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Mielecki D, Detman A, Aleksandrzak-Piekarczyk T, Widomska M, Chojnacka A, Stachurska-Skrodzka A, Walczak P, Grzesiuk E, Sikora A. Unlocking the genome of the non-sourdough Kazachstania humilis MAW1: insights into inhibitory factors and phenotypic properties. Microb Cell Fact 2024; 23:111. [PMID: 38622625 PMCID: PMC11017505 DOI: 10.1186/s12934-024-02380-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Ascomycetous budding yeasts are ubiquitous environmental microorganisms important in food production and medicine. Due to recent intensive genomic research, the taxonomy of yeast is becoming more organized based on the identification of monophyletic taxa. This includes genera important to humans, such as Kazachstania. Until now, Kazachstania humilis (previously Candida humilis) was regarded as a sourdough-specific yeast. In addition, any antibacterial activity has not been associated with this species. RESULTS Previously, we isolated a yeast strain that impaired bio-hydrogen production in a dark fermentation bioreactor and inhibited the growth of Gram-positive and Gram-negative bacteria. Here, using next generation sequencing technologies, we sequenced the genome of this strain named K. humilis MAW1. This is the first genome of a K. humilis isolate not originating from a fermented food. We used novel phylogenetic approach employing the 18 S-ITS-D1-D2 region to show the placement of the K. humilis MAW1 among other members of the Kazachstania genus. This strain was examined by global phenotypic profiling, including carbon sources utilized and the influence of stress conditions on growth. Using the well-recognized bacterial model Escherichia coli AB1157, we show that K. humilis MAW1 cultivated in an acidic medium inhibits bacterial growth by the disturbance of cell division, manifested by filament formation. To gain a greater understanding of the inhibitory effect of K. humilis MAW1, we selected 23 yeast proteins with recognized toxic activity against bacteria and used them for Blast searches of the K. humilis MAW1 genome assembly. The resulting panel of genes present in the K. humilis MAW1 genome included those encoding the 1,3-β-glucan glycosidase and the 1,3-β-glucan synthesis inhibitor that might disturb the bacterial cell envelope structures. CONCLUSIONS We characterized a non-sourdough-derived strain of K. humilis, including its genome sequence and physiological aspects. The MAW1, together with other K. humilis strains, shows the new organization of the mating-type locus. The revealed here pH-dependent ability to inhibit bacterial growth has not been previously recognized in this species. Our study contributes to the building of genome sequence-based classification systems; better understanding of K.humilis as a cell factory in fermentation processes and exploring bacteria-yeast interactions in microbial communities.
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Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
- Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, Warsaw, 02-106, Poland
| | - Anna Detman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | | | - Małgorzata Widomska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
- Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776, Poland
| | | | - Paulina Walczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Anna Sikora
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland.
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Gallotti AC, Lombera M, Pinto K, Pinilla I, Zaragoza O, Cuétara MS. Kazachstania slooffiae, an emerging pathogen to watch for in humans? Med Mycol Case Rep 2023; 42:100604. [PMID: 37693216 PMCID: PMC10482886 DOI: 10.1016/j.mmcr.2023.08.007] [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: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
In an 80-year-old man with long-term dysphagia, an upper endoscopy was performed and biopsy samples collected for microbiological and pathological tests, showing fungal structures. Kazachstania slooffiae was isolated in microbiological cultures that were later confirmed with DNA sequencing. Susceptibility tests were performed, and antifungal treatment was initiated with a clinical, pathological, and microbiological response.
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Affiliation(s)
- Ana Cristina Gallotti
- Department of Microbiology and Parasitology, Severo Ochoa University Hospital, Madrid, Spain
| | - Mar Lombera
- Digestive Unit, Severo Ochoa University Hospital, Madrid, Spain
| | - Karen Pinto
- Department of Microbiology and Parasitology, Severo Ochoa University Hospital, Madrid, Spain
| | - Ignacio Pinilla
- Department of Anathomopathology, Severo Ochoa University Hospital, Madrid, Spain
| | - Oscar Zaragoza
- Mycology Reference Laboratory, National Center for Microbiology, Carlos III Health Institute, Madrid, Spain
- Center for Biomedical Research in Network in Infectious Diseases (CIBERINFEC-CB21/13/00105), Carlos III Health Institute, Madrid, Spain
| | - María Soledad Cuétara
- Department of Microbiology and Parasitology, Severo Ochoa University Hospital, Madrid, Spain
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Balarezo-Cisneros LN, Timouma S, Hanak A, Currin A, Valle F, Delneri D. High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries. Commun Biol 2023; 6:918. [PMID: 37679437 PMCID: PMC10484914 DOI: 10.1038/s42003-023-05285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Kazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals including organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing long read sequencing we report a high-quality phased genome assembly for three strains of K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14 Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array and mating type locus. This high-quality reference genome provides a resource to advance our fundamental knowledge of biotechnologically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts in biotechnological processes.
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Affiliation(s)
| | - Soukaina Timouma
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Alistair Hanak
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew Currin
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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El Khaider K, Chafik I, Hamouda A, Afechtal M, Ismaili Alaoui M, Mounir M. Selection of mixed starters for the preparation of traditional Moroccan bread. JOURNAL OF BIOLOGICAL RESEARCH - BOLLETTINO DELLA SOCIETÀ ITALIANA DI BIOLOGIA SPERIMENTALE 2023. [DOI: 10.4081/jbr.2023.10697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The main objective of this work was the selection of mixed starters with a combination of Lactic Acid Bacteria (LAB) and yeasts strains for traditional bread production in Morocco. For this, a total of 21 LAB strains and 36 yeast strains were isolated from different traditional sourdough. Dough fermentation were assessed by monitoring physicochemical parameters including, titratable acidity, decrease of pH and lactic acid, ethanol and CO2 production. A total of six yeasts and four LAB were selected for their technological performances. Morphological, physiological and biochemical identification performed using API identification kits confirmed that these strains belonged to Saccharomyes cerevisiae, Candida humilis and Saccharomyces exiguus species, and Lactobacillus plantarum and Lactobacillus casei species for yeasts and LAB respectively. The yeast S3-L2 and the LAB OD-BL5 strains exhibited the best performances among the selected ones; S3-L2 yeast strain were able to produce ΔV=23mL of CO2 and showed the highest values of ethanol and biomass production (2.87 g/L and 1.25 10^9 UFC/mL, respectively). Whereas OD-BL5 LAB strains produced 13.9 g/L of lactate in dough. These findings lead to consider these two strains very good candidates for the formulation of an effective mixed starter for bread preparation. Subsequently, sensorial analysis results showed that bread prepared using mixed starter No. 24 composed of the two selected species exhibited better exterior appearance, golden and crispy crust, large volume and honeycomb crumb, compared to the control.
