LAB species are typically associated with cultivar, e.g., Lactobacillus parafarraginis with Spanish Manzanilla, or L. paraplantarum with Greek Kalamata and Conservolea, Portuguese Galega, and Italian Tonda di Cagliari. Despite the potential of native LAB to serve as starter cultures, extensive research and development efforts are still needed before this becomes a commercial reality in table olive fermentation.
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Benítez-Cabello A, Romero-Gil V, Medina-Pradas E, Garrido-Fernández A, Arroyo-López FN. Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis. Sci Rep 2020; 10:11381. [PMID: 32647238 PMCID: PMC7347591 DOI: 10.1038/s41598-020-68305-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/23/2020] [Indexed: 11/12/2022] Open
Abstract
In this work, a total of 72 samples of non-thermally treated commercial table olives were obtained from different markets of the world. Then, prokaryotic diversity in olive biofilms was investigated by metataxonomic analysis. A total of 660 different OTUs were obtained, belonging to Archaea (2.12%) and Bacteria domains (97.88%). From these, 41 OTUs with a proportion of sequences ≥ 0.01% were studied by compositional data analysis. Only two genera were found in all samples, Lactobacillus, which was the predominant bacteria in the biofilm consortium (median 54.99%), and Pediococcus (26.09%). Celerinatantimonas, Leuconostoc, Alkalibacterium, Pseudomonas, Marinilactibacillus, Weissella, and the family Enterobacteriaceae were also present in at least 80% of samples. Regarding foodborne pathogens, only Enterobacteriaceae, Vibrio, and Staphylococcus were detected in at least 91.66%, 75.00%, and 54.10% of samples, respectively, but their median values were always below 0.15%. Compositional data analysis allowed discriminating between lye treated and natural olive samples, as well as between olives packaged in glass, PET and plastic bags. Leuconostoc, Celerinatantimonas, and Alkalibacterium were the bacteria genera with a higher discriminant power among samples. These results expand our knowledge of the bacteria diversity in olive biofilms, providing information about the sanitary and hygienic status of this ready-to-eat fermented vegetable.
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Affiliation(s)
- Antonio Benítez-Cabello
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain
| | - Verónica Romero-Gil
- Technological Applications for Improvement of Quality and Safety in Foods, Carretera de Marbella nº22. Planta-1, 29108, Guaro, Málaga, Spain
| | - Eduardo Medina-Pradas
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain
| | - Antonio Garrido-Fernández
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain
| | - Francisco Noé Arroyo-López
- Food Technology Department, Instituto de La Grasa (CSIC), Crta Utrera km 1, Campus Universitario Pablo de Olavide. Building 46, 41013, Seville, Spain.
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7
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Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis. Microorganisms 2020; 8:microorganisms8050672. [PMID: 32384669 PMCID: PMC7284738 DOI: 10.3390/microorganisms8050672] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 11/23/2022] Open
Abstract
Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this study was the identification of bacterial and yeast/fungal microbiota of both olives and brines obtained from 29 cv. Kalamata olive samples industrially fermented in the two main producing geographical regions of Greece, namely Aitoloakarnania and Messinia/Lakonia. The potential microbial biogeography association between certain taxa and geographical area was also assessed. The dominant bacterial family identified in olive and brine samples from both regions was Lactobacillaceae, presenting, however, higher average abundances in the samples from Aitoloakarnania compared to Messinia/Lakonia. At the genus level, Lactobacillus, Celerinatantimonas, Propionibacterium and Pseudomonas were the most abundant. In addition, the yeasts/fungal communities were less diverse compared to those of bacteria, with Pichiaceae being the dominant family and Pichia, Ogataea, and Saccharomyces being the most abundant genera. To the best of our knowledge, this is the first report on the microbiota of both olives and brines of cv. Kalamata black olives fermented on an industrial scale between two geographical regions of Greece using metagenomics analysis.
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019. EFSA J 2020; 18:e05965. [PMID: 32874211 PMCID: PMC7448003 DOI: 10.2903/j.efsa.2020.5965] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.
