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Rappaport HB, Senewiratne NPJ, Lucas SK, Wolfe BE, Oliverio AM. Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes. mSystems 2024; 9:e0053724. [PMID: 39287380 PMCID: PMC11498085 DOI: 10.1128/msystems.00537-24] [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: 04/15/2024] [Accepted: 08/22/2024] [Indexed: 09/19/2024] Open
Abstract
While research on the sourdough microbiome has primarily focused on lactic acid bacteria (LAB) and yeast, recent studies have found that acetic acid bacteria (AAB) are also common members. However, the ecology, genomic diversity, and functional contributions of AAB in sourdough remain unknown. To address this gap, we sequenced 29 AAB genomes, including three that represent putatively novel species, from a collection of over 500 sourdough starters surveyed globally from community scientists. We found variations in metabolic traits related to carbohydrate utilization, nitrogen metabolism, and alcohol production, as well as in genes related to mobile elements and defense mechanisms. Sourdough AAB genomes did not cluster when compared to AAB isolated from other environments, although a subset of gene functions was enriched in sourdough isolates. The lack of a sourdough-specific genomic cluster may reflect the nomadic lifestyle of AAB. To assess the consequences of AAB on the emergent function of sourdough starter microbiomes, we constructed synthetic starter microbiomes, varying only the AAB strain included. All AAB strains increased the acidification of synthetic sourdough starters relative to yeast and LAB by 18.5% on average. Different strains of AAB had distinct effects on the profile of synthetic starter volatiles. Taken together, our results begin to define the ways in which AAB shape emergent properties of sourdough and suggest that differences in gene content resulting from intraspecies diversification can have community-wide consequences on emergent function. IMPORTANCE This study is a comprehensive genomic and ecological survey of acetic acid bacteria (AAB) isolated from sourdough starters. By combining comparative genomics with manipulative experiments using synthetic microbiomes, we demonstrate that even strains with >97% average nucleotide identity can shift important microbiome functions, underscoring the importance of species and strain diversity in microbial systems. We also demonstrate the utility of sourdough starters as a model system to understand the consequences of genomic diversity at the strain and species level on multispecies communities. These results are also relevant to industrial and home-bakers as we uncover the importance of AAB in shaping properties of sourdough starters that have direct impacts on sensory notes and the quality of sourdough bread.
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Affiliation(s)
- H. B. Rappaport
- Department of Biology,
Syracuse University,
Syracuse, New York, USA
| | | | - Sarah K. Lucas
- Department of Biology,
Syracuse University,
Syracuse, New York, USA
| | - Benjamin E. Wolfe
- Department of Biology,
Tufts University, Medford,
Massachusetts, USA
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2
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Barron AJ, Agrawal S, Lesperance DNA, Doucette J, Calle S, Broderick NA. Microbiome-derived acidity protects against microbial invasion in Drosophila. Cell Rep 2024; 43:114087. [PMID: 38583152 PMCID: PMC11163447 DOI: 10.1016/j.celrep.2024.114087] [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: 10/13/2023] [Revised: 02/16/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Microbial invasions underlie host-microbe interactions resulting in pathogenesis and probiotic colonization. In this study, we explore the effects of the microbiome on microbial invasion in Drosophila melanogaster. We demonstrate that gut microbes Lactiplantibacillus plantarum and Acetobacter tropicalis improve survival and lead to a reduction in microbial burden during infection. Using a microbial interaction assay, we report that L. plantarum inhibits the growth of invasive bacteria, while A. tropicalis reduces this inhibition. We further show that inhibition by L. plantarum is linked to its ability to acidify its environment via lactic acid production by lactate dehydrogenase, while A. tropicalis diminishes the inhibition by quenching acids. We propose that acid from the microbiome is a gatekeeper to microbial invasions, as only microbes capable of tolerating acidic environments can colonize the host. The methods and findings described herein will add to the growing breadth of tools to study microbe-microbe interactions in broad contexts.
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Affiliation(s)
- Alexander J Barron
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Sneha Agrawal
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Danielle N A Lesperance
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jeremy Doucette
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Sthefany Calle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Nichole A Broderick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
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3
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Pause L, Weimer A, Wirth NT, Nguyen AV, Lenz C, Kohlstedt M, Wittmann C, Nikel PI, Lai B, Krömer JO. Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system. Microb Biotechnol 2024; 17:e14375. [PMID: 37990843 PMCID: PMC10832537 DOI: 10.1111/1751-7915.14375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Providing an anodic potential in a bio-electrochemical system to the obligate aerobe Pseudomonas putida enables anaerobic survival and allows the cells to overcome redox imbalances. In this setup, the bacteria could be exploited to produce chemicals via oxidative pathways at high yield. However, the absence of anaerobic growth and low carbon turnover rates remain as obstacles for the application of such an electro-fermentation technology. Growth and carbon turnover start with carbon uptake into the periplasm and cytosol. P. putida KT2440 has three native transporting systems for glucose, each differing in energy and redox demand. This architecture previously led to the hypothesis that internal redox and energy constraints ultimately limit cytoplasmic carbon utilization in a bio-electrochemical system. However, it remains largely unclear which uptake route is predominantly used by P. putida under electro-fermentative conditions. To elucidate this, we created three gene deletion mutants of P. putida KT2440, forcing the cells to exclusively utilize one of the routes. When grown in a bio-electrochemical system, the pathway mutants were heavily affected in terms of sugar consumption, current output and product formation. Surprisingly, however, we found that about half of the acetate formed in the cytoplasm originated from carbon that was put into the system via the inoculation biomass, while the other half came from the consumption of substrate. The deletion of individual sugar uptake routes did not alter significantly the secreted acetate concentrations among different strains even with different carbon sources. This means that the stoichiometry of the sugar uptake routes is not a limiting factor during electro-fermentation and that the low rates might be caused by other reasons, for example energy limitations or a yet-to-be-identified oxygen-dependent regulatory mechanism.
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Affiliation(s)
- Laura Pause
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Anna Weimer
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | - Nicolas T. Wirth
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Anh Vu Nguyen
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Claudius Lenz
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrückenGermany
| | | | - Pablo I. Nikel
- Systems Environmental Microbiology Group, The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkLyngbyDenmark
| | - Bin Lai
- BMBF Junior Research Group BiophotovoltaicsHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Jens O. Krömer
- Systems Biotechnology groupHelmholtz Centre for Environmental Research – UFZLeipzigGermany
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4
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Román-Camacho JJ, García-García I, Santos-Dueñas IM, García-Martínez T, Mauricio JC. Latest Trends in Industrial Vinegar Production and the Role of Acetic Acid Bacteria: Classification, Metabolism, and Applications-A Comprehensive Review. Foods 2023; 12:3705. [PMID: 37835358 PMCID: PMC10572879 DOI: 10.3390/foods12193705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Vinegar is one of the most appreciated fermented foods in European and Asian countries. In industry, its elaboration depends on numerous factors, including the nature of starter culture and raw material, as well as the production system and operational conditions. Furthermore, vinegar is obtained by the action of acetic acid bacteria (AAB) on an alcoholic medium in which ethanol is transformed into acetic acid. Besides the highlighted oxidative metabolism of AAB, their versatility and metabolic adaptability make them a taxonomic group with several biotechnological uses. Due to new and rapid advances in this field, this review attempts to approach the current state of knowledge by firstly discussing fundamental aspects related to industrial vinegar production and then exploring aspects related to AAB: classification, metabolism, and applications. Emphasis has been placed on an exhaustive taxonomic review considering the progressive increase in the number of new AAB species and genera, especially those with recognized biotechnological potential.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
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5
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Van de Voorde D, Díaz-Muñoz C, Hernandez CE, Weckx S, De Vuyst L. Yeast strains do have an impact on the production of cured cocoa beans, as assessed with Costa Rican Trinitario cocoa fermentation processes and chocolates thereof. Front Microbiol 2023; 14:1232323. [PMID: 37621398 PMCID: PMC10445768 DOI: 10.3389/fmicb.2023.1232323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023] Open
Abstract
The microbiological and metabolic outcomes of good cocoa fermentation practices can be standardized and influenced through the addition of starter culture mixtures composed of yeast and bacterial strains. The present study performed two spontaneous and 10 starter culture-initiated (SCI) cocoa fermentation processes (CFPs) in Costa Rica with local Trinitario cocoa. The yeast strains Saccharomyces cerevisiae IMDO 050523, Hanseniaspora opuntiae IMDO 020003, and Pichia kudriavzevii IMDO 060005 were used to compose starter culture mixtures in combination with the lactic acid bacterium strain Limosilactobacillus fermentum IMDO 0611222 and the acetic acid bacterium strain Acetobacter pasteurianus IMDO 0506386. The microbial community and metabolite dynamics of the cocoa pulp-bean mass fermentation, the metabolite dynamics of the drying cocoa beans, and the volatile organic compound (VOC) profiles of the chocolate production were assessed. An amplicon sequence variant approach based on full-length 16S rRNA gene sequencing instead of targeting the V4 region led to a highly accurate monitoring of the starter culture strains added, in particular the Liml. fermentum IMDO 0611222 strain. The latter strain always prevailed over the background lactic acid bacteria. A similar approach, based on the internal transcribed spacer (ITS1) region of the fungal rRNA transcribed unit, was used for yeast strain monitoring. The SCI CFPs evolved faster when compared to the spontaneous ones. Moreover, the yeast strains applied did have an impact. The presence of S. cerevisiae IMDO 050523 was necessary for successful fermentation of the cocoa pulp-bean mass, which was characterized by the production of higher alcohols and esters. In contrast, the inoculation of H. opuntiae IMDO 020003 as the sole yeast strain led to underfermentation and a poor VOC profile, mainly due to its low competitiveness. The P. kudriavzevii IMDO 060005 strain tested in the present study did not contribute to a richer VOC profile. Although differences in VOCs could be revealed in the cocoa liquors, no significant effect on the final chocolates could be obtained, mainly due to a great impact of cocoa liquor processing during chocolate-making. Hence, optimization of the starter culture mixture and cocoa liquor processing seem to be of pivotal importance.
