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Zhao N, Kokawa M, Suzuki T, Khan AR, Dong W, Nguyen MQ, Kitamura Y. Refermentation with yeast and lactic acid bacteria isolates: a strategy to improve the flavor of green coffee beans. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 39007339 DOI: 10.1002/jsfa.13735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/14/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND Yeast and lactic acid bacteria (LAB) play an important part in the post-harvest fermentation of coffee. This study applied lab-scale fermentation to commercial green coffee beans using dry coffee pulp as the substrate, with the aim of modifying coffee-bean flavor. In addition to spontaneous fermentation, yeast and LAB isolated from coffee beans and dried coffee pulp were added during fermentation. RESULTS Co-inoculation of yeast and LAB showed a significant effect on the chlorogenic acid content after between 24 and 72 h of fermentation. Acetic, citric, malic, lactic, and quinic acids were shown to be affected significantly (P < 0.05) by fermentation and inoculation. Gas chromatography detected that esters, alcohols, aldehydes, furans, and pyrazines were the primary compounds in the coffee beans. Certain volatile groups were present in greater concentrations and broader varieties within the inoculated beans. The highest cupping scores were given to beans that had been co-inoculated with yeast and LAB. CONCLUSION Overall, the use of yeasts and LAB starters showed potential to create coffee beverages with desirable characteristics by standardized fermentation. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Na Zhao
- Graduate School of Science and Technology, University of Tsukuba, Ibaraki, Japan
| | - Mito Kokawa
- Institute of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Taroh Suzuki
- Graduate School of Science and Technology, University of Tsukuba, Ibaraki, Japan
- SAZA COFFEE HOLDINGS LTD, Hitachinaka, Japan
| | | | - Weixue Dong
- Graduate School of Science and Technology, University of Tsukuba, Ibaraki, Japan
| | - Minh-Quan Nguyen
- Graduate School of Science and Technology, University of Tsukuba, Ibaraki, Japan
| | - Yutaka Kitamura
- Institute of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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Zhao N, Kokawa M, Amini RK, Dong W, Kitamura Y. Isolation of Yeast and LAB from Dry Coffee Pulp and Monitoring of Organic Acids in Inoculated Green Beans. Foods 2023; 12:2622. [PMID: 37444360 DOI: 10.3390/foods12132622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Yeast and lactic acid bacteria (LAB) are known to play an important role in the fermentation process of coffee post-harvest. This study aimed to isolate and screen yeast and LAB to be applied in lab-scale refermentation of commercial green coffee beans and coffee pulp with the aim of modifying the composition of organic acids (OAs) in coffee beans. Yeast and LAB strains were isolated from green coffee beans and dry coffee pulp and identified, and their effect on OA concentration in the coffee beans was quantified. In addition, the effects of different fermentation conditions (additional carbon source, different inoculum dose, and different types of coffee pulp) were evaluated based on OA quantification. Nine yeast isolates of Rhodotorula mucilaginosa and Wickerhamomyces anomalus were identified, and 11 LAB isolates of the species Enterococcus mundtii were identified. Of the 7 OAs quantified, quinic acid was the most abundant. The inoculation of isolated yeasts and LAB led to higher concentrations of OAs, showing the potential to realize modification of the OA composition of green coffee beans by re-fermentation with coffee-originated isolates.