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Hernández-Parada N, González-Ríos O, Suárez-Quiroz ML, Hernández-Estrada ZJ, Figueroa-Hernández CY, Figueroa-Cárdenas JDD, Rayas-Duarte P, Figueroa-Espinoza MC. Exploiting the Native Microorganisms from Different Food Matrices to Formulate Starter Cultures for Sourdough Bread Production. Microorganisms 2022; 11:microorganisms11010109. [PMID: 36677402 PMCID: PMC9865925 DOI: 10.3390/microorganisms11010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The use of sourdough for bread production involves fermentation, which is dominated by lactic acid bacteria (LAB) and yeast. Sourdough can be inoculated with a starter culture or through a food matrix containing microorganisms to initiate sourdough fermentation. Sourdough is used as leavening agent for bread making, and metabolites produced by LAB and yeast confer a specific aroma and flavor profile to bread, thus improving its sensory attributes. However, few publications report the effect of microorganisms from different food products and by-products on sourdough fermentation. This review focuses on using different starter cultures from various food sources, from wheat flour to starter cultures. Additionally, included are the types of sourdough, the sourdough fermentation process, and the biochemical transformations that take place during the sourdough fermentation process.
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Affiliation(s)
- Natali Hernández-Parada
- Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, M.A. de Quevedo 2779, Col. Formando Hogar, Veracruz C.P. 91897, Mexico
| | - Oscar González-Ríos
- Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, M.A. de Quevedo 2779, Col. Formando Hogar, Veracruz C.P. 91897, Mexico
| | - Mirna Leonor Suárez-Quiroz
- Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, M.A. de Quevedo 2779, Col. Formando Hogar, Veracruz C.P. 91897, Mexico
| | - Zorba Josué Hernández-Estrada
- Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, M.A. de Quevedo 2779, Col. Formando Hogar, Veracruz C.P. 91897, Mexico
| | - Claudia Yuritzi Figueroa-Hernández
- CONACYT-Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, Unidad de Investigación y Desarrollo en Alimentos, M.A. de Quevedo 2779, Veracruz C.P. 91897, Mexico
| | - Juan de Dios Figueroa-Cárdenas
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV Unidad Querétaro), Libramiento Norponiente 2000, Fracc. Real de Juriquilla, Querétaro C.P. 76230, Mexico
| | - Patricia Rayas-Duarte
- Robert M. Kerr Food & Agricultural Products Center, Oklahoma State University, 123 FAPC, Stillwater, OK 74078-6055, USA
- Correspondence: (P.R.-D.); (M.C.F.-E.)
| | - María Cruz Figueroa-Espinoza
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de la Réunion, F-34398 Montpellier, France
- Correspondence: (P.R.-D.); (M.C.F.-E.)
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Impact of Leavening Agent and Wheat Variety on Bread Organoleptic and Nutritional Quality. Microorganisms 2022; 10:microorganisms10071416. [PMID: 35889135 PMCID: PMC9317705 DOI: 10.3390/microorganisms10071416] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 02/06/2023] Open
Abstract
Leavened bread can be made with different wheat varieties and leavening agents. Several studies have now demonstrated that each of these factors can play a role in bread quality. However, their relative impact in artisanal bread making remains to be elucidated. Here, we assessed the impact of two wheat varieties as well as the impact of sourdoughs and yeasts on multiple components of bread organoleptic and nutritional quality. Using a participatory research approach including scientists and bakers, we compared breads leavened with three different sourdoughs and three different commercial yeasts as well as a mix of sourdough and yeast. Breads were made from two wheat varieties commonly used in organic farming: the variety “Renan” and the landrace “Barbu”. Except for bread minerals contents that mostly depended on wheat variety, bread quality was mostly driven by the fermenting agent. Sourdough breads had lower sugar and organic acids contents. These differences were mostly attributable to lower amounts of maltose and malate. They also had a higher proportion of soluble proteins than yeast breads, with specific aroma profiles. Finally, their aroma profiles were specific and more diverse compared to yeast breads. Interestingly, we also found significant nutritional and organoleptic quality differences between sourdough breads. These results highlight the value of sourdough bread and the role of sourdough microbial diversity in bread nutritional and organoleptic quality.
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Boyaci Gunduz CP, Agirman B, Gaglio R, Franciosi E, Francesca N, Settanni L, Erten H. Evaluation of the variations in chemical and microbiological properties of the sourdoughs produced with selected lactic acid bacteria strains during fermentation. Food Chem X 2022; 14:100357. [PMID: 35693452 PMCID: PMC9178471 DOI: 10.1016/j.fochx.2022.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/18/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022] Open
Abstract
Chemical, microbiological and VOCs profile showed the relevance of starter addition. MiSeq Illumina confirmed that Lactobacillus spp. constituted the major LAB group. Fructilactobacillus sanfranciscensis was the most isolated LAB species. Rapid acidifying LAB strains should be preferred for sourdough production. Number of VOCs increased in sourdoughs produced with starter culture.
