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Giangeri G, Morlino MS, De Bernardini N, Ji M, Bosaro M, Pirillo V, Antoniali P, Molla G, Raga R, Treu L, Campanaro S. Preliminary investigation of microorganisms potentially involved in microplastics degradation using an integrated metagenomic and biochemical approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157017. [PMID: 35777567 DOI: 10.1016/j.scitotenv.2022.157017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/23/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Plastic pollution is becoming an emerging environmental issue due to inappropriate disposal at the end of the materials life cycle. When plastics are released, they undergo physical and chemical corrosion, leading to the formation of small particles, commonly referred to as microplastics. In this study, a microbial community derived from the leachate of a bioreactor containing a mixture of soil and plastic collected during a landfill mining process underwent an enrichment protocol in order to select the microbial species specifically involved in plastic degradation. The procedure was set up and tested on polyethylene, polyvinyl chloride, and polyethylene terephthalate, both in anaerobic and aerobic conditions. The evolution of the microbiome has been monitored using a combined approach based on microscopy, marker-gene amplicon sequencing, genome-centric metagenomics, degradation assays, and GC-MS analyses. This procedure permitted us to deeply investigate the metabolic pathways potentially involved in plastic degradation and to depict the route for microplastics metabolization from the enriched microbial community. Six enzymes, among the ones already identified, were found in our samples (alkane 1-monooxygenase, cutinase, feruloyl esterase, triacylglycerol lipase, medium-chain acyl-CoA dehydrogenase, and protocatechuate 4,5-dioxygenase) and new enzymes, addressed as MHETases most probably for the presence of the catalytic triad (His-Asp-Ser), were detected. Among the enzymes involved in plastics degradation, alkane 1-monooxygenase was found in high copy number (between ten and 62 copies) in the metagenomes that resulted most abundant in the microbiome enriched with polyethylene, while protocatechuate 4,5-dioxygenase was found between one and eight copies in the most abundant metagenomes of the microbial culture enriched with polyethylene terephthalate. Degradation assays, performed using both bacterial lysates and supernatants, revealed interesting results on polyethylene terephthalate degradation. Moreover, this study demonstrates to what extent different types of microplastics can affect the microbial community composition. The results obtained significantly increase the knowledge of the plastic degradation process.
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Affiliation(s)
- Ginevra Giangeri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Maria Silvia Morlino
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Nicola De Bernardini
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Mengyuan Ji
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Matteo Bosaro
- Italiana Biotecnologie, Via Vigazzolo 112, 36054 Montebello Vicentino, Italy
| | - Valentina Pirillo
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Paolo Antoniali
- Italiana Biotecnologie, Via Vigazzolo 112, 36054 Montebello Vicentino, Italy
| | - Gianluca Molla
- Department of Biotechnology and Life Sciences, University of Insubria, via J. H. Dunant 3, 21100 Varese, Italy
| | - Roberto Raga
- ICEA, Department of Civil, Environmental and Architectural Engineering, University of Padua, via Marzolo 9, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy; CRIBI biotechnology center, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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Lemos Junior WJF, Guerra AF, Tarrah A, da Silva Duarte V, Giacomini A, Luchese RH, Corich V. Safety and Stability of Two Potentially Probiotic Lactobacillus Strains After In Vitro Gastrointestinal Transit. Probiotics Antimicrob Proteins 2021; 12:657-666. [PMID: 31214943 DOI: 10.1007/s12602-019-09565-2] [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] [Indexed: 02/08/2023]
Abstract
According to FAO and WHO, probiotics are defined as live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Most probiotic bacteria used today belong to the genera Lactobacillus and Bifidobacterium and are of animal or human origin. The fundamental characteristic routinely evaluated in potential probiotics strains is their limited viability loss during gastrointestinal transit (GIT), but to date, no studies reported whether probiotics, besides viability, still also maintain their beneficial properties intact. To study this aspect, we considered two strains, Lactobacillus rhamnosus DTA 79 and L. paracasei DTA 83, previously characterised for the presence of some probiotic properties, isolated from faeces of 7- to 21-day-old babies. Here, we examined some additional properties, namely antibiotic resistance, resistance to lysozyme, presence of haemolytic activity and inhibition of pathogen biofilm formation. We then tested the effect of in vitro GIT on all these features and our results show evidence that this procedure had in some cases limited and in others no significant effects on them. Additionally, we examined the gastrointestinal resistance of the strains after skim milk fermentation and successive storage of the product for 20 and 40 days at refrigeration temperature, to see whether prolonged storage could weaken cell resistance to GIT. Our results demonstrate that a protracted refrigeration period before in vitro GIT did not affect or influenced very weakly this essential probiotic property.