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Affiliation(s)
- Na Zhao
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Ibaraki, Japan
| | - Mito Kokawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnodai, Tsukuba 305-8572, Ibaraki, Japan
| | - Rasool Khan Amini
- Saza Coffee Holdings Ltd., 8-18 Kyoeicho, Hitachinaka 312-0043, Ibaraki, Japan
| | - Weixue Dong
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572, Ibaraki, Japan
| | - Yutaka Kitamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennnodai, Tsukuba 305-8572, Ibaraki, Japan
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Peñuela-Martínez AE, Velasquez-Emiliani AV, Angel CA. Microbial Diversity Using a Metataxonomic Approach, Associated with Coffee Fermentation Processes in the Department of Quindío, Colombia. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Coffee fermentation is a complex process, mainly involving bacteria and yeasts, whose interaction influences beverage quality. The way this process is conducted affects the interactions between these microorganisms. To identify microbial diversity in fermenting coffee, samples were collected from 20 farms in the Department of Quindío, Colombia. Metataxonomic analyses using high-throughput sequencing and volatile organic compound identification in green coffee beans were performed with HS-SPME and GC-MS. Potential relationships between some families and genera with different fermentation types and coffee quality were evaluated. In our results, samples presented with high richness and diversity were greater for bacteria than for yeast/fungi. The Enterobacteriaceae family dominated at the beginning of fermentation, while Leuconostoc, Lactobacillus, Gluconobacter, and Acetobacter genera dominated at the end, a finding related to pH reduction and final coffee quality. Overall, 167 fungal families were identified, but Saccharomyceaceae dominated from the beginning. Alcohols and esters were the main chemical classes identified in green coffee bean samples from these fermentations. These results will facilitate the identification process conditions that influence the presence and abundance of microorganisms related to quality as well as contributing to the design of strategies to conduct fermentations to improve the final quality of coffee.
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Braga AVU, Miranda MA, Aoyama H, Schmidt FL. Study on coffee quality improvement by self-induced anaerobic fermentation: Microbial diversity and enzymatic activity. Food Res Int 2023; 165:112528. [PMID: 36869528 DOI: 10.1016/j.foodres.2023.112528] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/12/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023]
Abstract
The postharvest fermentation process of coffee has rapidly advanced in the last few years due to the search for quality and diversity of sensorial profiles. A new type of fermentation, named self-induced-anaerobic fermentation (SIAF), is a promising process that has been increasingly used. This study aims to evaluate the sensorial improvement of coffee beverages during SIAF and the influence of microorganism's community and enzymatic activity. The SIAF process was conducted in Brazilian farms for up to 8 days. The sensorial quality of coffee was evaluated by Q-graders; the microbial community was identified by the high-throughput sequencing of 16S rRNA and ITS regions; and the enzymatic activity (invertase, polygalacturonase, and endo-β-mannanase) was also investigated. SIAF increased up to 3.8 points in the total score of sensorial evaluation (compared to the non-fermented sample), in addition to presenting more flavor diversity (especially within the fruity and sweetness descriptors). The high-throughput sequencing identified 655 bacterial and 296 fungal species during the three processes. The bacteria Enterobacter sp., Lactobacillus sp., Pantoea sp., and the fungi Cladosporium sp. and Candida sp. were the predominant genera. Fungi that are potential producers of mycotoxin were identified throughout the process, which indicates a risk of contamination since some of them are not degraded in the roasting process. Thirty-one species of microorganisms were described for the first time in coffee fermentation. The microbial community was influenced by the place where the process was carried out, mainly in relation to the diversity of fungi. Washing the coffee fruits before fermenting led to a fast reduction of pH; a fast development of Lactobacillus sp. and a fast dominance of Candida sp.; a reduction of the fermentation time necessary to achieve the best sensorial score; an increase in the invertase activity in the seed; a more expressive invertase activity in the husk; and a decreasing trend in polygalacturonase activity in the coffee husk. The increase in endo-β-mannanase activity suggests that coffee starts germinating during the process. SIAF has a huge potential to increase the quality and add value to coffee, but further studies must be conducted to access its safety. The study allowed a better knowledge of the spontaneous microbial community and the enzymes that were present in the fermentation process.
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Affiliation(s)
- Ana Valéria Ulhano Braga
- Laboratory of Fruits and Vegetables, Department of Food Engineering and Technology, School of Food Engineering, Universidade Estadual de Campinas, Rua Monteiro Lobato, n°80 - ZIP Code 13083-862. Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, Brazil.