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Affiliation(s)
- Dario Van de Voorde
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Carlos Eduardo Hernandez
- Laboratorio de Calidad e Innovación Agroalimentaria, Escuela de Ciencias Agrarias, Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | - 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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6
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Guzmán-Armenteros TM, Ramos-Guerrero LA, Guerra LS, Weckx S, Ruales J. Optimization of cacao beans fermentation by native species and electromagnetic fields. Heliyon 2023; 9:e15065. [PMID: 37077687 PMCID: PMC10106516 DOI: 10.1016/j.heliyon.2023.e15065] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/21/2023] Open
Abstract
Acid and bitter notes of the cocoa clone Cacao Castro Naranjal 51 (CCN 51) negatively affect the final quality of the chocolate. Thence, the fermentative process of cocoa beans using native species and electromagnetic fields (EMF) was carried out to evaluate the effect on the yield and quality of CCN 51 cocoa beans. The variables magnetic field density (D), exposure time (T), and inoculum concentration (IC) were optimized through response surface methodology to obtain two statistically validated second-order models, explaining 88.39% and 92.51% of the variability in the yield and quality of the beans, respectively. In the coordinate: 5 mT(D), 22.5 min (T), and 1.6% (CI), yield and bean quality improved to 110% and 120% above the control (without magnetic field). The metagenomic analysis showed that the changes in the microbial communities favored the aroma profile at low and intermediate field densities (5-42 mT) with high yields and floral, fruity, and nutty notes. Conversely, field densities (80 mT) were evaluated with low yields and undesirable notes of acidity and bitterness. The findings revealed that EMF effectively improves the yield and quality of CCN 51 cocoa beans with future applications in the development and quality of chocolate products.
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Affiliation(s)
- Tania María Guzmán-Armenteros
- Departamento de Ciencia de Alimentos y Biotecnología (DECAB), Escuela Politécnica Nacional (EPN), Quito, Ecuador
- Corresponding author.
| | | | - Luis Santiago Guerra
- Department of Pathology, Faculty of Medical Sciences, Universidad Central del Ecuador (UCE), Capus El Dorador, Quito, 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
- Departamento de Ciencia de Alimentos y Biotecnología (DECAB), Escuela Politécnica Nacional (EPN), Quito, Ecuador
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7
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New insights into the role of key microorganisms and wooden barrels during lambic beer fermentation and maturation. Int J Food Microbiol 2023; 394:110163. [PMID: 36913841 DOI: 10.1016/j.ijfoodmicro.2023.110163] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/08/2023]
Abstract
Belgian lambic beers are still produced through traditional craftsmanship. They rely on a spontaneous fermentation and maturation process that is entirely carried out in wooden barrels. The latter are used repetitively and may introduce some batch-to-batch variability. The present systematic and multiphasic study dealt with two parallel lambic beer productions carried out in nearly identical wooden barrels making use of the same cooled wort. It encompassed a microbiological and metabolomic approach. Further, a taxonomic classification and metagenome-assembled genome (MAG) investigation was based on shotgun metagenomics. These investigations provided new insights into the role of these wooden barrels and key microorganisms for this process. Indeed, besides their role in traditionality, the wooden barrels likely helped in establishing the stable microbial ecosystem of lambic beer fermentation and maturation by acting as an inoculation source of the necessary microorganisms, thereby minimizing batch-to-batch variations. They further provided a microaerobic environment, which aided in achieving the desirable succession of the different microbial communities for a successful lambic beer production process. Moreover, these conditions prevented excessive growth of acetic acid bacteria and, therefore, uncontrolled production of acetic acid and acetoin, which may lead to flavor deviations in lambic beer. Concerning the role of less studied key microorganisms for lambic beer production, it was shown that the Acetobacter lambici MAG contained several acid tolerance mechanisms toward the harsh environment of maturing lambic beer, whereas genes related to sucrose and maltose/maltooligosaccharide consumption and the glyoxylate shunt were absent. Further, a Pediococcus damnosus MAG possessed a gene encoding ferulic acid decarboxylase, possibly contributing to 4-vinyl compound production, as well as several genes, likely plasmid-based, related to hop resistance and biogenic amine production. Finally, contigs related to Dekkera bruxellensis and Brettanomyces custersianus did not possess genes involved in glycerol production, emphasizing the need for alternative external electron acceptors for redox balancing.
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Erazo Solorzano CY, Disca V, Muñoz-Redondo JM, Tuárez García DA, Sánchez-Parra M, Carrilo Zenteno MD, Moreno-Rojas JM, Rodríguez-Solana R. Effect of Drying Technique on the Volatile Content of Ecuadorian Bulk and Fine-Flavor Cocoa. Foods 2023; 12:foods12051065. [PMID: 36900586 PMCID: PMC10001102 DOI: 10.3390/foods12051065] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 03/06/2023] Open
Abstract
Cocoa (Theobroma cacao L.) is one of the most widely consumed edible seeds in the world affected by on-farm processing. This study investigated the effect of different drying techniques, namely oven drying (OD), sun drying (SD), and a modification of sun drying using black plastic sheeting (SBPD), on the volatile profile of fine-flavor and bulk cocoa varieties analyzed by HS-SPME-GC-MS. A total of sixty-four volatile compounds were identified in fresh and dried cocoa. As expected, the volatile profile was clearly modified after the drying step, showing strong differences among cocoa varieties, this factor and its interaction with the drying technique having greater influence according to the ANOVA simultaneous component analysis. A principal component analysis revealed a close relationship between the volatile content of bulk cocoa samples dried by the OD and SD techniques, whereas slight volatile modifications were perceived among fine-flavor samples dried using the three different techniques under study. Overall, the results provide the basis for the potential application of the simplest inexpensive SBPD technique in order to accelerate the drying process of sun drying and produce cocoa with similar (fine-flavor cocoa) or improved (bulk cocoa) aromatic quality to that formed using the traditional SD or the small-scale OD.
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Affiliation(s)
- Cyntia Yadira Erazo Solorzano
- Faculty of Industry and Production Sciences, State Technical University of Quevedo, Av. Walter Andrade, km 1.5 Via Santo Domingo, Quevedo 120301, Ecuador
| | - Vincenzo Disca
- Dipartimento di Scienze del Farmaco, Università degli Studi del Piemonte Orientale “A. Avogadro”, 28100 Novara, Italy
| | - José Manuel Muñoz-Redondo
- Department of Agrifood Industry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Diego Armando Tuárez García
- Faculty of Industry and Production Sciences, State Technical University of Quevedo, Av. Walter Andrade, km 1.5 Via Santo Domingo, Quevedo 120301, Ecuador
| | - Mónica Sánchez-Parra
- Department of Agrifood Industry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Manuel Danilo Carrilo Zenteno
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Tropical Pichilingue (EETP), Departamento de Manejo de Suelos y Aguas (DMSA), km 5 Via Quevedo–El Empalme, Cantón Mocache, Quevedo 120313, Ecuador
| | - José Manuel Moreno-Rojas
- Department of Agrifood Industry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda Menéndez Pidal s/n, 14004 Córdoba, Spain
- Foods for Health Group, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), 14004 Córdoba, Spain
- Correspondence: (J.M.M.-R.); (R.R.-S.)
| | - Raquel Rodríguez-Solana
- Department of Agrifood Industry and Food Quality, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda Menéndez Pidal s/n, 14004 Córdoba, Spain
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- Correspondence: (J.M.M.-R.); (R.R.-S.)
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9
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Herrera-Rocha F, Fernández-Niño M, Cala MP, Duitama J, Barrios AFG. Omics approaches to understand cocoa processing and chocolate flavor development: A review. Food Res Int 2023; 165:112555. [PMID: 36869541 DOI: 10.1016/j.foodres.2023.112555] [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: 09/13/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023]
Abstract
The global market of chocolate has increased worldwide during the last decade and is expected to reach a value of USD 200 billion by 2028. Chocolate is obtained from different varieties of Theobroma cacao L, a plant domesticated more than 4000 years ago in the Amazon rainforest. However, chocolate production is a complex process requiring extensive post-harvesting, mainly involving cocoa bean fermentation, drying, and roasting. These steps have a critical impact on chocolate quality. Standardizing and better understanding cocoa processing is, therefore, a current challenge to boost the global production of high-quality cocoa worldwide. This knowledge can also help cocoa producers improve cocoa processing management and obtain a better chocolate. Several recent studies have been conducted to dissect cocoa processing via omics analysis. A vast amount of data has been produced regarding omics studies of cocoa processing performed worldwide. This review systematically analyzes the current data on cocoa omics using data mining techniques and discusses opportunities and gaps for cocoa processing standardization from this data. First, we observed a recurrent report in metagenomics studies of species of the fungi genus Candida and Pichia as well as bacteria from the genus Lactobacillus, Acetobacter, and Bacillus. Second, our analyzes of the available metabolomics data showed clear differences in the identified metabolites in cocoa and chocolate from different geographical origin, cocoa type, and processing stage. Finally, our analysis of peptidomics data revealed characteristic patterns in the gathered data including higher diversity and lower size distribution of peptides in fine-flavor cocoa. In addition, we discuss the current challenges in cocoa omics research. More research is still required to fill gaps in central matter in chocolate production as starter cultures for cocoa fermentation, flavor evolution of cocoa, and the role of peptides in the development of specific flavor notes. We also offer the most comprehensive collection of multi-omics data in cocoa processing gathered from different research articles.
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Affiliation(s)
- Fabio Herrera-Rocha
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia
| | - Miguel Fernández-Niño
- Leibniz-Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, D-06120 Halle, Germany.
| | - Mónica P Cala
- MetCore - Metabolomics Core Facility, Vice-Presidency for Research, Universidad de los Andes, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá 111711, Colombia.
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10
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Barron AJ, Lesperance DNA, Doucette J, Calle S, Broderick NA. Microbiome derived acidity protects against microbial invasion in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523836. [PMID: 36711873 PMCID: PMC9882140 DOI: 10.1101/2023.01.12.523836] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbial invasions underlie host-microbe interactions that result in microbial pathogenesis and probiotic colonization. While these processes are of broad interest, there are still gaps in our understanding of the barriers to entry and how some microbes overcome them. In this study, we explore the effects of the microbiome on invasions of foreign microbes in Drosophila melanogaster. We demonstrate that gut microbes Lactiplantibacillus plantarum and Acetobacter tropicalis improve survival during invasion of a lethal gut pathogen and lead to a reduction in microbial burden. Using a novel multi-organism interactions assay, we report that L. plantarum inhibits the growth of three invasive Gram-negative bacteria, while A. tropicalis prevents this inhibition. A series of in vitro and in vivo experiments revealed that inhibition by L. plantarum is linked to its ability to acidify both internal and external environments, including culture media, fly food, and the gut itself, while A. tropicalis diminishes the inhibition by quenching acids. We propose that acid produced by the microbiome serves as an important gatekeeper to microbial invasions, as only microbes capable of tolerating acidic environments can colonize the host. The methods described herein will add to the growing breadth of tools to study microbe-microbe interactions in broad contexts.