This research aimed to analyze variations in chemical properties, microbiological characteristics and generated volatile organic compounds (VOCs) profile during sourdough fermentation. Sourdoughs were collected from different cities in Turkey at two different times and lactic acid bacteria (LAB) in the samples were identified with culture-independent and culture-dependent molecular methods. According to culture-dependent methodology, thirteen LAB species were identified. Lactobacillus spp. were identified as the major group according to MiSeq Illumina analysis. Technological potential of commonly isolated LAB species was evaluated. Due to high frequency of isolation, Fructilactobacillus sanfranciscensis and Lactiplantibacillus plantarum strains were better investigated for their technological traits useful in sourdough production. Experimental sourdoughs were produced with mono- and dual-culture of the selected strains and chemical properties and microbiological characteristics, as well as VOCs profile of the sourdoughs, were subjected to multivariate analysis which showed the relevance of added starter, in terms of acidification and VOCs profile.
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Pino A, Russo N, Solieri L, Sola L, Caggia C, Randazzo CL. Microbial Consortia Involved in Traditional Sicilian Sourdough: Characterization of Lactic Acid Bacteria and Yeast Populations. Microorganisms 2022; 10:microorganisms10020283. [PMID: 35208738 PMCID: PMC8875953 DOI: 10.3390/microorganisms10020283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Sourdough is one of the oldest starters traditionally used for making baked goods, offering several advantages to the sensory, rheology, and shelf life of final products. The present study investigated, for the first time, the microbiota of spontaneously fermented Maiorca dough samples collected from bakeries located in Sicily (Italy). Four sourdough samples (M1, M2, M3, and M4), were produced using Triticum vulgare Host. var. albidum Koern (Maiorca grain) were subjected to LAB and yeasts isolation and identification at the species level. The in-depth characterization of the lactobacilli population revealed that Lactiplantibacillus plantarum and Levilactobacillus brevis unquestionably dominated the Maiorca sourdough ecosystem. Concerning the yeasts community, high species diversity was found. Saccharomyces cerevisiae and Wickerhamomyces anomalus were the most frequently isolated species. In addition, Torulaspora delbrueckii, Pichia kluyveri, Candida boidinii, and Candida diddensiae were also detected. Investigations on both pro-technological and functional traits of the isolated strains could lead to the selection of starters for the production of baked goods.
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Affiliation(s)
- Alessandra Pino
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (C.C.)
- ProBioEtna srl, Spin-off of University of Catania, 95123 Catania, Italy
| | - Nunziatina Russo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (C.C.)
- ProBioEtna srl, Spin-off of University of Catania, 95123 Catania, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy; (L.S.); (L.S.)
| | - Laura Sola
- Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy; (L.S.); (L.S.)
| | - Cinzia Caggia
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (C.C.)
- ProBioEtna srl, Spin-off of University of Catania, 95123 Catania, Italy
| | - Cinzia Lucia Randazzo
- Department of Agricultural, Food and Environment, University of Catania, 95123 Catania, Italy; (A.P.); (N.R.); (C.C.)
- ProBioEtna srl, Spin-off of University of Catania, 95123 Catania, Italy
- Correspondence:
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Yang Q, Rutherfurd-Markwick K, Mutukumira AN. Identification of dominant lactic acid bacteria and yeast in rice sourdough produced in New Zealand. Curr Res Food Sci 2021; 4:729-736. [PMID: 34729499 PMCID: PMC8546371 DOI: 10.1016/j.crfs.2021.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/21/2022] Open
Abstract
This study characterised a commercial New Zealand gluten free (GF) rice sourdough and its starter culture composition. Acidity of the mother sourdough, dough before proofing and dough after proofing was determined during the production of rice sourdough bread, and colour was measured for the baked bread. Yeast and lactic acid bacteria (LAB) were enumerated in the rice sourdough samples and representative colonies characterised using API kits and sequenced by the Internal Transcribed Spacer and 16 S rRNA region. Sourdough LAB isolates were identified as Lactobacillus (L.) papraplantarum DSM 10667 and L. fermentarum CIP 102980 and the yeast isolates as Saccharomyces (S.) cerevisiae CBS 1171. Dough acidity increased significantly (p < 0.05) during fermentation due to the metabolic activities of the sourdough cultures. After baking, the colour of the rice sourdough bread crust was similar to that of unleavened wheat bread (golden brown). The improved colour of the rice sourdough bread crust may be a result of combined use of sourdough technique and optimal baking conditions. The results of this study may allow bakers to improve the overall quality of GF rice sourdough baked bread by selecting suitable fermentation and baking parameters. Gluten-free rice sourdough bread. Rice sourdough fermentation of gluten-free bread improved bread crust colour Rice sourdough LAB identified as Lactobacillus paraplantarum CIP 102980 and Lactobacillus fermentarum DSM 10667 Yeast isolated from rice sourdough was identified as S. cerevisiae CBS 1171.
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Affiliation(s)
- Qiwei Yang
- School of Food and Advanced Technology, Massey University, Auckland, 0745, New Zealand
| | - Kay Rutherfurd-Markwick
- School of Health Sciences, College of Health, Massey University, Auckland, 0745, New Zealand
| | - Anthony N. Mutukumira
- School of Food and Advanced Technology, Massey University, Auckland, 0745, New Zealand
- Corresponding author.