| | - Márcio André Miranda
- Laboratory of Enzymology, Institute of Biology, Universidade Estadual de Campinas, Rua Monteiro Lobato, n°255 - ZIP Code 13083-862. Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de São Paulo. Rua Heitor Lacerda Guedes, n °1000 - ZIP Code 13059-581. Cidade Satélite Íris, Campinas, São Paulo, Brazil
| | - Hiroshi Aoyama
- Laboratory of Enzymology, Institute of Biology, Universidade Estadual de Campinas, Rua Monteiro Lobato, n°255 - ZIP Code 13083-862. Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, Brazil
| | - Flavio Luís Schmidt
- Laboratory of Fruits and Vegetables, Department of Food Engineering and Technology, School of Food Engineering, Universidade Estadual de Campinas, Rua Monteiro Lobato, n°80 - ZIP Code 13083-862. Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, Brazil
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Cruz-O’Byrne R, Gamez-Guzman A, Piraneque-Gambasica N, Aguirre-Forero S. Genomic sequencing in Colombian coffee fermentation reveals new records of yeast species. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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FERNANDEZ-GÜIMAC SLJ, PEREZ J, MENDOZA JE, BUSTAMANTE DE, CALDERON MS. Exploring the diversity of microorganisms and potential pectinase activity isolated from wet fermentation of coffee in northeastern Peru. FOOD SCIENCE AND TECHNOLOGY 2023. [DOI: 10.1590/fst.81922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | - Jhordy PEREZ
- Universidad Nacional Toribio Rodríguez de Mendoza, Peru
| | | | - Danilo Edson BUSTAMANTE
- Universidad Nacional Toribio Rodríguez de Mendoza, Peru; Universidad Nacional Toribio Rodríguez de Mendoza, Peru
| | - Martha Steffany CALDERON
- Universidad Nacional Toribio Rodríguez de Mendoza, Peru; Universidad Nacional Toribio Rodríguez de Mendoza, Peru
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7
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Guerra LS, Cevallos-Cevallos JM, Weckx S, Ruales J. Traditional Fermented Foods from Ecuador: A Review with a Focus on Microbial Diversity. Foods 2022; 11:foods11131854. [PMID: 35804670 PMCID: PMC9265738 DOI: 10.3390/foods11131854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 11/23/2022] Open
Abstract
The development of early civilizations was greatly associated with populations’ ability to exploit natural resources. The development of methods for food preservation was one of the pillars for the economy of early societies. In Ecuador, food fermentation significantly contributed to social advances and fermented foods were considered exclusive to the elite or for religious ceremonies. With the advancement of the scientific research on bioprocesses, together with the implementation of novel sequencing tools for the accurate identification of microorganisms, potential health benefits and the formation of flavor and aroma compounds in fermented foods are progressively being described. This review focuses on describing traditional fermented foods from Ecuador, including cacao and coffee as well as less popular fermented foods. It is important to provide new knowledge associated with nutritional and health benefits of the traditional fermented foods.
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Affiliation(s)
- Luis Santiago Guerra
- Department of Food Science and Biotechnology, Escuela Politécnica Nacional, P.O. Box 17-01-2759, Quito 170517, Ecuador;
| | - Juan Manuel Cevallos-Cevallos
- Centro de Investigaciones Biotecnologicas del Ecuador (CIBE), Campus Gustavo Galindo, Escuela Superior Politécnica del Litoral (ESPOL), Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil 090112, Ecuador;
| | - Stefan Weckx
- 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;
| | - Jenny Ruales
- Department of Food Science and Biotechnology, Escuela Politécnica Nacional, P.O. Box 17-01-2759, Quito 170517, Ecuador;
- Correspondence:
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8
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da Silva Vale A, de Melo Pereira GV, de Carvalho Neto DP, Sorto RD, Goés-Neto A, Kato R, Soccol CR. Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:470-481. [PMID: 33399261 DOI: 10.1111/1758-2229.12921] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.