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Affiliation(s)
| | - André Fioravante Guerra
- Federal Center of Technological Education Celso Suckow da Fonseca, Valença, Rio de Janeiro, Brazil
| | - Armin Tarrah
- Department of Agronomy Food Natural resources Animals and Environment, University of Padova, Legnaro, Padua, Italy
| | - Vinícius da Silva Duarte
- Department of Agronomy Food Natural resources Animals and Environment, University of Padova, Legnaro, Padua, Italy
| | - Alessio Giacomini
- Department of Agronomy Food Natural resources Animals and Environment, University of Padova, Legnaro, Padua, Italy.
| | - Rosa Helena Luchese
- Department of Food Technology, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Viviana Corich
- Department of Agronomy Food Natural resources Animals and Environment, University of Padova, Legnaro, Padua, Italy
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3
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Tlais AZA, Da Ros A, Filannino P, Vincentini O, Gobbetti M, Di Cagno R. Biotechnological re-cycling of apple by-products: A reservoir model to produce a dietary supplement fortified with biogenic phenolic compounds. Food Chem 2020; 336:127616. [PMID: 32763733 DOI: 10.1016/j.foodchem.2020.127616] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
This study is an example of apple by-products (AP) recycling through a designed fermentation by selected autochthonous Lactobacillus plantarum AFI5 and Lactobacillus fabifermentans ALI6 used singly or as binary cultures with the selected Saccharomyces cerevisiae AYI7. Compared to Raw-, Unstarted- and Chemically Acidified-AP, Fermented-AP promoted the highest levels of total and insoluble dietary fibers, DPPH scavenging capacity, and free phenolics. The binary culture of L. plantarum AFI5 and S. cerevisiae AYI7 had the best effect on the bioavailability phenolic compounds as resulted by the LC-MS/MS validated method. The accumulation of phenolic acids derivatives highlighted the microbial metabolism during AP fermentation. Bio-converted phenolics were likely responsible for the increased DPPH scavenging capacity. The potential health-promoting effects of Fermented-AP were highlighted using Caco-2 cells. With variations among single and binary cultures, fermented-AP counteracted the inflammatory processes and the effects of oxidative stress in Caco-2 cells, and preserved the integrity of tight junctions.
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Affiliation(s)
- Ali Z A Tlais
- Faculty of Sciences and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Alessio Da Ros
- Faculty of Sciences and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Olimpia Vincentini
- U.O Alimentazione, Nutrizione e Salute, Dipartimento Sicurezza Alimentare, Nutrizione e Sanità Pubblica Veterinaria, Istituto Superiore di Sanità, Roma, Italy
| | - Marco Gobbetti
- Faculty of Sciences and Technology, Libera Università di Bolzano, Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Sciences and Technology, Libera Università di Bolzano, Bolzano, Italy.
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Tarrah A, Pakroo S, Lemos Junior WJF, Guerra AF, Corich V, Giacomini A. Complete Genome Sequence and Carbohydrates-Active EnZymes (CAZymes) Analysis of Lactobacillus paracasei DTA72, a Potential Probiotic Strain with Strong Capability to Use Inulin. Curr Microbiol 2020; 77:2867-2875. [PMID: 32623485 DOI: 10.1007/s00284-020-02089-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023]
Abstract
The whole genome sequence of Lactobacillus paracasei DTA72, isolated from healthy infant feces, is reported, along with the Carbohydrates-Active enZymes (CAZymes) analysis and an in silico safety assessment. Strain DTA72 had previously demonstrated some interesting potential probiotic features, such as a good resistance to gastrointestinal conditions and an anti-Listeria activity. The 3.1 Mb sequenced genome consists of 3116 protein-coding sequences distributed on 340 SEED subsystems. In the present study, we analyzed the fermentation capability of strain DTA72 on six different carbohydrate sources, namely, glucose, fructose, lactose, galactose, xylose, and inulin by using phenotypical and genomic approaches. Interestingly, L. paracasei DTA72 evidenced the best growth performances on inulin with a much shorter lag phase and higher number of cells at the stationary phase in comparison with all the sugars tested. The CAZyme analysis using the predicted amino acid sequences detected 80 enzymes, distributed into the five CAZymes classes. Moreover, the in silico analysis revealed the absence of blood hemolytic genes, transmissible antibiotic resistances, and plasmids in DTA72. The results described in this study, together with those previously reported and particularly the strong capability to utilize inulin as energy source, make DTA72 a very interesting potential probiotic strain to be considered for the production of synbiotic foods. The complete genome data have been deposited in GenBank under the accession number WUJH00000000.