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Lau SW, Chong AQ, Chin NL, Talib RA, Basha RK. Sourdough Microbiome Comparison and Benefits. Microorganisms 2021; 9:microorganisms9071355. [PMID: 34201420 PMCID: PMC8306212 DOI: 10.3390/microorganisms9071355] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
Sourdough is the oldest form of leavened bread used as early as 2000 BC by the ancient Egyptians. It may have been discovered by accident when wild yeast drifted into dough that had been left out resulting in fermentation of good microorganisms, which made bread with better flavour and texture. The discovery was continued where sourdough was produced as a means of reducing wastage with little known (at that point of time) beneficial effects to health. With the progress and advent of science and technology in nutrition, sourdough fermentation is now known to possess many desirable attributes in terms of health benefits. It has become the focus of attention and practice in modern healthy eating lifestyles when linked to the secret of good health. The sourdough starter is an excellent habitat where natural and wild yeast plus beneficial bacteria grow by ingesting only water and flour. As each sourdough starter is unique, with different activities, populations and interactions of yeast and bacteria due to different ingredients, environment, fermentation time and its carbohydrate fermentation pattern, there is no exact elucidation on the complete make-up of the sourdough microbiome. Some lactic acid bacteria (LAB) strains that are part of the sourdough starter are considered as probiotics which have great potential for improving gastrointestinal health. Hence, from a wide literature surveyed, this paper gives an overview of microbial communities found in different sourdough starters. This review also provides a systematic analysis that identifies, categorises and compares these microbes in the effort of linking them to specific functions, particularly to unlock their health benefits.
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Affiliation(s)
| | | | - Nyuk Ling Chin
- Correspondence: ; Tel.: +603-9769-6353; Fax: +603-9769-4440
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Liu Z, Li J, Zhou X, Wei B, Xie S, Du T, Zhao X, Jiang L, Xiong T. The lactic acid bacteria and yeast community of home-made sauerkraut from three provinces in Southwest China. Arch Microbiol 2021; 203:3171-3182. [PMID: 33825934 DOI: 10.1007/s00203-021-02222-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/28/2020] [Accepted: 02/11/2021] [Indexed: 10/21/2022]
Abstract
The aim of this study was to investigate the lactic acid bacteria (LAB) and yeast community from home-made sauerkraut collected from Southwest China through culture-dependent and culture-independent technology. Forty-eight samples of home-made sauerkraut were collected from households at three different locations in Southwest China. The pH, total acidity and salt contents among these fermented vegetables were 3.69 ± 0.42, 0.86 ± 0.43 g/100 ml, and 3.86 ± 2.55 g/100 ml, respectively. The number of lactic acid bacteria (LAB) and yeasts were 7.25 ± 1.05 log10 colony-forming units (CFU)/ml and 3.74 ± 1.01 log CFU/ml, respectively. A total of 182 LAB and 81 yeast isolates were identified. The dominant isolates were Lactobacillus plantarum, L. brevis, Pediococcus ethanolidurans, Pichia membranifaciens, P. fermentans and Kazachstania bulderi. Denaturing gradient gel electrophoresis (DGGE) showed that L. plantarum, uncultured Lactobacillus sp, P. ethanolidurans, and K. exigua were the predominant microflora. Our studies demonstrated that the DGGE technique combined with a culture-dependent method is very effective for studying the LAB and yeast community in Chinese traditional fermentation vegetables. The results will give us an understanding of LAB and yeast community of Chinese sauerkraut and improve the knowledge of LAB and yeast community of Chinese sauerkraut.
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Affiliation(s)
- Zhanggen Liu
- State Key Laboratory of Food Science and Technology, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China.,School of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China
| | - Junyi Li
- State Key Laboratory of Food Science and Technology, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China.,School of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China
| | - Xiaowei Zhou
- Department of Nutrition, Henry Fok School of Food Science and Engineering, Shaoguan University, Shaoguan, 512005, China
| | - Benliang Wei
- State Key Laboratory of Food Science and Technology, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China.,School of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China
| | - Shuhu Xie
- State Key Laboratory of Food Science and Technology, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China.,School of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China
| | - Tonghao Du
- State Key Laboratory of Food Science and Technology, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China.,School of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China
| | - Xueting Zhao
- State Key Laboratory of Food Science and Technology, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China.,School of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China
| | - Li Jiang
- Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, Jiangxi, People's Republic of China
| | - Tao Xiong
- State Key Laboratory of Food Science and Technology, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China. .,School of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang, 330047, Jiangxi, People's Republic of China.
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Boudaoud S, Aouf C, Devillers H, Sicard D, Segond D. Sourdough yeast-bacteria interactions can change ferulic acid metabolism during fermentation. Food Microbiol 2021; 98:103790. [PMID: 33875218 DOI: 10.1016/j.fm.2021.103790] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/03/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022]
Abstract
The metabolism of ferulic acid (FA) was studied during fermentation with different species and strains of lactic acid bacteria (LAB) and yeasts, in synthetic sourdough medium. Yeast strains of Kazachstania humilis, Kazachstania bulderi, and Saccharomyces cerevisiae, as well as lactic acid bacteria strains of Fructilactobacillus sanfranciscensis, Lactiplantibacillus plantarum, Lactiplantibacillus xiangfangensis, Levilactobacillus hammesii, Latilactobacillus curvatus and Latilactobacillus sakei were selected from French natural sourdoughs. Fermentation in presence or absence of FA was carried out in LAB and yeasts monocultures, as well as in LAB/yeast co-cultures. Our results indicated that FA was mainly metabolized into 4-vinylguaiacol (4-VG) by S. cerevisiae strains, and into dihydroferulic acid (DHFA) and 4-VG in the case of LAB. Interactions of LAB and yeasts led to the modification of FA metabolism, with a major formation of DHFA, even by the strains that do not produce it in monoculture. Interestingly, FA was almost completely consumed by the F. sanfranciscensis bFs17 and K. humilis yKh17 pair and converted into DHFA in 89.5 ± 19.6% yield, while neither bFs17, nor yKh17 strains assimilated FA in monoculture.
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Affiliation(s)
- Sonia Boudaoud
- UMR 1083 SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Chahinez Aouf
- UMR 1208 IATE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Hugo Devillers
- UMR 1083 SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Delphine Sicard
- UMR 1083 SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Diego Segond
- UMR 1083 SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France.