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Affiliation(s)
- Alexander da Silva Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, 81531-970, Brazil
| | | | - Dão Pedro de Carvalho Neto
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, 81531-970, Brazil
| | | | - Aristóteles Goés-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Rodrigo Kato
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, 81531-970, Brazil
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9
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Cruz-O'Byrne R, Piraneque-Gambasica N, Aguirre-Forero S. Microbial diversity associated with spontaneous coffee bean fermentation process and specialty coffee production in northern Colombia. Int J Food Microbiol 2021; 354:109282. [PMID: 34140187 DOI: 10.1016/j.ijfoodmicro.2021.109282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/15/2021] [Accepted: 05/30/2021] [Indexed: 01/16/2023]
Abstract
Coffee fermentation involves the action of microorganisms, whose metabolism has a significant influence on the composition of the beans and, consequently, on the beverage's sensory characteristics. In this study, the microbial diversity during the wet fermentation of Coffea arabica L. in the Sierra Nevada of Santa Marta (SNSM) in Colombia was explored by high-throughput sequencing and the resulting cup quality through the standards of the Specialty Coffee Association. The taxonomic assignment of sequence reads showed a high microbial diversity comprised of 695 bacterial and 156 fungal genera. The microbial community was dominated by the Lactic Acid Bacteria (LAB) Leuconostoc, the yeast Kazachstania, and the Acetic Acid Bacteria (AAB) Acetobacter. Co-occurrence relationships suggested synergistic patterns between populations of LAB-AAB, yeasts-AAB, Leuconostoc-Prevotella, LAB-ABB-Selenomonas, and yeasts-fungi-nonLAB-nonAAB, which may result in the production of metabolites that positively impact the sensory attributes of coffee. The beverages produced were classified as specialty coffees, and their score was positively influenced by the fungal richness and the abundance of unclassified Lactobacillales, Pichia, and Pseudomonas. The findings show the richness and microbial diversity of the SNSM and serve as input for future research such as the analysis of microbial-derived metabolites and the establishment of starter cultures in coffee processing that guarantee the generation of high-quality beverages, the standardization of processes, the reduction of economic losses, and the production of value-added products that allow taking advantage of specialty coffee market.
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Méndez-Zamora A, Gutiérrez-Avendaño DO, Arellano-Plaza M, De la Torre González FJ, Barrera-Martínez I, Gschaedler Mathis A, Casas-Godoy L. The non-Saccharomyces yeast Pichia kluyveri for the production of aromatic volatile compounds in alcoholic fermentation. FEMS Yeast Res 2020; 20:6034014. [PMID: 33316048 DOI: 10.1093/femsyr/foaa067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Alcoholic fermentation is influenced by yeast strain, culture media, substrate concentration and fermentation conditions, which contribute to taste and aroma. Some non-Saccharomyces yeasts are recognized as volatile compound producers that enrich aromatic profile of alcoholic beverages. In this work, 21 strains of Pichia kluyveri isolated from different fermentative processes and regions were evaluated. A principal component analysis (PCA) showed statistical differences between strains mainly associated with the variety and concentration of the compounds produced. From the PCA, two strains (PK1 and PK8) with the best volatile compound production were selected to evaluate the impact of culture media (M12 medium and Agave tequilana juice), stirring speeds (100 and 250 rpm) and temperatures (20°C, 25°C and 30°C). Increased ester production was observed at 250 rpm. Greatest effect in alcohols and ester production was found with A. tequilana, identifying PK1 as higher alcohol producer, and PK8 as better ester producer. Regarding temperature, PK1 increased ester production with decreased fermentation temperature. PK8 presented maximum levels of ethyl acetate and ethyl dodecanoate at 20°C, and finally isoamyl acetate increased its production at 30°C. Therefore, P. kluyveri strains are of great interest to produce different aromatic profiles that are affected by factors including medium, agitation and temperature.
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Affiliation(s)
- Andrés Méndez-Zamora
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Unidad de Biotecnología Industrial, Camino Arenero 1227, El Bajío del Arenal, 45019 Zapopan, Jalisco, México
| | - Daniel Oswaldo Gutiérrez-Avendaño
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Unidad de Biotecnología Industrial, Camino Arenero 1227, El Bajío del Arenal, 45019 Zapopan, Jalisco, México
| | - Melchor Arellano-Plaza
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Unidad de Biotecnología Industrial, Camino Arenero 1227, El Bajío del Arenal, 45019 Zapopan, Jalisco, México
| | - Francisco Javier De la Torre González
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Unidad de Biotecnología Industrial, Camino Arenero 1227, El Bajío del Arenal, 45019 Zapopan, Jalisco, México
| | - Iliana Barrera-Martínez
- CONACYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Unidad de Biotecnología Industrial, Camino Arenero 1227, El Bajío del Arenal, 45019 Zapopan, Jalisco, México
| | - Anne Gschaedler Mathis
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Unidad de Biotecnología Industrial, Camino Arenero 1227, El Bajío del Arenal, 45019 Zapopan, Jalisco, México
| | - Leticia Casas-Godoy
- CONACYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Unidad de Biotecnología Industrial, Camino Arenero 1227, El Bajío del Arenal, 45019 Zapopan, Jalisco, México
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Duong B, Marraccini P, Maeght JL, Vaast P, Lebrun M, Duponnois R. Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.607935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.