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Affiliation(s)
- Alexander J. Barron
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218 U.S.A
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Danielle N. A. Lesperance
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218 U.S.A
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Jeremy Doucette
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Sthefany Calle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
| | - Nichole A. Broderick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218 U.S.A
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 U.S.A
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11
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Xia M, Zhang X, Xiao Y, Sheng Q, Tu L, Chen F, Yan Y, Zheng Y, Wang M. Interaction of acetic acid bacteria and lactic acid bacteria in multispecies solid-state fermentation of traditional Chinese cereal vinegar. Front Microbiol 2022; 13:964855. [PMID: 36246224 PMCID: PMC9557190 DOI: 10.3389/fmicb.2022.964855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The microbial community plays an important role on the solid-state fermentation (SSF) of Chinese cereal vinegar, where acetic acid bacteria (AAB) and lactic acid bacteria (LAB) are the dominant bacteria. In this study, the top-down (in situ) and bottom-up (in vitro) approaches were employed to reveal the interaction of AAB and LAB in SSF of Shanxi aged vinegar (SAV). The results of high-throughput sequencing indicates that Acetobacter pasteurianus and Lactobacillus helveticus are the predominant species of AAB and LAB, respectively, and they showed negative interrelationship during the fermentation. A. pasteurianus CGMCC 3089 and L. helveticus CGMCC 12062, both of which were isolated from fermentation of SAV, showed no nutritional competition when they were co-cultured in vitro. However, the growth and metabolism of L. helveticus CGMCC 12062 were inhibited during SSF due to the presence of A. pasteurianus CGMCC 3089, indicating an amensalism phenomenon between these two species. The transcriptomic results shows that there are 831 differentially expressed genes (|log2 (Fold Change)| > 1 and, p ≤ 0.05) in L. helveticus CGMCC 12062 under co-culture condition comparing to its mono-culture, which are mainly classified into Gene Ontology classification of molecular function, biological process, and cell composition. Of those 831 differentially expressed genes, 202 genes are up-regulated and 629 genes are down-regulated. The down-regulated genes were enriched in KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism. The transcriptomic results for A. pasteurianus CGMCC 3089 under co-culture condition reveals 529 differentially expressed genes with 393 up-regulated and 136 down-regulated, and the genes within KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism are up-regulated. Results indicate an amensalism relationship in co-culture of A. pasteurianus and L. helveticus. Therefore, this work gives a whole insight on the interaction between the predominant species in SSF of cereal vinegar from nutrient utilization, endogenous factors inhibition and the regulation of gene transcription.
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Affiliation(s)
- Menglei Xia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaofeng Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yun Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qing Sheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Linna Tu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
| | - Yufeng Yan
- Shanxi Zilin Vinegar Industry Co., Ltd., Shanxi Province Key Laboratory of Vinegar Fermentation Science and Engineering, Taiyuan, China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China,*Correspondence: Yu Zheng, Min Wang,
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China,*Correspondence: Yu Zheng, Min Wang,
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12
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Bouchez A, De Vuyst L. Acetic Acid Bacteria in Sour Beer Production: Friend or Foe? Front Microbiol 2022; 13:957167. [PMID: 35992674 PMCID: PMC9386357 DOI: 10.3389/fmicb.2022.957167] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Beer is the result of a multistep brewing process, including a fermentation step using in general one specific yeast strain. Bacterial presence during beer production (or presence in the beer itself) is considered as bad, since bacteria cause spoilage, produce off-flavors, and/or turbidity. Although most problems in the past related to lack of hygiene and/or cleaning, bacteria do still cause problems nowadays. Despite this negative imago, certain bacteria play an irreplaceable role during fermentation and/or maturation of more unique, funky, and especially refreshing sour beers. The term sour beers or sours is not restricted to one definition but covers a wide variety of beers produced via different techniques. This review proposes an uncluttered sour beer classification scheme, which includes all sour beer production techniques and pays special attention to the functional role of acetic acid bacteria. Whereas their oxidation of ethanol and lactate into acetic acid and acetoin usually spoils beer, including sour beers, organoleptically, a controlled growth leads to a desirable acidic flavor in sour beers, such as lambic-style, lambic-based, and red-brown acidic ales.
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13
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Yeasts as Producers of Flavor Precursors during Cocoa Bean Fermentation and Their Relevance as Starter Cultures: A Review. FERMENTATION 2022. [DOI: 10.3390/fermentation8070331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During the fermentation of cocoa beans, the yeasts produce volatile organic compounds (VOCs). Through reactions associated with amino acid metabolism, yeasts generate important aroma precursors as acetate esters and fatty acid ethyl esters are essential in developing fruity flavors and aromas in the final product (usually chocolate). In addition, some yeasts may have pectinolytic and antifungal activity, which is desirable in the post-harvest process of cocoa. The main yeast species in cocoa fermentation are Saccharomyces cerevisiae, Pichia kudriavzevii, and Hanseniaspora opuntiae. These produce higher alcohols and acetyl-CoA to make acetate–esters, compounds that produce floral and fruity notes. However, there are still controversies in scientific reports because some mention that there are no significant differences in the sensory characteristics of the final product. Others mention that the fermentation of cocoa by yeast has a significant influence on improving the sensory attributes of the final product. However, using yeasts as starter cultures for cocoa bean fermentation is recommended to homogenize sensory attributes such as notes and flavors in chocolate.
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14
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Román-Camacho JJ, Mauricio JC, Santos-Dueñas IM, García-Martínez T, García-García I. Unraveling the Role of Acetic Acid Bacteria Comparing Two Acetification Profiles From Natural Raw Materials: A Quantitative Approach in Komagataeibacter europaeus. Front Microbiol 2022; 13:840119. [PMID: 35572698 PMCID: PMC9100681 DOI: 10.3389/fmicb.2022.840119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
The industrial production of vinegar is carried out by the activity of a complex microbiota of acetic acid bacteria (AAB) working, mainly, within bioreactors providing a quite specific and hard environment. The “omics” sciences can facilitate the identification and characterization analyses of these microbial communities, most of which are difficult to cultivate by traditional methods, outside their natural medium. In this work, two acetification profiles coming from the same AAB starter culture but using two natural raw materials of different alcoholic origins (fine wine and craft beer), were characterized and compared and the emphasis of this study is the effect of these raw materials. For this purpose, the composition and natural behavior of the microbiota present throughout these profiles were analyzed by metaproteomics focusing, mainly, on the quantitative protein profile of Komagataeibacter europaeus. This species provided a protein fraction significantly higher (73.5%) than the others. A submerged culture system and semi-continuous operating mode were employed for the acetification profiles and liquid chromatography with tandem mass spectrometry (LC-MS/MS) for the protein analyses. The results showed that neither of two raw materials barely modified the microbiota composition of the profiles, however, they had an effect on the protein expression changes in different biological process. A molecular strategy in which K. europaeus would prevail over other species by taking advantage of the different features offered by each raw material has been suggested. First, by assimilating the excess of inner acetic acid through the TCA cycle and supplying biosynthetic precursors to replenish the cellular material losses; second, by a previous assimilation of the excess of available glucose, mainly in the beer medium, through the glycolysis and the pentose phosphate pathway (PPP); and third, by triggering membrane mechanisms dependent on proton motive force to detoxify the cell at the final moments of acetification. This study could complement the current knowledge of these bacteria as well as to expand the use of diverse raw materials and optimize operating conditions to obtain quality vinegars.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
- *Correspondence: Juan C. Mauricio,
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Institute of Nanochemistry (IUNAN), University of Córdoba, Córdoba, Spain
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Institute of Nanochemistry (IUNAN), University of Córdoba, Córdoba, Spain
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15
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Schulze D, Kohlstedt M, Becker J, Cahoreau E, Peyriga L, Makowka A, Hildebrandt S, Gutekunst K, Portais JC, Wittmann C. GC/MS-based 13C metabolic flux analysis resolves the parallel and cyclic photomixotrophic metabolism of Synechocystis sp. PCC 6803 and selected deletion mutants including the Entner-Doudoroff and phosphoketolase pathways. Microb Cell Fact 2022; 21:69. [PMID: 35459213 PMCID: PMC9034593 DOI: 10.1186/s12934-022-01790-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cyanobacteria receive huge interest as green catalysts. While exploiting energy from sunlight, they co-utilize sugar and CO2. This photomixotrophic mode enables fast growth and high cell densities, opening perspectives for sustainable biomanufacturing. The model cyanobacterium Synechocystis sp. PCC 6803 possesses a complex architecture of glycolytic routes for glucose breakdown that are intertwined with the CO2-fixing Calvin-Benson-Bassham (CBB) cycle. To date, the contribution of these pathways to photomixotrophic metabolism has remained unclear. RESULTS Here, we developed a comprehensive approach for 13C metabolic flux analysis of Synechocystis sp. PCC 6803 during steady state photomixotrophic growth. Under these conditions, the Entner-Doudoroff (ED) and phosphoketolase (PK) pathways were found inactive but the microbe used the phosphoglucoisomerase (PGI) (63.1%) and the oxidative pentose phosphate pathway (OPP) shunts (9.3%) to fuel the CBB cycle. Mutants that lacked the ED pathway, the PK pathway, or phosphofructokinases were not affected in growth under metabolic steady-state. An ED pathway-deficient mutant (Δeda) exhibited an enhanced CBB cycle flux and increased glycogen formation, while the OPP shunt was almost inactive (1.3%). Under fluctuating light, ∆eda showed a growth defect, different to wild type and the other deletion strains. CONCLUSIONS The developed approach, based on parallel 13C tracer studies with GC-MS analysis of amino acids, sugars, and sugar derivatives, optionally adding NMR data from amino acids, is valuable to study fluxes in photomixotrophic microbes to detail. In photomixotrophic cells, PGI and OPP form glycolytic shunts that merge at switch points and result in synergistic fueling of the CBB cycle for maximized CO2 fixation. However, redirected fluxes in an ED shunt-deficient mutant and the impossibility to delete this shunt in a GAPDH2 knockout mutant, indicate that either minor fluxes (below the resolution limit of 13C flux analysis) might exist that could provide catalytic amounts of regulatory intermediates or alternatively, that EDA possesses additional so far unknown functions. These ideas require further experiments.