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13
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Recent research advances of lactic acid bacteria in sourdough: origin, diversity, and function. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Mercier V, Desnos-Ollivier M, Lamy A, Mahul M, Sasso M. Kazachstania slooffiae: An unexpected journey to a human pleural sample. J Mycol Med 2020; 31:101109. [PMID: 33422936 DOI: 10.1016/j.mycmed.2020.101109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022]
Abstract
We report a case of a 50-year-old shepherd hospitalized in intensive care unit for hiatal hernia complicated by an occlusive syndrome. In post-surgery, an acute respiratory distress occurs due to mediastinitis with large pleural effusion. At the laboratory, direct examination of the pleural sample revealed the presence of pseudohyphae. Kazachstania slooffiae was identified by Mass Spectrometry and confirmed by DNA sequencing. This uncommon yeast has never been previously described in human infections. Although its pathogenicity is not well known, K. slooffiae should be considered in the case of critically ill patients.
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Affiliation(s)
- Victor Mercier
- MIVEGEC, University Montpellier, CHU de Nîmes, CNRS, IRD, Montpellier, France
| | - Marie Desnos-Ollivier
- Institut Pasteur, CNRS, Molecular Mycology Unit, National Reference Center for Invasive Mycoses & Antifungals, UMR 2000, Paris, France
| | - Anaïs Lamy
- Department of Parasitology and Mycology, Nîmes University Hospital, Nîmes, France
| | - Martin Mahul
- Department of Intensive Care Unit, Nîmes University Hospital, Nîmes, France
| | - Milène Sasso
- MIVEGEC, University Montpellier, CHU de Nîmes, CNRS, IRD, Montpellier, France.
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15
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Yeast Biodiversity in Fermented Doughs and Raw Cereal Matrices and the Study of Technological Traits of Selected Strains Isolated in Spain. Microorganisms 2020; 9:microorganisms9010047. [PMID: 33375367 PMCID: PMC7824024 DOI: 10.3390/microorganisms9010047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022] Open
Abstract
Bakers use pure microorganisms and/or traditional sourdoughs as the leavening agent for making bread. The performance of each starter and the substances produced by the microorganisms greatly affect the dough rheology and features of breads. Modern sourdoughs inoculated with selected lactic acid bacteria and yeasts are microbiologically stable, safer than traditional sourdoughs, and easy to use. However, the commercial repertoire of baker’s yeasts is still limited. Therefore, there is a demand for new strains of yeast species, capable of conferring distinctive traits to breads made from a variety of agri-food matrices, in the design of innovative starters. In this context, we report the first comprehensive study on yeasts isolated from a wide range of fermented doughs, cereal flours, and grains of Spain. Nine yeast species were identified from 433 isolates, which were distributed among separate clades. Moreover, phenotypic traits of potential technological relevance were identified in selected yeast strains. Mother doughs (MDs) showed the greatest yeast biodiversity, whereas commercial Saccharomyces starters or related and wild strains often dominated the bakery doughs. A metataxonomic analysis of wheat and tritordeum MDs revealed a greater richness of yeast species and percentage variations related to the consistency, flour type, and fermentation time of MDs.
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16
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Sustainable Food Supply Chains: Is Shortening the Answer? A Literature Review for a Research and Innovation Agenda. SUSTAINABILITY 2020. [DOI: 10.3390/su12239831] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Short food supply chains (SFSCs) are increasingly garnering attention in food systems research, owing to their rising popularity among consumers, producers and policy-makers in the last few decades. Written with the aim to identify research gaps for the Horizon Europe research and innovation programme, this literature review provides a state of play of the definition and characterisation of SFSCs, and of their sustainability. Drawing on hypotheses about SFSC sustainability elaborated in an expert network in France, this review summarises a wide range of papers from various disciplines in the SFSC literature, written in English or French, while specifically highlighting the empirical results derived from European projects. Though the literature tends to generally agree on the social benefits of SFSCs, their economic and environmental impacts typically elicit more heterogeneous outcomes, while their health/nutrition and governance dimensions remain under-explored. Based on this review, recommendations for a future research and innovation programme are outlined, addressing the contribution of SFSCs to agrifood system transition and resilience in the current context of the Covid-19 crisis and of the Green New Deal objectives.
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17
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Lahue C, Madden AA, Dunn RR, Smukowski Heil C. History and Domestication of Saccharomyces cerevisiae in Bread Baking. Front Genet 2020; 11:584718. [PMID: 33262788 PMCID: PMC7686800 DOI: 10.3389/fgene.2020.584718] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.
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Affiliation(s)
- Caitlin Lahue
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Anne A. Madden
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Caiti Smukowski Heil
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
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18
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Gaglio R, Cirlincione F, Di Miceli G, Franciosi E, Di Gerlando R, Francesca N, Settanni L, Moschetti G. Microbial dynamics in durum wheat kernels during aging. Int J Food Microbiol 2020; 324:108631. [DOI: 10.1016/j.ijfoodmicro.2020.108631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/11/2020] [Indexed: 12/18/2022]
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19
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Boyaci‐Gunduz CP, Erten H. Predominant yeasts in the sourdoughs collected from some parts of Turkey. Yeast 2020; 37:449-466. [DOI: 10.1002/yea.3500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Cennet Pelin Boyaci‐Gunduz
- Faculty of Agriculture, Food Engineering Department Cukurova University Adana Turkey
- Faculty of Engineering, Food Engineering Department Adana Alparslan Turkes Science and Technology University Adana Turkey
| | - Huseyin Erten
- Faculty of Agriculture, Food Engineering Department Cukurova University Adana Turkey
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20
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Suo B, Nie W, Wang Y, Ma J, Xing X, Huang Z, Xu C, Li Z, Ai Z. Microbial diversity of fermented dough and volatile compounds in steamed bread prepared with traditional Chinese starters. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109350] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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21
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Carbonetto B, Nidelet T, Guezenec S, Perez M, Segond D, Sicard D. Interactions between Kazachstania humilis Yeast Species and Lactic Acid Bacteria in Sourdough. Microorganisms 2020; 8:microorganisms8020240. [PMID: 32053958 PMCID: PMC7074792 DOI: 10.3390/microorganisms8020240] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/25/2020] [Accepted: 02/06/2020] [Indexed: 11/24/2022] Open
Abstract
Sourdoughs harbor simple microbial communities usually composed of a few prevailing lactic acid bacteria species (LAB) and yeast species. However, yeast and LAB found in sourdough have been described as highly diverse. Even if LAB and yeast associations have been widely documented, the nature of the interactions between them has been poorly described. These interactions define the composition and structure of sourdough communities, and therefore, the characteristics of the final bread product. In this study, the nature of the interactions between strains of two commonly found sourdough yeast species, Kazachstania humilis and Saccharomyces cerevisiae, and lactic acid bacteria isolated from sourdoughs has been analyzed. Population density analysis showed no evidence of positive interactions, but instead revealed neutral or negative asymmetric interaction outcomes. When in coculture, the yeasts´ population size decreased in the presence of LAB regardless of the strain, while the LAB´s population size was rarely influenced by the presence of yeasts. However, a higher maltose depletion was shown in maltose-negative K. humilis and maltose-positive obligately heterofermentative LAB cocultures compared to monocultures. In addition, tested pairs of obligately heterofermentative LAB and K. humilis strains leavened dough as much as couples of LAB and S. cerevisiae strains, while K. humilis strains never leavened dough as much as S. cerevisiae when in monoculture. Taken together, our results demonstrate that even if higher fermentation levels with increased maltose depletion were detected for K. humilis and obligately heterofermentative LAB pairs, these interactions cannot be ecologically classified as positive, leading us to rethink the established hypothesis of coexistence by facilitation in sourdoughs.