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12
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Pothakos V, De Vuyst L, Zhang SJ, De Bruyn F, Verce M, Torres J, Callanan M, Moccand C, Weckx S. Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria. CURRENT RESEARCH IN BIOTECHNOLOGY 2020. [DOI: 10.1016/j.crbiot.2020.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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13
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Bressani APP, Martinez SJ, Sarmento ABI, Borém FM, Schwan RF. Organic acids produced during fermentation and sensory perception in specialty coffee using yeast starter culture. Food Res Int 2020; 128:108773. [DOI: 10.1016/j.foodres.2019.108773] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 01/05/2023]
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15
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Zhang SJ, De Bruyn F, Pothakos V, Contreras GF, Cai Z, Moccand C, Weckx S, De Vuyst L. Influence of Various Processing Parameters on the Microbial Community Dynamics, Metabolomic Profiles, and Cup Quality During Wet Coffee Processing. Front Microbiol 2019; 10:2621. [PMID: 31798557 PMCID: PMC6863779 DOI: 10.3389/fmicb.2019.02621] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
Post-harvest wet coffee processing is a commonly applied method to transform coffee cherries into green coffee beans through depulping or demucilaging, fermentation, washing, soaking, drying, and dehulling. Multiple processing parameters can be modified and thus influence the coffee quality (green coffee beans and cup quality). The present study aimed to explore the impacts of these parameters, including processing type (depulping or demucilaging), fermentation duration, and application of soaking, on the microbial community dynamics, metabolite compositions of processing waters (fermentation and soaking) and coffee beans, and resulting cup quality through a multiphasic approach. A large-scale wet coffee processing experiment was conducted with Coffea arabica var. Catimor in Yunnan (China) in duplicate. The fermentation steps presented a dynamic interaction between constant nutrient release (mainly from the cherry mucilage) into the surrounding water and active microbial activities led by lactic acid bacteria, especially Leuconostoc and Lactococcus. The microbial communities were affected by both the processing type and fermentation duration. At the same time, the endogenous coffee bean metabolism remained active at different stages along the processing, as could be seen through changes in the concentrations of carbohydrates, organic acids, and free amino acids. Among all the processing variants tested, the fermentation duration had the greatest impact on the green coffee bean compositions and the cup quality. A long fermentation duration resulted in a fruitier and more acidic cup. As an ecological alternative for the depulped processing, the demucilaged processing produced a beverage quality comparable to the depulped one. The application of soaking, however, tempered the positive fermentation effects and standardized the green coffee bean quality, regardless of the preceding processing practices applied. Lastly, the impact strength of each processing parameter would also depend on the coffee variety used and the local geographical conditions. All these findings provide a considerable margin of opportunities for future coffee research.
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Affiliation(s)
- Sophia Jiyuan Zhang
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Florac De Bruyn
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vasileios Pothakos
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Zhiying Cai
- Yunnan Institute of Tropical Crops, Kunming, China
| | | | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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de Oliveira Junqueira AC, de Melo Pereira GV, Coral Medina JD, Alvear MCR, Rosero R, de Carvalho Neto DP, Enríquez HG, Soccol CR. First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing. Sci Rep 2019; 9:8794. [PMID: 31217528 PMCID: PMC6584692 DOI: 10.1038/s41598-019-45002-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/27/2019] [Indexed: 12/12/2022] Open
Abstract
In Colombia, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. This process has a great influence on sensory quality and prestige of Colombian coffee in international markets, but has never been studied. Here we use an Illumina-based amplicon sequencing to investigate bacterial and fungal communities associated with spontaneous coffee-bean fermentation in Colombia. Microbial-derived metabolites were further analysed by high-performance liquid chromatography and gas chromatography-mass spectrometry. Highly diverse bacterial groups, comprising 160 genera belonging to 10 phyla, were found. Lactic acid bacteria (LAB), mainly represented by the genera Leuconostoc and Lactobacillus, showed relative prevalence over 60% at all sampling times. The structure of the fungal community was more homogeneous, with Pichia nakasei dominating throughout the fermentation process. Lactic acid and acetaldehyde were the major end-metabolites produced by LAB and Pichia, respectively. In addition, 20 volatile compounds were produced, comprising alcohols, organic acids, aldehydes, esters, terpenes, phenols, and hydrocarbons. Interestingly, 56 microbial genera, associated with native soil, seawater, plants, insects, and human contact, were detected for the first time in coffee fermentation. These microbial groups harbour a remarkable phenotypic diversity and may impart flavours that yield clues to the terroir of Colombian coffees.