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Affiliation(s)
- Dennis Schulze
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Edern Cahoreau
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, Inserm U1031, CNRS 5070, UPS, EFS, Toulouse, France
| | - Lindsay Peyriga
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, Inserm U1031, CNRS 5070, UPS, EFS, Toulouse, France
| | | | | | - Kirstin Gutekunst
- Institute of Botany, Christian-Albrecht University, Kiel, Germany.,Molecular Plant Physiology, Bioenergetics in Photoautotrophs, University of Kassel, Kassel, Germany
| | - Jean-Charles Portais
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics & Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, Inserm U1031, CNRS 5070, UPS, EFS, Toulouse, France
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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16
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Tangyu M, Fritz M, Ye L, Aragão Börner R, Morin-Rivron D, Campos-Giménez E, Bolten CJ, Bogicevic B, Wittmann C. Co-cultures of Propionibacterium freudenreichii and Bacillus amyloliquefaciens cooperatively upgrade sunflower seed milk to high levels of vitamin B 12 and multiple co-benefits. Microb Cell Fact 2022; 21:48. [PMID: 35346203 PMCID: PMC8959080 DOI: 10.1186/s12934-022-01773-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/02/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Sunflower seeds (Helianthus annuus) display an attractive source for the rapidly increasing market of plant-based human nutrition. Of particular interest are press cakes of the seeds, cheap residuals from sunflower oil manufacturing that offer attractive sustainability and economic benefits. Admittedly, sunflower seed milk, derived therefrom, suffers from limited nutritional value, undesired flavor, and the presence of indigestible sugars. Of specific relevance is the absence of vitamin B12. This vitamin is required for development and function of the central nervous system, healthy red blood cell formation, and DNA synthesis, and displays the most important micronutrient for vegans to be aware of. Here we evaluated the power of microbes to enrich sunflower seed milk nutritionally as well as in flavor. RESULTS Propionibacterium freudenreichii NCC 1177 showed highest vitamin B12 production in sunflower seed milk out of a range of food-grade propionibacteria. Its growth and B12 production capacity, however, were limited by a lack of accessible carbon sources and stimulants of B12 biosynthesis in the plant milk. This was overcome by co-cultivation with Bacillus amyloliquefaciens NCC 156, which supplied lactate, amino acids, and vitamin B7 for growth of NCC 1177 plus vitamins B2 and B3, potentially supporting vitamin B12 production by the Propionibacterium. After several rounds of optimization, co-fermentation of ultra-high-temperature pre-treated sunflower seed milk by the two microbes, enabled the production of 17 µg (100 g)-1 vitamin B12 within four days without any further supplementation. The fermented milk further revealed significantly enriched levels of L-lysine, the most limiting essential amino acid, vitamin B3, vitamin B6, improved protein quality and flavor, and largely eliminated indigestible sugars. CONCLUSION The fermented sunflower seed milk, obtained by using two food-grade microbes without further supplementation, displays an attractive, clean-label product with a high level of vitamin B12 and multiple co-benefits. The secret of the successfully upgraded plant milk lies in the multifunctional cooperation of the two microbes, which were combined, based on their genetic potential and metabolic signatures found in mono-culture fermentations. This design by knowledge approach appears valuable for future development of plant-based milk products.
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Affiliation(s)
- Muzi Tangyu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michel Fritz
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lijuan Ye
- Nestlé Research Center, Lausanne, Switzerland
| | | | | | | | - Christoph J. Bolten
- Nestlé Research Center, Lausanne, Switzerland
- Nestlé Product Technology Center Food, Singen, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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17
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Ibacache-Quiroga C, González-Pizarro K, Charifeh M, Canales C, Díaz-Viciedo R, Schmachtenberg O, Dinamarca MA. Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods 2022; 11:foods11070900. [PMID: 35406987 PMCID: PMC8997647 DOI: 10.3390/foods11070900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.
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Affiliation(s)
- Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
| | - Karoll González-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Mariam Charifeh
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Christian Canales
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción 4080871, Chile;
| | - Rodrigo Díaz-Viciedo
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
| | - Oliver Schmachtenberg
- Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2360102, Chile;
- Centro Interdisciplinario de Neurociencias (CINV), Universidad de Valparaíso, Valparaíso 2381850, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
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18
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Song J, Wang J, Wang X, Zhao H, Hu T, Feng Z, Lei Z, Li W, Zheng Y, Wang M. Improving the Acetic Acid Fermentation of Acetobacter pasteurianus by Enhancing the Energy Metabolism. Front Bioeng Biotechnol 2022; 10:815614. [PMID: 35350179 PMCID: PMC8957916 DOI: 10.3389/fbioe.2022.815614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Energy metabolism is important for cell growth and tolerance against environment stress. In acetic acid fermentation by Acetobacter pasteurianus, the correlation coefficients of acid production rate with energy charge and ATP content were 0.9981 and 0.9826, respectively. The main energy metabolism pathway, including glycolysis pathway, TCA cycle, ethanol oxidation, pentose phosphate pathway, and ATP production, was constructed by transcriptome analysis. The effects of fermentation conditions, including dissolved oxygen, initial acetic acid concentration, and total concentration, on acetic acid fermentation and energy metabolism of A. pasteurianus were analyzed by using the RT-PCR method. The results showed the high energy charge inhibited glucose catabolism, and associated with the high ethanol oxidation rate. Consequently, a virtuous circle of increased ethanol oxidation, increased energy generation, and acetic acid tolerance was important for improving acetic acid fermentation.
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Affiliation(s)
- Jia Song
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xinyu Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Tao Hu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhiwei Feng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhi Lei
- Tian Di No. 1 Beverage Inc., Jiangmen, China
| | - Weizhao Li
- Tian Di No. 1 Beverage Inc., Jiangmen, China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Yu Zheng, ; Min Wang,
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Yu Zheng, ; Min Wang,
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19
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Ndoye B, Shafiei R, Sanaei NS, Cleenwerck I, Somda MK, Dicko MH, Tounkara LS, Guiro AT, Delvigne F, Thonart P. Acetobacter senegalensis Isolated from Mango Fruits: Its Polyphasic Characterization and Adaptation to Protect against Stressors in the Industrial Production of Vinegar: A Review. J Appl Microbiol 2022; 132:4130-4149. [PMID: 35182093 DOI: 10.1111/jam.15495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/03/2022] [Accepted: 02/12/2022] [Indexed: 11/26/2022]
Abstract
It has been more than a decade since Acetobacter senegalensis was isolated, identified, and described as a thermotolerant strain of acetic acid bacteria. It was isolated from mango fruits in Senegal and used for industrial vinegar production in developing countries, mainly in sub-Saharan Africa. The strain was tested during several spirit vinegar fermentation processes at relatively high temperatures in accordance with African acclimation. The upstream fermentation process had significant stress factors, which are highlighted in this review so that the fermentation process can be better controlled. Due to its high industrial potential, this strain was extensively investigated by diverse industrial microbiologists worldwide; they concentrated on its microbiological, physiological, and genomic features. A research group based in Belgium proposed an important project for the investigation of the whole-genome sequence of A. senegalensis. It would use a 454-pyrosequencing technique to determine and corroborate features that could give this strain significant diverse bioindustrial applications. For instance, its application in cocoa bean fermentation has made it a more suitable acetic acid bacterium for the making of chocolate than Acetobacter pasteurianus. Therefore, in this paper, we present a review that summarizes the current research on A. senegalensis at its microbial and genomic levels and also its specific bioindustrial applications, which can provide economic opportunities for African agribusiness.
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Affiliation(s)
- Bassirou Ndoye
- University of Sine Saloum El Hadji Ibrahima Niasse (USSEIN), BP, Kaolack, Senegal.,Walloon Centre of Industrial Biology, Gembloux Agro-Bio Tech, University of Liège, Belgique
| | - Rasoul Shafiei
- Department of Cell, Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
| | - Nastaran Shah Sanaei
- Department of Cell, Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Marius K Somda
- Biochemistry, Biotechnology, Food Technology and Nutrition Laboratory, University Pr Joseph Ki Zerbo, PO, Ouagadougou, Burkina Faso
| | - Mamoudou Hama Dicko
- Biochemistry, Biotechnology, Food Technology and Nutrition Laboratory, University Pr Joseph Ki Zerbo, PO, Ouagadougou, Burkina Faso
| | | | - Amadou Tidiane Guiro
- University of Sine Saloum El Hadji Ibrahima Niasse (USSEIN), BP, Kaolack, Senegal
| | - Frank Delvigne
- Walloon Centre of Industrial Biology, Gembloux Agro-Bio Tech, University of Liège, Belgique
| | - Philippe Thonart
- Walloon Centre of Industrial Biology, Gembloux Agro-Bio Tech, University of Liège, Belgique
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20
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Abstract
Individuals are constantly exposed to microbial organisms that may or may not colonize their gut microbiome, and newborn individuals assemble their microbiomes through a number of these acquisition events. Since microbiome composition has been shown to influence host physiology, a mechanistic understanding of community assembly has potentially therapeutic applications. In this paper we study microbiome acquisition in a highly controlled setting using germ-free fruit flies inoculated with specific bacterial species at known abundances. Our approach revealed that acquisition events are stochastic, and the colonization odds of different species in different contexts encode ecological information about interactions. These findings have consequences for microbiome-based therapies like fecal microbiota transplantation that attempt to modify a person’s gut microbiome by deliberately introducing foreign microbes. Observational studies reveal substantial variability in microbiome composition across individuals. Targeted studies in gnotobiotic animals underscore this variability by showing that some bacterial strains colonize deterministically, while others colonize stochastically. While some of this variability can be explained by external factors like environmental, dietary, and genetic differences between individuals, in this paper we show that for the model organism Drosophila melanogaster, interactions between bacteria can affect the microbiome assembly process, contributing to a baseline level of microbiome variability even among isogenic organisms that are identically reared, housed, and fed. In germ-free flies fed known combinations of bacterial species, we find that some species colonize more frequently than others even when fed at the same high concentration. We develop an ecological technique that infers the presence of interactions between bacterial species based on their colonization odds in different contexts, requiring only presence/absence data from two-species experiments. We use a progressive sequence of probabilistic models, in which the colonization of each bacterial species is treated as an independent stochastic process, to reproduce the empirical distributions of colonization outcomes across experiments. We find that incorporating context-dependent interactions substantially improves the performance of the models. Stochastic, context-dependent microbiome assembly underlies clinical therapies like fecal microbiota transplantation and probiotic administration and should inform the design of synthetic fecal transplants and dosing regimes.
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21
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Herrera-Rocha F, Cala MP, Aguirre Mejía JL, Rodríguez-López CM, Chica MJ, Olarte HH, Fernández-Niño M, Gonzalez Barrios AF. Dissecting fine-flavor cocoa bean fermentation through metabolomics analysis to break down the current metabolic paradigm. Sci Rep 2021; 11:21904. [PMID: 34754023 PMCID: PMC8578666 DOI: 10.1038/s41598-021-01427-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/14/2021] [Indexed: 12/05/2022] Open
Abstract
Cocoa fermentation plays a crucial role in producing flavor and bioactive compounds of high demand for food and nutraceutical industries. Such fermentations are frequently described as a succession of three main groups of microorganisms (i.e., yeast, lactic acid, and acetic acid bacteria), each producing a relevant metabolite (i.e., ethanol, lactic acid, and acetic acid). Nevertheless, this view of fermentation overlooks two critical observations: the role of minor groups of microorganisms to produce valuable compounds and the influence of environmental factors (other than oxygen availability) on their biosynthesis. Dissecting the metabolome during spontaneous cocoa fermentation is a current challenge for the rational design of controlled fermentations. This study evaluates variations in the metabolic fingerprint during spontaneous fermentation of fine flavor cocoa through a multiplatform metabolomics approach. Our data suggested the presence of two phases of differential metabolic activity that correlate with the observed variations on temperature over fermentations: an exothermic and an isothermic phase. We observed a continuous increase in temperature from day 0 to day 4 of fermentation and a significant variation in flavonoids and peptides between phases. While the second phase, from day four on, was characterized for lower metabolic activity, concomitant with small upward and downward fluctuations in temperature. Our work is the first to reveal two phases of metabolic activity concomitant with two temperature phases during spontaneous cocoa fermentation. Here, we proposed a new paradigm of cocoa fermentation that considers the changes in the global metabolic activity over fermentation, thus changing the current paradigm based only on three main groups of microorganism and their primary metabolic products.