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22
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Shi F, Zhao H, Song H, Guo W, Wang L, Cui X, Zhang W, Li S. Effects of electron-beam irradiation on inoculated Listeria innocua, microbiological and physicochemical quality of fresh noodles during refrigerated storage. Food Sci Nutr 2020; 8:114-123. [PMID: 31993138 PMCID: PMC6977504 DOI: 10.1002/fsn3.1277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/06/2019] [Accepted: 10/09/2019] [Indexed: 11/06/2022] Open
Abstract
As a nonthermal sterilization technology, electron-beam irradiation (EBI) has attracted great interests for microbial inactivation in food preservation. In this study, the inactivation of inoculated Listeria innocua, natural microbiota, and quality of fresh noodles treated by EBI during refrigerated storage were evaluated. Results showed that the initial L. innocua population (6.38 log CFU/g) was significantly reduced to an undetectable level by treatment with 3.0 kGy EBI. Moreover, treatment with 3 kGy EBI significantly reduced the initial total bacteria counts and fungal counts (mold and yeast) from 5.66 and 3.15 log CFU/g to 2.90 and 2.11 log CFU/g, respectively. However, along with the storage process, the inoculated L. innocua and natural microbiota were recovered resulting in the increased populations of the spoilage microorganisms. Increasing the dose of EBI to 4.0 kGy or 5.0 kGy, the L. innocua population was inhibited to the undetectable level and the microbiological quality of the fresh noodles was kept in the acceptable level during the 28 day storage. In addition, changes of the physicochemical indicators including pH value, color, cooking characteristics, texture, and sensory of fresh noodles treated with EBI were delayed during storage. These results reveal that EBI treatment can improve the microbiological safety and shelf life of fresh noodles without impairing quality.
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Affiliation(s)
- Feifei Shi
- Department of Food and Biological EngineeringBeijing Vocational College of AgricultureBeijingChina
- College of Food ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Hongwei Zhao
- Qingdao University of Science and TechnologyQingdaoChina
- Shandong Provincial Key Laboratory of Biochemical EngineeringQingdaoChina
| | - Hongbo Song
- College of Food ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Weiling Guo
- College of Food ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Li Wang
- Department of Food and Biological EngineeringBeijing Vocational College of AgricultureBeijingChina
| | - Xiaorui Cui
- Department of Food and Biological EngineeringBeijing Vocational College of AgricultureBeijingChina
- College of Food ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | | | - Shurong Li
- Department of Food and Biological EngineeringBeijing Vocational College of AgricultureBeijingChina
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23
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Liu Z, Peng Z, Huang T, Xiao Y, Li J, Xie M, Xiong T. Comparison of bacterial diversity in traditionally homemade paocai and Chinese spicy cabbage. Food Microbiol 2019; 83:141-149. [DOI: 10.1016/j.fm.2019.02.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 01/22/2019] [Accepted: 02/22/2019] [Indexed: 01/02/2023]
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24
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Gänzle MG, Zheng J. Lifestyles of sourdough lactobacilli – Do they matter for microbial ecology and bread quality? Int J Food Microbiol 2019; 302:15-23. [DOI: 10.1016/j.ijfoodmicro.2018.08.019] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/09/2018] [Accepted: 08/18/2018] [Indexed: 12/11/2022]
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25
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Winters M, Panayotides D, Bayrak M, Rémont G, Viejo CG, Liu D, Le B, Liu Y, Luo J, Zhang P, Howell K. Defined co-cultures of yeast and bacteria modify the aroma, crumb and sensory properties of bread. J Appl Microbiol 2019; 127:778-793. [PMID: 31211891 DOI: 10.1111/jam.14349] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/27/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022]
Abstract
AIMS Yeast and bacterial communities inhabit a sourdough starter to make artisanal bread. This study shows whether the interactions of micro-organisms derived from Australian sourdough starters provide some of the positive flavour, and aroma properties to bread by using defined sourdough cultures as the sole leaven in bread production. METHODS AND RESULTS An investigation of Australian sourdough starters found that they contained Saccharomyces cerevisiae and Kazachstania exigua yeasts. When these yeasts were inoculated alone to ferment wheat flour in an extended fermentation, the bread had a heterogeneous crumb structure, a deeper colour and a distinctive chemical aroma profile than those made with commercial baker's yeast. When bread was made combining these yeasts individually and in combinations with lactic acid bacteria also isolated from these sourdough starters, including Lactobacillus plantarum, L. brevis, L. rossiae, L. casei, the bread aroma profiles and crumb structure were more distinctive, with compounds associated with sour aromas produced, and preferred by sensory panels. CONCLUSIONS The use of defined mixed cultures as the leaven in bread making, by exploiting the microbial diversity of artisanal Australian starters, can produce bread with distinctive and attractive aromas. SIGNIFICANCE AND IMPACT OF THE STUDY Understanding and identifying the community ecosystems found in sourdough cultures and using them as the sole leaven in bread production provide novel insights into microbial interactions and how they affect food quality by removing the effects of commercial yeast strains.