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Affiliation(s)
- Ana C de Oliveira Junqueira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
| | - Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
| | - Jesus D Coral Medina
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - María C R Alvear
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - Rubens Rosero
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - Dão P de Carvalho Neto
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
| | - Hugo G Enríquez
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil.
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17
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Viable and Total Bacterial Populations Undergo Equipment- and Time-Dependent Shifts during Milk Processing. Appl Environ Microbiol 2019; 85:AEM.00270-19. [PMID: 31028031 DOI: 10.1128/aem.00270-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
We set out to identify the viable and total bacterial content in milk as it passes through a large-scale, dairy product manufacturing plant for pasteurization, concentration, separation, blending, and storage prior to cheese manufacture. A total of 142 milk samples were collected from up to 10 pieces of equipment for a period spanning 21 h on two collection dates in the spring and late summer of 2014. Bacterial composition in the milk was determined by 16S rRNA marker gene, high-throughput DNA sequencing. Milk samples from the late summer were paired such that half were treated with propidium monoazide (PMA) to enrich for viable cells prior to quantification by PCR and identification by DNA sequence analysis. Streptococcus had the highest median relative abundance across all sampling sites within the facility on both sampling dates. The proportions of Anoxybacillus, Thermus, Lactococcus, Lactobacillus, Micrococcaceae, and Pseudomonas were also elevated in some samples. Viable cells detected by PMA treatment showed that Turicibacter was enriched after high-temperature short-time pasteurization, whereas proportions of Staphylococcus were significantly reduced. Using clean-in-place (CIP) times as a reference point, Bacillus, Pseudomonas, and Anoxybacillus were found in high relative proportions in several recently cleaned silos (<19 h since CIP). At later times (>19 h after CIP), 10 of 11 silos containing elevated viable cell numbers were enriched in Acinetobacter and/or Lactococcus These results show the tremendous point-to-point and sample-dependent variations in bacterial composition in milk during processing.IMPORTANCE Milk undergoes sustained contact with the built environment during processing into finished dairy products. This contact has the potential to influence the introduction, viability, and growth of microorganisms within the milk. Currently, the population dynamics of bacteria in milk undergoing processing are not well understood. Therefore, we measured for total and viable bacterial composition and cell numbers in milk over time and at different processing points in a cheese manufacturing facility in California. Our results provide new perspectives on the dramatic variations in microbial populations in milk during processing even over short amounts of time. Although some of the changes in the milk microbiota were predictable (e.g., reduced viable cell numbers after pasteurization), other findings could not be easily foreseen based on knowledge of bacteria contained in raw milk or when the equipment was last cleaned. This information is important for predicting and controlling microbial spoilage contaminants in dairy products.