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Affiliation(s)
- Fabio Herrera-Rocha
- grid.7247.60000000419370714Grupo de Diseño de Productos Y Procesos (GDPP), Departamento de Ingeniería Química Y de Alimentos, Universidad de los Andes, 111711 Bogotá, Colombia
| | - Mónica P. Cala
- grid.7247.60000000419370714MetCore - Metabolomics Core Facility. Vice-Presidency for Research, Universidad de los Andes, Bogotá, Colombia
| | | | | | | | | | - Miguel Fernández-Niño
- Grupo de Diseño de Productos Y Procesos (GDPP), Departamento de Ingeniería Química Y de Alimentos, Universidad de los Andes, 111711, Bogotá, Colombia. .,Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany.
| | - Andrés Fernando Gonzalez Barrios
- Grupo de Diseño de Productos Y Procesos (GDPP), Departamento de Ingeniería Química Y de Alimentos, Universidad de los Andes, 111711, Bogotá, Colombia.
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22
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Cielecka I, Ryngajłło M, Maniukiewicz W, Bielecki S. Response surface methodology-based improvement of the yield and differentiation of properties of bacterial cellulose by metabolic enhancers. Int J Biol Macromol 2021; 187:584-593. [PMID: 34324907 DOI: 10.1016/j.ijbiomac.2021.07.147] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/30/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
This study aims to examine the effect of ethanol and lactic acid on the production of bacterial cellulose, and determine the optimal composition of a co-supplemented culture using response surface methodology. Both ethanol and lactic acid, when added separately or jointly, affected the yield and properties of the biomaterial. Optimization resulted in an increase of 470% in the yield, compared to the Schramm-Hestrin medium. Culture growth profiles, substrate consumption and by-products generation, were examined. The growth rate was increased for cultures supplemented with lactic acid and both lactic acid and ethanol, while the production of gluconic acid was diminished for all modified cultures. The properties of BNC, such as the structure, crystallinity, water holding capacity and tensile strength, were also determined. BNC produced in optimal conditions is more porous and characterized by wider fibers. Despite a decrease in crystallinity, by the addition of ethanol, lactic acid and both additives, the ratio of cellulose Iα was almost unchanged. The stress, strain, young modulus and toughness were improved 2.8-4.2 times, 1-1.9 times, 2.4-3.5 times and 2.5-6.8 times, respectively. The new approach to improving BNC yields and properties presented here could contribute to more economical production and wider application of this biopolymer.
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Affiliation(s)
- Izabela Cielecka
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland.
| | - Małgorzata Ryngajłło
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland.
| | - Waldemar Maniukiewicz
- Institute of General and Ecological Chemistry, Lodz University of Technology, Łódź, Poland.
| | - Stanisław Bielecki
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Łódź, Poland.
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23
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Influence of Taxonomic and Functional Content of Microbial Communities on the Quality of Fermented Cocoa Pulp-Bean Mass. Appl Environ Microbiol 2021; 87:e0042521. [PMID: 33990301 DOI: 10.1128/aem.00425-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial metabolism drives changes in the physicochemical properties and, consequently, the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function, and metabolic potential of microbial communities' present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physicochemical, microbiological, quality, and sensory analyses to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, the fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavors. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin, and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri, and Acetobacter pasteurianus were the most prevalent. Fermentation time and roasting are the most important determinants of cocoa quality, while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is urgently needed for developing fermentation protocols according to regions, countries, and cocoa varieties to guarantee safety and desirable flavor development. IMPORTANCE Monitoring the composition, structure, functionalities, and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.
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24
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Viesser JA, de Melo Pereira GV, de Carvalho Neto DP, Favero GR, de Carvalho JC, Goés-Neto A, Rogez H, Soccol CR. Global cocoa fermentation microbiome: revealing new taxa and microbial functions by next generation sequencing technologies. World J Microbiol Biotechnol 2021; 37:118. [PMID: 34131809 DOI: 10.1007/s11274-021-03079-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 12/01/2022]
Abstract
This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.
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Affiliation(s)
- Jéssica A Viesser
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil.
| | | | - Gabriel R Favero
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Júlio Cesar de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | - Aristóteles Goés-Neto
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Hervé Rogez
- Centre for Valorisation of Amazonian Bioactive Compounds (CVACBA), Federal University of Pará, Belém, PA, Brazil
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil
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25
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Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis. Sci Rep 2021; 11:8638. [PMID: 33883642 PMCID: PMC8060343 DOI: 10.1038/s41598-021-88048-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/04/2021] [Indexed: 01/12/2023] Open
Abstract
The global demand for fine-flavour cocoa has increased worldwide during the last years. Fine-flavour cocoa offers exceptional quality and unique fruity and floral flavour attributes of high demand by the world's elite chocolatiers. Several studies have highlighted the relevance of cocoa fermentation to produce such attributes. Nevertheless, little is known regarding the microbial interactions and biochemistry that lead to the production of these attributes on farms of industrial relevance, where traditional fermentation methods have been pre-standardized and scaled up. In this study, we have used metagenomic approaches to dissect on-farm industrial fermentations of fine-flavour cocoa. Our results revealed the presence of a shared core of nine dominant microorganisms (i.e. Limosilactobacillus fermentum, Saccharomyces cerevisiae, Pestalotiopsis rhododendri, Acetobacter aceti group, Bacillus subtilis group, Weissella ghanensis group, Lactobacillus_uc, Malassezia restricta and Malassezia globosa) between two farms located at completely different agro-ecological zones. Moreover, a community metabolic model was reconstructed and proposed as a tool to further elucidate the interactions among microorganisms and flavour biochemistry. Our work is the first to reveal a core of microorganisms shared among industrial farms, which is an essential step to process engineering aimed to design starter cultures, reducing fermentation times, and controlling the expression of undesirable phenotypes.
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26
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Abstract
Acetic acid bacteria are involved in many food and beverage fermentation processes. They play an important role in cocoa bean fermentation through their acetic acid production. They initiate the development of some of the flavor precursors that are necessary for the organoleptic quality of cocoa, and for the beans’ color. The development of starter cultures with local strains would enable the preservation of the microbial biodiversity of each country in cocoa-producing areas, and would also control the fermentation. This approach could avoid the standardization of cocoa bean fermentation in the producing countries. One hundred and thirty acetic acid bacteria were isolated from three different cocoa-producing countries, and were identified based on their 16S rRNA gene sequence. The predominate strains were grown in a cocoa pulp simulation medium (CPSM-AAB) in order to compare their physiological traits regarding their specific growth rate, ethanol and lactic acid consumption, acetic acid production, and relative preferences of carbon sources. Finally, the intraspecific diversity of the strains was then assessed through the analysis of their genomic polymorphism by (GTG)5-PCR fingerprinting. Our results showed that Acetobacter pasteurianus was the most recovered species in all of the origins, with 86 isolates out of 130 cultures. A great similarity was observed between the strains according to their physiological characterization and genomic polymorphisms. However, the multi-parametric clustering results in the different groups highlighted some differences in their basic metabolism, such as their efficiency in converting carbon substrates to acetate, and their relative affinity to lactic acid and ethanol. The A. pasteurianus strains showed different behaviors regarding their ability to oxidize ethanol and lactic acid into acetic acid, and in their relative preference for each substrate. The impact of these behaviors on the cocoa quality should be investigated, and should be considered as a criterion for the selection of acetic acid bacteria starters.
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27
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De Vuyst L, Leroy F. Functional role of yeasts, lactic acid bacteria and acetic acid bacteria in cocoa fermentation processes. FEMS Microbiol Rev 2021; 44:432-453. [PMID: 32420601 DOI: 10.1093/femsre/fuaa014] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/16/2020] [Indexed: 01/07/2023] Open
Abstract
Cured cocoa beans are obtained through a post-harvest, batchwise process of fermentation and drying carried out on farms in the equatorial zone. Fermentation of cocoa pulp-bean mass is performed mainly in heaps or boxes. It is made possible by a succession of yeast, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) activities. Yeasts ferment the glucose of the cocoa pulp into ethanol, perform pectinolysis and produce flavour compounds, such as (higher) alcohols, aldehydes, organic acids and esters. LAB ferment the glucose, fructose and citric acid of the cocoa pulp into lactic acid, acetic acid, mannitol and pyruvate, generate a microbiologically stable fermentation environment, provide lactate as carbon source for the indispensable growth of AAB, and contribute to the cocoa and chocolate flavours by the production of sugar alcohols, organic acids, (higher) alcohols and aldehydes. AAB oxidize the ethanol into acetic acid, which penetrates into the bean cotyledons to prevent seed germination. Destruction of the subcellular seed structure in turn initiates enzymatic and non-enzymatic conversions inside the cocoa beans, which provides the necessary colour and flavour precursor molecules (hydrophilic peptides, hydrophobic amino acids and reducing sugars) for later roasting of the cured cocoa beans, the first step of the chocolate-making.
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Affiliation(s)
- Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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28
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Blasche S, Kim Y, Mars RAT, Machado D, Maansson M, Kafkia E, Milanese A, Zeller G, Teusink B, Nielsen J, Benes V, Neves R, Sauer U, Patil KR. Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nat Microbiol 2021; 6:196-208. [PMID: 33398099 PMCID: PMC7610452 DOI: 10.1038/s41564-020-00816-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/19/2020] [Indexed: 01/28/2023]
Abstract
Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures or synthetic assemblies. Here, we show how kefir, a natural milk-fermenting community of prokaryotes (predominantly lactic and acetic acid bacteria) and yeasts (family Saccharomycetaceae), realizes stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microorganisms) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open the niche for the followers by making available metabolites such as amino acids and lactate. Through metabolomics, transcriptomics and large-scale mapping of inter-species interactions, we show how microorganisms poorly suited for milk survive in-and even dominate-the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.