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Affiliation(s)
- M Winters
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - D Panayotides
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - M Bayrak
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - G Rémont
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia.,AgroParisTech, Paris, France
| | - C G Viejo
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - D Liu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - B Le
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - Y Liu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - J Luo
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - P Zhang
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
| | - K Howell
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Vic, Australia
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26
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Det-Udom R, Gilbert C, Liu L, Prakitchaiwattana C, Ellis T, Ledesma-Amaro R. Towards semi-synthetic microbial communities: enhancing soy sauce fermentation properties in B. subtilis co-cultures. Microb Cell Fact 2019; 18:101. [PMID: 31159886 PMCID: PMC6547557 DOI: 10.1186/s12934-019-1149-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/22/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Many fermented foods and beverages are produced through the action of complex microbial communities. Synthetic biology approaches offer the ability to genetically engineer these communities to improve the properties of these fermented foods. Soy sauce is a fermented condiment with a vast global market. Engineering members of the microbial communities responsible for soy sauce fermentation may therefore lead to the development of improved products. One important property is the colour of soy sauce, with recent evidence pointing to a consumer preference for more lightly-coloured soy sauce products for particular dishes. RESULTS Here we show that a bacterial member of the natural soy sauce fermentation microbial community, Bacillus, can be engineered to reduce the 'browning' reaction during soy sauce production. We show that two approaches result in 'de-browning': engineered consumption of xylose, an important precursor in the browning reaction, and engineered degradation of melanoidins, the major brown pigments in soy sauce. Lastly, we show that these two strategies work synergistically using co-cultures to result in enhanced de-browning. CONCLUSIONS Our results demonstrate the potential of using synthetic biology and metabolic engineering methods for fine-tuning the process of soy sauce fermentation and indeed for many other natural food and beverage fermentations for improved products.
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Affiliation(s)
- Rachatida Det-Udom
- Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand
| | - Charlie Gilbert
- Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Long Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cheunjit Prakitchaiwattana
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand
| | - Tom Ellis
- Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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27
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Urien C, Legrand J, Montalent P, Casaregola S, Sicard D. Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour. Front Microbiol 2019; 10:201. [PMID: 30833935 PMCID: PMC6387954 DOI: 10.3389/fmicb.2019.00201] [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: 08/07/2018] [Accepted: 01/24/2019] [Indexed: 02/04/2023] Open
Abstract
Microbial communities are essential for the maintenance and functioning of ecosystems, including fermented food ecosystems. The analysis of food microbial communities is mainly focused on lactic acid bacteria (LAB), while yeast diversity is less understood. Here, we describe the fungal diversity of a typical food fermented product, sourdough bread. The species diversity of 14 sourdoughs collected from bakeries located all over France was analyzed. Bakeries were chosen to represent diverse bakery practices and included bakers and farmer-bakers. Both non-culture-based (pyrosequencing of Internal Transcribed Spacer 1 amplicons) and culture-based methods were used. While both identification methods were in agreement regarding the dominant yeast species of each sourdough, the ITS1 metabarcoding analysis identified an increased number of fungal species in sourdough communities. Two third of the identified sequences obtained from sourdoughs were Saccharomycetales, mostly in the Kazachstania genus. No Saccharomycetales species was shared by all the sourdoughs, whereas five other fungal species, mainly known plant pathogens, were found in all sourdoughs. Interestingly, Saccharomyces cerevisiae, known as “baker’s yeast,” was identified as the dominant species in only one sourdough. By contrast, five Kazachstania species were identified as the dominant sourdough species, including one recently described Kazachstania species, Kazachstania saulgeensis and an undescribed Kazachstania sp. Sourdoughs from farmer-bakers harbored Kazachstania bulderi, Kazachstania unispora and two newly described Kazachstania species, while sourdough from bakers mostly carried Kazachstania humilis as the dominant species. Such yeast diversity has not been found in sourdoughs before, highlighting the need to maintain different traditional food practices to conserve microbial diversity.
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Affiliation(s)
- Charlotte Urien
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Judith Legrand
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Montalent
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphine Sicard
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France.,SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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28
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Carbonetto B, Ramsayer J, Nidelet T, Legrand J, Sicard D. Bakery yeasts, a new model for studies in ecology and evolution. Yeast 2018; 35:591-603. [DOI: 10.1002/yea.3350] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Belén Carbonetto
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
- Instituto Gulbenkian de Ciência; Bioinformatics and Computational Biology Unit; Oeiras Portugal
| | - Johan Ramsayer
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
| | - Thibault Nidelet
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
| | - Judith Legrand
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Gif-sur-Yvette France
| | - Delphine Sicard
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
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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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Hernández A, Pérez-Nevado F, Ruiz-Moyano S, Serradilla MJ, Villalobos MC, Martín A, Córdoba MG. Spoilage yeasts: What are the sources of contamination of foods and beverages? Int J Food Microbiol 2018; 286:98-110. [PMID: 30056262 DOI: 10.1016/j.ijfoodmicro.2018.07.031] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
Foods and beverages are nutrient-rich ecosystems in which most microorganisms are able to grow. Moreover, several factors, such as physicochemical characteristics, storage temperature, culinary practices, and application of technologies for storage, also define the microbial population of foods and beverages. The yeast population has been well-characterised in fresh and processed fruit and vegetables, dairy products, dry-cured meat products, and beverages, among others. Some species are agents of alteration in different foods and beverages. Since the most comprehensive studies of spoilage yeasts have been performed in the winemaking process, hence, these studies form the thread of the discussion in this review. The natural yeast populations in raw ingredients and environmental contamination in the manufacturing facilities are the main modes by which food contamination occurs. After contamination, yeasts play a significant role in food and beverage spoilage, particularly in the alteration of fermented foods. Several mechanisms contribute to spoilage by yeasts, such as the production of lytic enzymes (lipases, proteases, and cellulases) and gas, utilisation of organic acids, discolouration, and off-flavours. This review addresses the role of yeasts in foods and beverages degradation by considering the modes of contamination and colonisation by yeasts, the yeast population diversity, mechanisms involved, and the analytical techniques for their identification, primarily molecular methods.