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Benítez-Cabello A, Romero-Gil V, Medina E, Sánchez B, Calero-Delgado B, Bautista-Gallego J, Jiménez-Díaz R, Arroyo-López FN. Metataxonomic analysis of the bacterial diversity in table olive dressing components. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.05.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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10
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Benítez-Cabello A, Calero-Delgado B, Rodríguez-Gómez F, Garrido-Fernández A, Jiménez-Díaz R, Arroyo-López FN. Biodiversity and Multifunctional Features of Lactic Acid Bacteria Isolated From Table Olive Biofilms. Front Microbiol 2019; 10:836. [PMID: 31057529 PMCID: PMC6479189 DOI: 10.3389/fmicb.2019.00836] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/01/2019] [Indexed: 01/24/2023] Open
Abstract
In the present study, a total of 554 lactic acid bacteria (LAB) isolates were obtained from the olive surface of Manzanilla, Gordal, and Aloreña cultivars processed as green Spanish-style or directly brined (natural) olives. The isolates obtained from industrial processes were genotyped by rep-PCR with primer GTG5, collecting a total of 79 different genotypes. The α-biodiversity indexes showed that the LAB diversity was higher in the biofilms on the fruits which followed the Spanish-style process than in those just brined. Sixteen genotypes had a frequency higher >1% and were identified, by multiplex PCR recA gene and 16S gene sequencing, as belonging to Lactobacillus pentosus (n = 13) and Lactobacillus plantarum (n = 3) species. A multivariate analysis based on a dataset with 89,744 cells, including technological (resistance to salt and pH, production of lactic acid, auto and co-aggregation with yeast species, β-glucosidase and esterase activities), and potential probiotic characteristics (survival to gastric and pancreatic digestions, resistance to antibiotics, inhibition of pathogens, presence of bsh genes, cholesterol removal, hemolytic, α-glucosidase, β-galactosidase, and phytase activities) showed that the 16 genotypes could be grouped into 3 great phenotypes. Thus, the genotype biodiversity in table olive biofilms was limited but, at phenotype level, it was even lower since L. pentosus predominated clearly (80.15% isolates). L. pentosus Lp13 was the genotype with the most promising characteristics for its use as a multifunctional starter, with this strain being and ubiquitous microorganism present in both natural and lye-treated olive fermentations.
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Affiliation(s)
- Antonio Benítez-Cabello
- Department of Food Biotechnology, Instituto de la Grasa, Agencia Estatal Consejo Superior de Investigaciones Científicas, Pablo de Olavide University, Seville, Spain
| | - Beatriz Calero-Delgado
- Department of Food Biotechnology, Instituto de la Grasa, Agencia Estatal Consejo Superior de Investigaciones Científicas, Pablo de Olavide University, Seville, Spain
| | - Francisco Rodríguez-Gómez
- Department of Food Biotechnology, Instituto de la Grasa, Agencia Estatal Consejo Superior de Investigaciones Científicas, Pablo de Olavide University, Seville, Spain
| | - Antonio Garrido-Fernández
- Department of Food Biotechnology, Instituto de la Grasa, Agencia Estatal Consejo Superior de Investigaciones Científicas, Pablo de Olavide University, Seville, Spain
| | - Rufino Jiménez-Díaz
- Department of Food Biotechnology, Instituto de la Grasa, Agencia Estatal Consejo Superior de Investigaciones Científicas, Pablo de Olavide University, Seville, Spain
| | - Francisco Noé Arroyo-López
- Department of Food Biotechnology, Instituto de la Grasa, Agencia Estatal Consejo Superior de Investigaciones Científicas, Pablo de Olavide University, Seville, Spain
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Multiple Genome Sequences of Lactobacillus pentosus Strains Isolated from Biofilms on the Skin of Fermented Green Table Olives. Microbiol Resour Announc 2019; 8:MRA01546-18. [PMID: 30834370 PMCID: PMC6386571 DOI: 10.1128/mra.01546-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/26/2019] [Indexed: 11/20/2022] Open
Abstract
The draft genome sequences of five Lactobacillus pentosus strains isolated from biofilms on the skin of green table olives are presented here. These genome sequences will assist in revealing the potential probiotic properties of these strains, as the intake of fermented olives implicates the passage of millions of Lactobacillus spp. throughout a consumer's gastrointestinal tract.
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Draft Genome Sequences of Six Lactobacillus pentosus Strains Isolated from Brines of Traditionally Fermented Spanish-Style Green Table Olives. GENOME ANNOUNCEMENTS 2018; 6:6/18/e00379-18. [PMID: 29724847 PMCID: PMC5940955 DOI: 10.1128/genomea.00379-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Here, we report the genome sequences of six Lactobacillus pentosus strains isolated from traditional noninoculated Spanish-style green table olive brines. The total genome sizes varied between 3.77 and 4.039 Mbp. These genome sequences will assist in revealing the genes responsible for both technological and probiotic properties of these strains.
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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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