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Affiliation(s)
- Sonja Blasche
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yongkyu Kim
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ruben A T Mars
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Machado
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Eleni Kafkia
- European Molecular Biology Laboratory, Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Georg Zeller
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bas Teusink
- Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jens Nielsen
- Chalmers University of Technology, Gothenburg, Sweden
| | - Vladimir Benes
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory, Heidelberg, Germany.
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK.
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29
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Metabolic network of ammonium in cereal vinegar solid-state fermentation and its response to acid stress. Food Microbiol 2020; 95:103684. [PMID: 33397616 DOI: 10.1016/j.fm.2020.103684] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/28/2022]
Abstract
Shanxi aged vinegar (SAV), a Chinese traditional vinegar, is produced by various microorganisms. Ammonium is an important nitrogen source for microorganisms and a key intermediate for the utilization of non-ammonium nitrogen sources. In this work, an ammonium metabolic network during SAV fermentation was constructed through the meta-transcriptomic analysis of in situ samples, and the potential mechanism of acid affecting ammonium metabolism was revealed. The results showed that ammonium was enriched as the acidity increased. Meta-transcriptomic analysis showed that the conversion of glutamine to ammonia is the key pathway of ammonium metabolism in vinegar and that Lactobacillus and Acetobacter are the dominant genera. The construction and analysis of the metabolic network showed that amino acid metabolism, nucleic acid metabolism, pentose phosphate pathway and energy metabolism were enhanced to resist acid damage to the intracellular environment and cell structures. The enhancement of nitrogen assimilation provides nitrogen for metabolic pathways that resist acid cytotoxicity. In addition, the concentration gradient allows ammonium to diffuse outside the cell, which causes ammonium to accumulate during fermentation.
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30
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Fang CJ, You HC, Huang ZL, Hsu CL, Tsai CF, Lin YT, Kao YM, Tseng SH, Wang DY, Su NW. Simultaneous Analysis of the Stable Carbon Isotope Ratios of Acetoin and Acetic Acid by GC-C-IRMS for Adulteration Detection in Brewed Rice Vinegar Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14252-14260. [PMID: 33215927 DOI: 10.1021/acs.jafc.0c05674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, we developed a method to simultaneously measure the stable carbon isotope ratio for acetic acid (δ 13Cacetic acid) and acetoin (δ13Cacetoin) in rice vinegar by gas chromatography-combustion-isotope ratio mass spectrometry. The method showed good precision and accuracy. With this method, data from 16 brewed rice vinegars and 10 acetic acid samples were used to evaluate the feasibility of adulteration detection. On the basis that all δ13Cacetoin values of brewed rice vinegars are nearly constant, a characteristic pattern of the stable carbon isotope in rice vinegar was built with the 95% confidence intervals for δ13Cacetic acid (-26.97 to -25.38‰), δ13Cacetoin (-28.14 to -27.09‰), and Δδ13C (0.61 to 2.27‰). An adulteration detection curve of Δδ13C was proposed based on the results of vinegar and acetic acid samples and confirmed by vinegar spiked with different amounts of acetic acid. This method could be useful in estimating the blending ratio of adulterated rice vinegar products. Products containing more than 10% of synthetic acetic acid could be possibly identified.
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Affiliation(s)
- Chun-Jen Fang
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road., Da'an District, Taipei City 106216, Taiwan
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Hsin-Cheng You
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Zih-Ling Huang
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Che-Lun Hsu
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Chia-Fen Tsai
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Ya-Tze Lin
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Ya-Min Kao
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Su-Hsiang Tseng
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Der-Yuan Wang
- Taiwan Food and Drug Administration, 161-2 Kunyang Street, Nangang District, Taipei City 115209, Taiwan
| | - Nan-Wei Su
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road., Da'an District, Taipei City 106216, Taiwan
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31
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Monitoring microbial succession and metabolic activity during manual and mechanical solid-state fermentation of Chinese cereal vinegar. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109868] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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McMullen JG, Peters-Schulze G, Cai J, Patterson AD, Douglas AE. How gut microbiome interactions affect nutritional traits of Drosophila melanogaster. ACTA ACUST UNITED AC 2020; 223:223/19/jeb227843. [PMID: 33051361 DOI: 10.1242/jeb.227843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022]
Abstract
Most research on the impact of the gut microbiome on animal nutrition is designed to identify the effects of single microbial taxa and single metabolites of microbial origin, without considering the potentially complex network of interactions among co-occurring microorganisms. Here, we investigated how different microbial associations and their fermentation products affect host nutrition, using Drosophila melanogaster colonized with three gut microorganisms (the bacteria Acetobacter fabarum and Lactobacillus brevis, and the yeast Hanseniaspora uvarum) in all seven possible combinations. Some microbial effects on host traits could be attributed to single taxa (e.g. yeast-mediated reduction of insect development time), while other effects were sex specific and driven by among-microbe interactions (e.g. male lipid content determined by interactions between the yeast and both bacteria). Parallel analysis of nutritional indices of microbe-free flies administered different microbial fermentation products (acetic acid, acetoin, ethanol and lactic acid) revealed a single consistent effect: that the lipid content of both male and female flies is reduced by acetic acid. This effect was recapitulated in male flies colonized with both yeast and A. fabarum, but not for any microbial treatment in females or males with other microbial complements. These data suggest that the effect of microbial fermentation products on host nutritional status is strongly context dependent, with respect to both the combination of associated microorganisms and host sex. Taken together, our findings demonstrate that among-microbe interactions can play a critically important role in determining the physiological outcome of host-microbiome interactions in Drosophila and, likely, in other animal hosts.
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Affiliation(s)
- John G McMullen
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | | | - Jingwei Cai
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA .,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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33
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Henriques SF, Dhakan DB, Serra L, Francisco AP, Carvalho-Santos Z, Baltazar C, Elias AP, Anjos M, Zhang T, Maddocks ODK, Ribeiro C. Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour. Nat Commun 2020; 11:4236. [PMID: 32843654 PMCID: PMC7447780 DOI: 10.1038/s41467-020-18049-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
The impact of commensal bacteria on the host arises from complex microbial-diet-host interactions. Mapping metabolic interactions in gut microbial communities is therefore key to understand how the microbiome influences the host. Here we use an interdisciplinary approach including isotope-resolved metabolomics to show that in Drosophila melanogaster, Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp) a syntrophic relationship is established to overcome detrimental host diets and identify Ap as the bacterium altering the host's feeding decisions. Specifically, we show that Ap uses the lactate produced by Lp to supply amino acids that are essential to Lp, allowing it to grow in imbalanced diets. Lactate is also necessary and sufficient for Ap to alter the fly's protein appetite. Our data show that gut bacterial communities use metabolic interactions to become resilient to detrimental host diets. These interactions also ensure the constant flow of metabolites used by the microbiome to alter reproduction and host behaviour.
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Affiliation(s)
- Sílvia F Henriques
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Darshan B Dhakan
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Lúcia Serra
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Ana Patrícia Francisco
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Zita Carvalho-Santos
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Célia Baltazar
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Ana Paula Elias
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Margarida Anjos
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Tong Zhang
- University of Glasgow Institute of Cancer Sciences, Switchback Road, Glasgow, G61 1QH, UK
| | - Oliver D K Maddocks
- University of Glasgow Institute of Cancer Sciences, Switchback Road, Glasgow, G61 1QH, UK
| | - Carlos Ribeiro
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal.
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Fang Y, Li R, Chu Z, Zhu K, Gu F, Zhang Y. Chemical and flavor profile changes of cocoa beans ( Theobroma cacao L.) during primary fermentation. Food Sci Nutr 2020; 8:4121-4133. [PMID: 32884693 PMCID: PMC7455942 DOI: 10.1002/fsn3.1701] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/23/2020] [Accepted: 05/14/2020] [Indexed: 11/11/2022] Open
Abstract
This survey reports for the first time the changed of quality of fermented cocoa (Theobroma cacao L.) beans. The quality evaluation and simultaneous detection of amino acids, flavor, procyanidin, color, fat, protein, antioxidant activity, and enthalpy were obtained for different fermentation stages of cocoa beans. The results showed that total essential amino acids contents ranged from 2.64 g/100 g to 3.68 g/100 g. A total of 88 compounds identified at the end of the fermentation belonged to alcohols, acids, esters, ketones, pyrazines, aldehydes, and terpenoids. One of the chemical groups that were present in highest abundance in the consummation treatments was acids, representing 56.04% of the total extracted area, followed by alcohols (22.95%) and ketones (9.40%). The colors of the beans in different fermentation stages were different, from deep purple to deep red-brown. Fermented cocoa beans were shown to be 53.45% and 13.51% bean butter and protein content, respectively. The value of denaturation enthalpy (ΔH) ranged from 30.4 (J/g) to 43.38 (J/g). The 3-day fermented sample had the highest ΔH (43.38 J/g). When the fermentation process was complete, the procyanidin concentration of the beans decreased, with the final yield of procyanidin at 6.2%. During fermentation, the antioxidant capacity of beans gradually reduced. The fermenting of cocoa beans had a significant effect on the quality formation. The findings of this study constitute a basis for further investigations on the quality formation of cocoa during fermentation.