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Affiliation(s)
- A Hernández
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain.
| | - F Pérez-Nevado
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - S Ruiz-Moyano
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - M J Serradilla
- Área de Vegetales, Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), A5 km 372, 06187 Guadajira, Spain
| | - M C Villalobos
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - A Martín
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
| | - M G Córdoba
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Instituto Universitario de Recursos Agrarios (INURA), Universidad de Extremadura, Ctra. de Cáceres s/n, 06007 Badajoz, Spain
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32
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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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Sarilar V, Sterck L, Matsumoto S, Jacques N, Neuvéglise C, Tinsley CR, Sicard D, Casaregola S. Genome sequence of the type strain CLIB 1764 T (= CBS 14374 T) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough. GENOMICS DATA 2017; 13:41-43. [PMID: 28725555 PMCID: PMC5501885 DOI: 10.1016/j.gdata.2017.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/23/2017] [Accepted: 07/04/2017] [Indexed: 12/21/2022]
Abstract
Kazachstania saulgeensis is a recently described species isolated from French organic sourdough. Here, we report the high quality genome sequence of a monosporic segregant of the type strain of this species, CLIB 1764T (= CBS 14374T). The genome has a total length of 12.9 Mb and contains 5326 putative protein-coding genes, excluding pseudogenes and transposons. The nucleotide sequences were deposited into the European Nucleotide Archive under the genome assembly accession numbers FXLY01000001–FXLY01000017.
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Affiliation(s)
- Véronique Sarilar
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Lieven Sterck
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Saki Matsumoto
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Colin R. Tinsley
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Delphine Sicard
- Sciences pour l'œnologie, INRA, Supagro, Université de Montpellier, 34060 Montpellier, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Corresponding author.
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Abstract
ABSTRACT
In this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.
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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: 71] [Impact Index Per Article: 10.1] [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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Yeast diversity of sourdoughs and associated metabolic properties and functionalities. Int J Food Microbiol 2016; 239:26-34. [DOI: 10.1016/j.ijfoodmicro.2016.07.018] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/09/2016] [Accepted: 07/11/2016] [Indexed: 12/30/2022]
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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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39
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Pontonio E, Rizzello CG, Di Cagno R, Dousset X, Clément H, Filannino P, Onno B, Gobbetti M. How organic farming of wheat may affect the sourdough and the nutritional and technological features of leavened baked goods. Int J Food Microbiol 2016; 239:44-53. [DOI: 10.1016/j.ijfoodmicro.2016.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/16/2016] [Accepted: 07/09/2016] [Indexed: 02/07/2023]
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40
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Jacques N, Sarilar V, Urien C, Lopes MR, Morais CG, Uetanabaro APT, Tinsley CR, Rosa CA, Sicard D, Casaregola S. Three novel ascomycetous yeast species of the Kazachstania clade, Kazachstania saulgeensis sp. nov., Kazachstania
serrabonitensis sp. nov. and Kazachstania australis sp. nov. Reassignment of Candida humilis to Kazachstania humilis f.a. comb. nov. and Candida pseudohumilis to Kazachstania pseudohumilis f.a. comb. nov. Int J Syst Evol Microbiol 2016; 66:5192-5200. [DOI: 10.1099/ijsem.0.001495] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Noémie Jacques
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Véronique Sarilar
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Charlotte Urien
- Génétique Quantitative et Evolution-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Mariana R. Lopes
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Camila G. Morais
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ana Paula T. Uetanabaro
- Departamento de Ciências Biológicas e Agroindústria, Universidade Estadual Santa Cruz, Ilhéus, BA 45662-900, Brazil
| | - Colin R. Tinsley
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Delphine Sicard
- Sciences pour l’œnologie, INRA, Supagro, 34060 Montpellier, France
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Klaedtke S, Jacques MA, Raggi L, Préveaux A, Bonneau S, Negri V, Chable V, Barret M. Terroir is a key driver of seed-associated microbial assemblages. Environ Microbiol 2015; 18:1792-804. [PMID: 26171841 DOI: 10.1111/1462-2920.12977] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/01/2015] [Indexed: 12/20/2022]
Abstract
Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces.
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Affiliation(s)
| | - Marie-Agnès Jacques
- UMR1345 Institut de Recherches en Horticulture et Semences, INRA, SFR4207 QUASAV, F-49071, Beaucouzé, France
| | - Lorenzo Raggi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Anne Préveaux
- UMR1345 Institut de Recherches en Horticulture et Semences, INRA, SFR4207 QUASAV, F-49071, Beaucouzé, France
| | - Sophie Bonneau
- UMR1345 Institut de Recherches en Horticulture et Semences, INRA, SFR4207 QUASAV, F-49071, Beaucouzé, France
| | - Valeria Negri
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Véronique Chable
- UR980, INRA SAD, 65 Rue de St. Brieuc, CS 84215, 35042, Rennes, France
| | - Matthieu Barret
- UMR1345 Institut de Recherches en Horticulture et Semences, INRA, SFR4207 QUASAV, F-49071, Beaucouzé, France
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