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Tinoco NAB, Pacheco S, Godoy RLO, Bizzo HR, de Aguiar PF, Leite SGF, Rezende CM. Reduction of βN-alkanoyl-5-hydroxytryptamides and diterpenes by yeast supplementation to green coffee during wet processing. Food Res Int 2019; 115:487-492. [PMID: 30599969 DOI: 10.1016/j.foodres.2018.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/20/2018] [Accepted: 10/02/2018] [Indexed: 02/07/2023]
Abstract
Coffee is one of the most consumed non-alcoholic beverages in the world. It is well known that some compounds present in coffee beans have important biological activities. In this study, evidence was turned to βN-alkanoyl-5-hydroxytryptamides (C-5HTs) and to the furokaurane diterpenes cafestol and kahweol, associated with gastric irritation and increasing of blood cholesterol, respectively. Fermentation in coffee post-harvest wet process was induced by three Saccharomyces cerevisiae yeasts (for bakery, white and sparkling wines) as starter cultures. Variations in mass, time, temperature and pH (56 experiments under fractional factorial and mixture experimental designs) were tested. Substantial reductions for C-5HTs (up to 38% reduction for C20-5HT and 26% for C22-5HT) as well as for diterpenes (54% for cafestol and 53% for kahweol) were obtained after treating green coffee beans with 0.6 g of a 1:1:1 mixture the three yeasts for 12 h at 15 °C and pH 4. Caffeine and 5-CQA content, monitored in the green coffee beans, did not change. Therefore, the use of starter cultures during coffee post-harvest wet process has influence on the amount of some important compounds related to health and improves the sensory quality of the beverage.
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Affiliation(s)
- Natália A B Tinoco
- Chemistry Institute, Federal University of Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil
| | - Sidney Pacheco
- Embrapa Agroindústria de Alimentos, 23020-470 Rio de Janeiro, RJ, Brazil
| | - Ronoel L O Godoy
- Embrapa Agroindústria de Alimentos, 23020-470 Rio de Janeiro, RJ, Brazil
| | - Humberto R Bizzo
- Embrapa Agroindústria de Alimentos, 23020-470 Rio de Janeiro, RJ, Brazil
| | - Paula F de Aguiar
- Chemistry Institute, Federal University of Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil
| | - Selma G F Leite
- Chemistry School, Federal University of Rio de Janeiro, 21949-900 Rio de Janeiro, RJ, Brazil
| | - Claudia M Rezende
- Chemistry Institute, Federal University of Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil.
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19
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Hameed A, Hussain SA, Ijaz MU, Ullah S, Pasha I, Suleria HAR. Farm to Consumer: Factors Affecting the Organoleptic Characteristics of Coffee. II: Postharvest Processing Factors. Compr Rev Food Sci Food Saf 2018; 17:1184-1237. [PMID: 33350164 DOI: 10.1111/1541-4337.12365] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 11/30/2022]
Abstract
The production and consumption of coffee are increasing despite the roadblocks to its agriculture and global trade. The unique, refreshing, and stimulating final cupping quality of coffee is the only reason for this rising production and consumption. Coffee quality is a multifaceted trait and is inevitably influenced by the way it is successively processed after harvesting. Reportedly, 60% of the quality attributes of coffee are governed by postharvest processing. The current review elaborates and establishes for the first time the relationship between different methods of postharvest processing of coffee and its varying organoleptic and sensory quality attributes. In view of the proven significance of each processing step, this review has been subdivided into three sections, secondary processing, primary processing, and postprocessing variables. Secondary processing addresses the immediate processing steps on the farm after harvest and storage before roasting. The primary processing section adheres specifically to roasting, grinding and brewing/extraction, topics which have been technically addressed more than any others in the literature and by industry. The postprocessing attribute section deals generally with interaction of the consumer with products of different visual appearance. Finally, there are still some bottlenecks which need to be addressed, not only to completely understand the relationship of varying postharvest processing methods with varying in-cup quality attributes, but also to devise the next generation of coffee processing technologies.