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Affiliation(s)
- Yiming Fang
- Spice and Beverage Research InstituteChinese Academy of Tropical Agricultural SciencesWanningChina
- National Center of Important Tropical Crops Engineering and Technology ResearchWanningChina
- Hainan Provincial Engineering Research Center of Tropical Spice and Beverage CropsWanningChina
| | - Rui Li
- Spice and Beverage Research InstituteChinese Academy of Tropical Agricultural SciencesWanningChina
- National Center of Important Tropical Crops Engineering and Technology ResearchWanningChina
- Hainan Provincial Engineering Research Center of Tropical Spice and Beverage CropsWanningChina
| | - Zhong Chu
- Spice and Beverage Research InstituteChinese Academy of Tropical Agricultural SciencesWanningChina
- National Center of Important Tropical Crops Engineering and Technology ResearchWanningChina
- Hainan Provincial Engineering Research Center of Tropical Spice and Beverage CropsWanningChina
| | - Kexue Zhu
- Spice and Beverage Research InstituteChinese Academy of Tropical Agricultural SciencesWanningChina
- National Center of Important Tropical Crops Engineering and Technology ResearchWanningChina
- Hainan Provincial Engineering Research Center of Tropical Spice and Beverage CropsWanningChina
| | - Fenglin Gu
- Spice and Beverage Research InstituteChinese Academy of Tropical Agricultural SciencesWanningChina
- National Center of Important Tropical Crops Engineering and Technology ResearchWanningChina
- Hainan Provincial Engineering Research Center of Tropical Spice and Beverage CropsWanningChina
| | - Yanjun Zhang
- Spice and Beverage Research InstituteChinese Academy of Tropical Agricultural SciencesWanningChina
- National Center of Important Tropical Crops Engineering and Technology ResearchWanningChina
- Hainan Provincial Engineering Research Center of Tropical Spice and Beverage CropsWanningChina
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Biological insights into non-model microbial hosts through stable-isotope metabolic flux analysis. Curr Opin Biotechnol 2020; 64:32-38. [DOI: 10.1016/j.copbio.2019.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/16/2022]
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Pelicaen R, Gonze D, De Vuyst L, Weckx S. Genome-scale metabolic modeling of Acetobacter pasteurianus 386B reveals its metabolic adaptation to cocoa fermentation conditions. Food Microbiol 2020; 92:103597. [PMID: 32950138 DOI: 10.1016/j.fm.2020.103597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Abstract
Acetobacter pasteurianus 386B has been selected as a candidate functional starter culture to better control the cocoa fermentation process. Previously, its genome has been sequenced and a genome-scale metabolic model (GEM) has been reconstructed. To understand its metabolic adaptation to cocoa fermentation conditions, different flux balance analysis (FBA) simulations were performed and compared with experimental data. In particular, metabolic flux distributions were simulated for two phases that characterize the growth of A. pasteurianus 386B under cocoa fermentation conditions, predicting a switch in respiratory chain usage in between these phases. The possible influence on the resulting energy production was shown using a reduced version of the GEM. FBA simulations revealed the importance of the compartmentalization of the ethanol oxidation reactions, namely in the periplasm or in the cytoplasm, and highlighted the potential role of ethanol as a source of carbon, energy, and NADPH. Regarding the latter, the physiological function of a proton-translocating NAD(P)+ transhydrogenase was further investigated in silico. This study revealed the potential of using a GEM to simulate the metabolism of A. pasteurianus 386B, and may provide a general framework toward a better physiological understanding of functional starter cultures in food fermentation processes.
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Affiliation(s)
- Rudy Pelicaen
- 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; ULB-VUB Interuniversity Institute of Bioinformatics in Brussels [(IB)(2)], Campus Plaine, CP 263, B-1050, Brussels, Belgium
| | - Didier Gonze
- Unité de Chronobiologie Théorique, Service de Chimie Physique, Faculté des Sciences, Université libre de Bruxelles (ULB), Campus Plaine, CP 231, Boulevard du Triomphe, B-1050, Brussels, Belgium; ULB-VUB Interuniversity Institute of Bioinformatics in Brussels [(IB)(2)], Campus Plaine, CP 263, B-1050, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium
| | - 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; ULB-VUB Interuniversity Institute of Bioinformatics in Brussels [(IB)(2)], Campus Plaine, CP 263, B-1050, Brussels, Belgium.
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De Roos J, Verce M, Weckx S, De Vuyst L. Temporal Shotgun Metagenomics Revealed the Potential Metabolic Capabilities of Specific Microorganisms During Lambic Beer Production. Front Microbiol 2020; 11:1692. [PMID: 32765478 PMCID: PMC7380088 DOI: 10.3389/fmicb.2020.01692] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/29/2020] [Indexed: 01/03/2023] Open
Abstract
Lambic beer production processes are characterized by a temporal succession of well-adapted microbial species. Temporal metagenomic analysis of a Belgian, traditional, lambic beer production process, which was examined microbiologically and metabolomically before, confirmed that the microbial diversity is limited. Moreover, it allowed to link the consumption and production of certain compounds to specific microbial groups or species. Fermentation characteristics, such as the conversion of malic acid into lactic acid and acetoin production, were retrieved and could be attributed to specific microorganisms, namely Pediococcus damnosus and Acetobacter species, respectively. Traits previously ascribed to brewery-specific Dekkera bruxellensis strains were confirmed during the lambic beer production process examined multiphasically; in particular, the higher production of 4-ethylguaiacol compared to 4-ethylphenol was further shown by mass spectrometric analysis. Moreover, the absence of phenolic acid decarboxylase in Brettanomyces custersianus was shown culture-independently and could explain its late occurrence during the maturation phase. Furthermore, the potential of maltooligosaccharide degradation could be ascribed metagenomically to not only Brettanomyces species but also Saccharomyces kudriavzevii, possibly explaining their degradation early in the lambic beer production process. Also, acetic acid bacteria (AAB) seemed to be able to consume maltooligosaccharides via their conversion into trehalose. Furthermore, these AAB possessed esterase genes, potentially capable of forming ethyl acetate, which may contribute to the flavor of lambic beer. Improved knowledge on the reasons behind certain community dynamics and the role of the different microorganisms in terms of potential functionality could improve brewery practices to assure to produce more quality-stable end-products.
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Affiliation(s)
- Jonas De Roos
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Modelling Acetification with Artificial Neural Networks and Comparison with Alternative Procedures. Processes (Basel) 2020. [DOI: 10.3390/pr8070749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Modelling techniques allow certain processes to be characterized and optimized without the need for experimentation. One of the crucial steps in vinegar production is the biotransformation of ethanol into acetic acid by acetic bacteria. This step has been extensively studied by using two predictive models: first-principles models and black-box models. The fact that first-principles models are less accurate than black-box models under extreme bacterial growth conditions suggests that the kinetic equations used by the former, and hence their goodness of fit, can be further improved. By contrast, black-box models predict acetic acid production accurately enough under virtually any operating conditions. In this work, we trained black-box models based on Artificial Neural Networks (ANNs) of the multilayer perceptron (MLP) type and containing a single hidden layer to model acetification. The small number of data typically available for a bioprocess makes it rather difficult to identify the most suitable type of ANN architecture in terms of indices such as the mean square error (MSE). This places ANN methodology at a disadvantage against alternative techniques and, especially, polynomial modelling.
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Consuegra J, Grenier T, Akherraz H, Rahioui I, Gervais H, da Silva P, Leulier F. Metabolic Cooperation among Commensal Bacteria Supports Drosophila Juvenile Growth under Nutritional Stress. iScience 2020; 23:101232. [PMID: 32563155 PMCID: PMC7305377 DOI: 10.1016/j.isci.2020.101232] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/13/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
The gut microbiota shapes animal growth trajectory in stressful nutritional environments, but the molecular mechanisms behind such physiological benefits remain poorly understood. The gut microbiota is mostly composed of bacteria, which construct metabolic networks among themselves and with the host. Until now, how the metabolic activities of the microbiota contribute to host juvenile growth remains unknown. Here, using Drosophila as a host model, we report that two of its major bacterial partners, Lactobacillus plantarum and Acetobacter pomorum, engage in a beneficial metabolic dialogue that boosts host juvenile growth despite nutritional stress. We pinpoint that lactate, produced by L. plantarum, is utilized by A. pomorum as an additional carbon source, and A. pomorum provides essential amino acids and vitamins to L. plantarum. Such bacterial cross-feeding provisions a set of anabolic metabolites to the host, which may foster host systemic growth despite poor nutrition. L. plantarum feeds lactate to A. pomorum A. pomorum supplies essential amino acids and vitamins to L. plantarum Microbiota metabolic dialogue boosts Drosophila's larval growth Lactate utilization by Acetobacter releases anabolic metabolites to larvae
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Affiliation(s)
- Jessika Consuegra
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, 69364 Cedex 07, Lyon, France.
| | - Théodore Grenier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, 69364 Cedex 07, Lyon, France
| | - Houssam Akherraz
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, 69364 Cedex 07, Lyon, France
| | - Isabelle Rahioui
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, UMR0203, 69621 Villeurbanne, France
| | - Hugo Gervais
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, 69364 Cedex 07, Lyon, France
| | - Pedro da Silva
- Laboratoire Biologie Fonctionnelle, Insectes et Interactions, Université de Lyon, Institut National des Sciences Appliquées, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, UMR0203, 69621 Villeurbanne, France
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, UMR5242, 69364 Cedex 07, Lyon, France.
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Wang W, Xu AL, Li ZC, Li Y, Xu SF, Sang HC, Zhi F. Combination of Probiotics and Salvia miltiorrhiza Polysaccharide Alleviates Hepatic Steatosis via Gut Microbiota Modulation and Insulin Resistance Improvement in High Fat-Induced NAFLD Mice. Diabetes Metab J 2020; 44:336-348. [PMID: 31950772 PMCID: PMC7188963 DOI: 10.4093/dmj.2019.0042] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) increases the risk of hepatocellular carcinoma, which is currently the leading cause of obesity-related cancer deaths in middle-aged men. METHODS Probiotics with lipid-lowering function were screened from the fecal microbiota of healthy adults. Polysaccharide from different sources was screened for improving insulin resistance. The combination of probiotics and Salvia miltiorrhiza polysaccharide (LBM) was investigated for alleviating hepatic steatosis. RESULTS First, Bifidobacterium bifidum V (BbV) and Lactobacillus plantarum X (LpX) were obtained from the fecal microbiota of healthy adults. Second, to improve insulin resistance, a Salvia miltiorrhiza Bunge polysaccharide showing good performance in reducing insulin resistance was obtained. The liver total cholesterol (TC) and total triglyceride (TG) levels and the serum levels of free fatty acid, alanine transaminase, aspartate transaminase, low density lipoprotein cholesterol, TG, and TC can be significantly reduced through supplementation with LpX-BbV (LB) in NAFLD mice. Interestingly, the function of the probiotic LB can be enhanced by S. miltiorrhiza Bunge polysaccharide. Furthermore, the gut microbiota was modulated by LpX-BbV+S. miltiorrhiza Bunge polysaccharide (LBM). The lipopolysaccharide concentration of the LBM group was decreased by 73.6% compared to the NAFLD group. Ultimately, the mRNA concentrations of the proinflammatory cytokines (tumor necrosis factor α, interleukin 1β [IL-1β], and IL-6) decreased with LB and LBM treatment. CONCLUSION The results of this this study indicate that the LBM combination can be used as a therapeutic for ameliorating NAFLD via modulating the gut microbiota and improving insulin resistance.
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Affiliation(s)
- Wei Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Ai Lei Xu
- Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Zheng Chao Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Li
- Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Shun Fu Xu
- Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Hua Chao Sang
- Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Pelicaen R, Gonze D, Teusink B, De Vuyst L, Weckx S. Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. Front Microbiol 2019; 10:2801. [PMID: 31921009 PMCID: PMC6915089 DOI: 10.3389/fmicb.2019.02801] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/18/2019] [Indexed: 01/17/2023] Open
Abstract
Acetobacter pasteurianus 386B is a candidate functional starter culture for the cocoa bean fermentation process. To allow in silico simulations of its related metabolism in response to different environmental conditions, a genome-scale metabolic model for A. pasteurianus 386B was reconstructed. This is the first genome-scale metabolic model reconstruction for a member of the genus Acetobacter. The metabolic network reconstruction process was based on extensive genome re-annotation and comparative genomics analyses. The information content related to the functional annotation of metabolic enzymes and transporters was placed in a metabolic context by exploring and curating a Pathway/Genome Database of A. pasteurianus 386B using the Pathway Tools software. Metabolic reactions and curated gene-protein-reaction associations were bundled into a genome-scale metabolic model of A. pasteurianus 386B, named iAp386B454, containing 454 genes, 322 reactions, and 296 metabolites embedded in two cellular compartments. The reconstructed model was validated by performing growth experiments in a defined medium, which revealed that lactic acid as the sole carbon source could sustain growth of this strain. Further, the reconstruction of the A. pasteurianus 386B genome-scale metabolic model revealed knowledge gaps concerning the metabolism of this strain, especially related to the biosynthesis of its cell envelope and the presence or absence of metabolite transporters.