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Affiliation(s)
- Armin Tarrah
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Shadi Pakroo
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
| | | | - Andre Fioravante Guerra
- Department of Food Engineering, Federal Center of Technological Education Celso Suckow da Fonseca, Valença, RJ, 27.600-000, Brazil
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy.
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
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Reque PM, Pinilla CMB, Tinello F, Corich V, Lante A, Giacomini A, Brandelli A. Biochemical and functional properties of wheat middlings bioprocessed by lactic acid bacteria. J Food Biochem 2020; 44:e13262. [PMID: 32361998 DOI: 10.1111/jfbc.13262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 11/30/2022]
Abstract
The present study aimed to investigate the bioprocessing of wheat middlings with different lactic acid bacteria (LAB) in order to improve biological activities of this by-product of wheat flour production. The concentration of lactic acid, reducing sugars, and total phenolics, as well as antioxidant, antibrowning, antibacterial and prebiotic activities of fermented samples were analyzed. All LAB strains were capable to growth on wheat middlings, and pH decreased in the medium associated with lactic acid production during cultivation. Samples inoculated with Lactobacillus plantarum DSM20174 presented the maximum growth, lactic acid concentration above 2 mg/ml, and pH values around 3.8. The amount or reducing sugars decreased after 24 hr growth, except for maltose. Bioprocessed wheat middlings exhibited antioxidant, antibrowning, antibacterial, and prebiotic properties, related with the increase of total phenolic content. Highest values for antioxidant activities were obtained for L. plantarum and Streptococcus thermophilus strains, reaching values around 400 and 640 μM Trolox equivalents (TE) ml-1 for 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric ion reducing antioxidant power (FRAP) assays, respectively. Bioprocessing techniques using LAB can be an interesting approach to improve the availability of compounds with health-promoting properties from lignocellulosic waste material. PRACTICAL APPLICATIONS: The processing of secondary products from wheat milling can represent an important benefit to the industry. Wheat middlings bioprocessed with LAB showed improved biological activities and may represent an interesting ingredient to be incorporated in food and feed formulations.
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Affiliation(s)
- Priscilla Magro Reque
- Department of Food Science, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristian Mauricio Barreto Pinilla
- Department of Food Science, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Federica Tinello
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), Università degli Studi di Padova, Padova, Italy
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), Università degli Studi di Padova, Padova, Italy
| | - Anna Lante
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), Università degli Studi di Padova, Padova, Italy
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), Università degli Studi di Padova, Padova, Italy
| | - Adriano Brandelli
- Department of Food Science, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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6
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Tarrah A, Pakroo S, Corich V, Giacomini A. Whole-genome sequence and comparative genome analysis of Lactobacillus paracasei DTA93, a promising probiotic lactic acid bacterium. Arch Microbiol 2020; 202:1997-2003. [DOI: 10.1007/s00203-020-01883-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/23/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022]
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7
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Gómez-Brandón M, Aira M, Santana N, Pérez-Losada M, Domínguez J. Temporal Dynamics of Bacterial Communities in a Pilot-Scale Vermireactor Fed with Distilled Grape Marc. Microorganisms 2020; 8:microorganisms8050642. [PMID: 32354197 PMCID: PMC7284424 DOI: 10.3390/microorganisms8050642] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 01/23/2023] Open
Abstract
Vermicomposting has been found as a profitable approach to dispose of and treat large quantities of raw grape marc. However, less information is available with regard to its efficiency for treating distillery winery byproducts, even though distillation has been widely used as a way to economically valorize grape marc. As such, we sought to characterize the compositional and functional changes in bacterial communities during vermicomposting of distilled grape marc by using 16S rRNA high-throughput sequencing. Samples were collected at the initiation of vermicomposting and at days 14, 21, 28, 35 and 42. There were significant changes (p < 0.0001) in the bacterial community composition of distilled grape marc after 14 days of vermicomposting that were accompanied by twofold increases in bacterial richness and diversity from a taxonomic and phylogenetic perspective. This was followed by significant increases in functional diversity of the bacterial community, including metabolic capacity, lignin and cellulose metabolism, and salicylic acid synthesis. These findings indicate that the most striking compositional and functional bacterial community changes took place during the active phase of the process. They also pinpoint functional attributes that may be related to the potential beneficial effects of distilled grape marc vermicompost when applied on soil and plants.