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Affiliation(s)
- Ahsan Hameed
- Laboratory for Yeast Molecular and Cell Biology, The Research Center of Fermentation Technology, School of Agricultural Engineering and Food Science, Shandong Univ. of Technology, Zibo, Shandong, 255000, China.,National Inst. of Food Science & Technology, Univ. of Agriculture Faisalabad, Pakistan
| | - Syed Ammar Hussain
- National Inst. of Food Science & Technology, Univ. of Agriculture Faisalabad, Pakistan.,Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong Univ. of Technology, Zibo, P.R. China
| | - Muhammad Umair Ijaz
- National Inst. of Food Science & Technology, Univ. of Agriculture Faisalabad, Pakistan.,Key Laboratory of Meat Processing & Quality Control, College of Food Sciences, Nanjing Agriculture Univ., Jiangsu, P.R China
| | - Samee Ullah
- National Inst. of Food Science & Technology, Univ. of Agriculture Faisalabad, Pakistan.,Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong Univ. of Technology, Zibo, P.R. China
| | - Imran Pasha
- National Inst. of Food Science & Technology, Univ. of Agriculture Faisalabad, Pakistan
| | - Hafiz Ansar Rasul Suleria
- UQ Diamantina Inst., Translational Research Inst. Faculty of Medicine, The Univ. of Queensland, 37 Kent Street Woolloongabba, Brisbane, QLD, 4102, Australia.,Dept. of Food, Nutrition, Dietetics and Health, Kansas State Univ., Manhattan, Kans., 66506, U.S.A.,Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin Univ., Pigdons Road, Waurn Ponds, VIC, 3216, Australia
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Broissin-Vargas L, Snell-Castro R, Godon J, González-Ríos O, Suárez-Quiroz M. Impact of storage conditions on fungal community composition of green coffee beansCoffea arabicaL. stored in jute sacks during 1 year. J Appl Microbiol 2018; 124:547-558. [DOI: 10.1111/jam.13656] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 11/26/2022]
Affiliation(s)
- L.M. Broissin-Vargas
- Tecnológico Nacional de México; Instituto Tecnológico de Veracruz; Unidad de Investigación y Desarrollo en Alimentos; Veracruz México
| | - R. Snell-Castro
- Departamento de Ingeniería Química; Universidad de Guadalajara-CUCEI; Guadalajara Jalisco México
| | | | - O. González-Ríos
- Tecnológico Nacional de México; Instituto Tecnológico de Veracruz; Unidad de Investigación y Desarrollo en Alimentos; Veracruz México
| | - M.L. Suárez-Quiroz
- Tecnológico Nacional de México; Instituto Tecnológico de Veracruz; Unidad de Investigación y Desarrollo en Alimentos; Veracruz México
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21
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Neto DPDC, Vinícius de Melo G, Pereira, César de Carvalho J, Soccol VT, Soccol CR. High-Throughput rRNA Gene Sequencing Reveals High
and Complex Bacterial Diversity Associated with
Brazilian Coffee Bean Fermentation. Food Technol Biotechnol 2017; 56:90-95. [PMID: 29796001 DOI: 10.17113/ftb.56.01.18.5441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Coffee bean fermentation is a spontaneous, on-farm process involving the action of different microbial groups, including bacteria and fungi. In this study, high-throughput sequencing approach was employed to study the diversity and dynamics of bacteria associated with Brazilian coffee bean fermentation. The total DNA from fermenting coffee samples was extracted at different time points, and the 16S rRNA gene with segments around the V4 variable region was sequenced by Illumina high-throughput platform. Using this approach, the presence of over eighty bacterial genera was determined, many of which have been detected for the first time during coffee bean fermentation, including Fructobacillus, Pseudonocardia, Pedobacter, Sphingomonas and Hymenobacter. The presence of Fructobacillus suggests an influence of these bacteria on fructose metabolism during coffee fermentation. Temporal analysis showed a strong dominance of lactic acid bacteria with over 97% of read sequences at the end of fermentation, mainly represented by the Leuconostoc and Lactococcus. Metabolism of lactic acid bacteria was associated with the high formation of lactic acid during fermentation, as determined by HPLC analysis. The results reported in this study confirm the underestimation of bacterial diversity associated with coffee fermentation. New microbial groups reported in this study may be explored as functional starter cultures for on-farm coffee processing.
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Affiliation(s)
- Dão Pedro de Carvalho Neto
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, PR 81531-980, Brazil
| | - Gilberto Vinícius de Melo
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, PR 81531-980, Brazil
| | - Pereira
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, PR 81531-980, Brazil
| | - Júlio César de Carvalho
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, PR 81531-980, Brazil
| | - Vanete Thomaz Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, PR 81531-980, Brazil
| | - Carlos Ricardo Soccol
- Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, PR 81531-980, Brazil
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22
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Zhao L, Li Y, Jiang L, Deng F. Determination of fungal community diversity in fresh and traditional Chinese fermented pepper by pyrosequencing. FEMS Microbiol Lett 2016; 363:fnw273. [DOI: 10.1093/femsle/fnw273] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/26/2016] [Accepted: 12/05/2016] [Indexed: 11/13/2022] Open
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