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Affiliation(s)
- Rudy Pelicaen
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- (IB) - Interuniversity Institute of Bioinformatics in Brussels (ULB-VUB), Brussels, Belgium
| | - Didier Gonze
- (IB) - Interuniversity Institute of Bioinformatics in Brussels (ULB-VUB), Brussels, Belgium
- Unité de Chronobiologie Théorique, Service de Chimie Physique, Faculté des Sciences, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bas Teusink
- Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- (IB) - Interuniversity Institute of Bioinformatics in Brussels (ULB-VUB), Brussels, Belgium
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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Ryngajłło M, Jacek P, Cielecka I, Kalinowska H, Bielecki S. Effect of ethanol supplementation on the transcriptional landscape of bionanocellulose producer Komagataeibacter xylinus E25. Appl Microbiol Biotechnol 2019; 103:6673-6688. [PMID: 31168651 PMCID: PMC6667682 DOI: 10.1007/s00253-019-09904-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 10/26/2022]
Abstract
Ethanol exerts a strong positive effect on the cellulose yields from the widely exploited microbial producers of the Komagataeibacter genus. Ethanol is postulated to provide an alternative energy source, enabling effective use of glucose for cellulose biosynthesis rather than for energy acquisition. In this paper, we investigate the effect of ethanol supplementation on the global gene expression profile of Komagataeibacter xylinus E25 using RNA sequencing technology (RNA-seq). We demonstrate that when ethanol is present in the culture medium, glucose metabolism is directed towards cellulose production due to the induction of genes related to UDP-glucose formation and the repression of genes involved in glycolysis and acetan biosynthesis. Transcriptional changes in the pathways of cellulose biosynthesis and c-di-GMP metabolism are also described. The transcript level profiles suggest that Schramm-Hestrin medium supplemented with ethanol promotes bacterial growth by inducing protein biosynthesis and iron uptake. We observed downregulation of genes encoding transposases of the IS110 family which may provide one line of evidence explaining the positive effect of ethanol supplementation on the genotypic stability of K. xylinus E25. The results of this study increase knowledge and understanding of the regulatory effects imposed by ethanol on cellulose biosynthesis, providing new opportunities for directed strain improvement, scaled-up bionanocellulose production, and wider industrial exploitation of the Komagataeibacter species as bacterial cellulose producers.
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Affiliation(s)
- Małgorzata Ryngajłło
- Institute of Technical Biochemistry, Lodz University of Technology, B. Stefanowskiego 4/10, 90-924, Lodz, Poland.
| | - Paulina Jacek
- Institute of Technical Biochemistry, Lodz University of Technology, B. Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Izabela Cielecka
- Institute of Technical Biochemistry, Lodz University of Technology, B. Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Halina Kalinowska
- Institute of Technical Biochemistry, Lodz University of Technology, B. Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Stanisław Bielecki
- Institute of Technical Biochemistry, Lodz University of Technology, B. Stefanowskiego 4/10, 90-924, Lodz, Poland
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Serra JL, Moura FG, Pereira GVDM, Soccol CR, Rogez H, Darnet S. Determination of the microbial community in Amazonian cocoa bean fermentation by Illumina-based metagenomic sequencing. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.02.038] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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45
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The challenges and perspectives of the selection of starter cultures for fermented cocoa beans. Int J Food Microbiol 2019; 301:41-50. [PMID: 31085407 DOI: 10.1016/j.ijfoodmicro.2019.05.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/12/2019] [Accepted: 05/03/2019] [Indexed: 12/11/2022]
Abstract
Fermentation is an essential process step to develop precursor compounds for aroma and flavour characteristics of chocolate, as well as preventing germination of the cocoa bean. Despite the importance of the role of microorganisms during the chocolate production, to date, there are some discrepancies of the "cocobiota" community found during fermentation and the impact of starter culture in fermented cocoa beans. This review provides both a detailed overview of the starter cultures used in fermented cocoa beans and the microbial diversity involved during this process, and an in-depth discussion of the methods used to identify these microorganisms. In this review, we included only published articles from 2008 to 2018 in English language. A total of forty-seven studies contributed to the description of the cocobiota from 13 different countries. In detail, we observed that the most common fermentation method used is the wooden box, followed by heap. Interestingly, 37% of the studies cited in this review did not mention the type of cocoa variety studied. Most of the techniques used to identify the microbiota are fingerprinting based (DGGE); however, few studies have been using next-generation technologies to elucidate the possible functions and interactions among microbes. Our results showed a greater diversity of yeasts if compared with bacterial involved in the fermentation. This review will help researchers seeking to design starter cultures to drive cocoa bean fermentation, and thus achieve a homogenous mass of fermented cocoa beans as well as serve as a guide for assessing methodologies for the identification of microorganisms.
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De Roos J, De Vuyst L. Microbial acidification, alcoholization, and aroma production during spontaneous lambic beer production. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:25-38. [PMID: 30246252 DOI: 10.1002/jsfa.9291] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/04/2018] [Accepted: 07/25/2018] [Indexed: 05/18/2023]
Abstract
Acidic beers, such as Belgian lambic beers and American and other coolship ales, are becoming increasingly popular worldwide thanks to their refreshing acidity and fruity notes. The traditional fermentation used to produce them does not apply pure yeast cultures but relies on spontaneous, environmental inoculation. The fermentation and maturation process is carried out in wooden barrels and can take up to three years. It is characterized by different microbial species belonging to the enterobacteria, acetic acid bacteria, lactic acid bacteria, and yeasts. This review provides an introduction to the technology and four fermentation strategies of beer production, followed by the microbiology of acidic beer production, focusing on the main microorganisms present during the long process used for the production of Belgian lambic beers. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jonas De Roos
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Metabolic Basis for Mutualism between Gut Bacteria and Its Impact on the Drosophila melanogaster Host. Appl Environ Microbiol 2019; 85:AEM.01882-18. [PMID: 30389767 DOI: 10.1128/aem.01882-18] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/27/2018] [Indexed: 01/05/2023] Open
Abstract
Interactions between species shape the formation and function of microbial communities. In the gut microbiota of animals, cross-feeding of metabolites between microbes can enhance colonization and influence host physiology. We examined a mutually beneficial interaction between two bacteria isolated from the gut microbiota of Drosophila, i.e., Acetobacter fabarum and Lactobacillus brevis After developing an in vitro coculture assay, we utilized a genetic screen to identify A. fabarum genes required for enhanced growth with L. brevis The screen, and subsequent genetic analyses, showed that the gene encoding pyruvate phosphate dikinase (ppdK) is required for A. fabarum to benefit fully from coculture. By testing strains with mutations in a range of metabolic genes, we provide evidence that A. fabarum can utilize multiple fermentation products of L. brevis Mutualism between the bacteria in vivo affects gnotobiotic Drosophila melanogaster; flies associated with A. fabarum and L. brevis showed >1,000-fold increases in bacterial cell density and significantly lower triglyceride storage than monocolonized flies. Mutation of ppdK decreased A. fabarum density in flies cocolonized with L. brevis, consistent with the model in which Acetobacter employs gluconeogenesis to assimilate Lactobacillus fermentation products as a source of carbon in vivo We propose that cross-feeding between these groups is a common feature of microbiota in Drosophila IMPORTANCE The digestive tracts of animals are home to a community of microorganisms, the gut microbiota, which affects the growth, development, and health of the host. Interactions among microbes in this inner ecosystem can influence which species colonize the gut and can lead to changes in host physiology. We investigated a mutually beneficial interaction between two bacterial species from the gut microbiota of fruit flies. By coculturing the bacteria in vitro, we were able to identify a metabolic gene required for the bacteria to grow better together than they do separately. Our data suggest that one species consumes the waste products of the other, leading to greater productivity of the microbial community and modifying the nutrients available to the host. This study provides a starting point for investigating how these and other bacteria mutually benefit by sharing metabolites and for determining the impact of mutualism on host health.
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Schwechheimer SK, Becker J, Wittmann C. Towards better understanding of industrial cell factories: novel approaches for 13C metabolic flux analysis in complex nutrient environments. Curr Opin Biotechnol 2018; 54:128-137. [DOI: 10.1016/j.copbio.2018.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
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Moreno-Zambrano M, Grimbs S, Ullrich MS, Hütt MT. A mathematical model of cocoa bean fermentation. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180964. [PMID: 30473841 PMCID: PMC6227950 DOI: 10.1098/rsos.180964] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/21/2018] [Indexed: 05/30/2023]
Abstract
Cocoa bean fermentation relies on the sequential activation of several microbial populations, triggering a temporal pattern of biochemical transformations. Understanding this complex process is of tremendous importance as it is known to form the precursors of the resulting chocolate's flavour and taste. At the same time, cocoa bean fermentation is one of the least controlled processes in the food industry. Here, a quantitative model of cocoa bean fermentation is constructed based on available microbiological and biochemical knowledge. The model is formulated as a system of coupled ordinary differential equations with two distinct types of state variables: (i) metabolite concentrations of glucose, fructose, ethanol, lactic acid and acetic acid and (ii) population sizes of yeast, lactic acid bacteria and acetic acid bacteria. We demonstrate that the model can quantitatively describe existing fermentation time series and that the estimated parameters, obtained by a Bayesian framework, can be used to extract and interpret differences in environmental conditions. The proposed model is a valuable tool towards a mechanistic understanding of this complex biochemical process, and can serve as a starting point for hypothesis testing of new systemic adjustments. In addition to providing the first quantitative mathematical model of cocoa bean fermentation, the purpose of our investigation is to show how differences in estimated parameter values for two experiments allow us to deduce differences in experimental conditions.
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Affiliation(s)
| | | | | | - Marc-Thorsten Hütt
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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Becker J, Wittmann C. From systems biology to metabolically engineered cells — an omics perspective on the development of industrial microbes. Curr Opin Microbiol 2018; 45:180-188. [DOI: 10.1016/j.mib.2018.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/06/2018] [Accepted: 06/08/2018] [Indexed: 10/28/2022]
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