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Affiliation(s)
- María Gómez-Brandón
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, E-36310 Vigo, Spain
- Correspondence:
| | - Manuel Aira
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, E-36310 Vigo, Spain
| | - Natielo Santana
- Department of Soil Science, Federal University of Santa Maria, 97119-900 Santa Maria, Rio Grande do Sul, Brazil
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Jorge Domínguez
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, E-36310 Vigo, Spain
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Nardi T. Microbial Resources as a Tool for Enhancing Sustainability in Winemaking. Microorganisms 2020; 8:microorganisms8040507. [PMID: 32252445 PMCID: PMC7232173 DOI: 10.3390/microorganisms8040507] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
In agriculture, the wine sector is one of the industries most affected by the sustainability issue. It is responsible for about 0.3% of annual global greenhouse gas emissions from anthropogenic activities. Sustainability in vitiviniculture was firstly linked to vineyard management, where the use of fertilizers, pesticides and heavy metals is a major concern. More recently, the contribution of winemaking, from grape harvest to bottling, has also been considered. Several cellar processes could be improved for reducing the environmental impact of the whole chain, including microbe-driven transformations. This paper reviews the potential of microorganisms and interactions thereof as a natural, environmentally friendly tool to improve the sustainability aspects of winemaking, all along the production chain. The main phases identified as potentially interesting for exploiting microbial activities to lower inputs are: (i) pre-fermentative stages, (ii) alcoholic fermentation, (iii) stage between alcoholic and malolactic fermentation, (iv) malolactic fermentation, (v) stabilization and spoilage risk management, and (vi) by-products and wastewater treatment. The presence of proper yeast or bacterial strains, the management and timing of inoculation of starter cultures, and some appropriate technological modifications that favor selected microbial activities can lead to several positive effects, including (among other) energy savings, reduction of chemical additives such as sulfites, and reuse of certain residues.
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Affiliation(s)
- Tiziana Nardi
- CREA-Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Viale XXVIII Aprile 26, 31015 Conegliano, Italy
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Zhao CC, Eun JB. Shotgun metagenomics approach reveals the bacterial community and metabolic pathways in commercial hongeo product, a traditional Korean fermented skate product. Food Res Int 2020; 131:109030. [PMID: 32247457 DOI: 10.1016/j.foodres.2020.109030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/22/2023]
Abstract
The aim of this study was to investigate the microbial diversity and microbial metabolic pathways using a metagenomic approach in commercial hongeo samples collected from five different fish processing plants. Community comparison analysis indicated that hongeo samples from different fish processing plants have a similar microbial structure at genus level, but the relative abundance of these genera showed a significant difference among different hongeo samples. Four bacterial genera including Psychrobacter, Pseudomonas, Clostridium, and Oblitimonas were detected in all hongeo samples with a high relative abundance, which associated with the nitrogen compound accumulation and ammonia flavor formation in hongeo samples. In addition, some alkaliphilic marine lactic acid bacteria (LAB) belonging to the genera Marinilactibacillus and Jeotgalibaca were detected in hongeo samples, indicating that this product might be a useful source for finding novel bacteria and possibly marine LAB. Through functional profiling analysis, it was found that hongeo samples had higher bacterial gene content related to amino acid metabolism, followed by carbohydrate metabolism and inorganic ion metabolism. The results of this study provide an important information for understanding the mechanism of quality characteristics and ammonia flavor formation in hongeo products.
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Affiliation(s)
- Chang-Cheng Zhao
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju 61186, South Korea
| | - Jong-Bang Eun
- Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju 61186, South Korea.
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10
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Probiotic potential and biofilm inhibitory activity of Lactobacillus casei group strains isolated from infant feces. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.02.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Bovo B, Nadai C, Lemos Junior WJF, Carlot M, Giacomini A, Corich V. The Different Physical and Chemical Composition of Grape Juice and Marc Influence Saccharomyces cerevisiae Strains Distribution During Fermentation. J Food Sci 2018; 83:2191-2196. [PMID: 30028508 DOI: 10.1111/1750-3841.14274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/28/2018] [Accepted: 06/04/2018] [Indexed: 01/15/2023]
Abstract
During white-grape winemaking, grape marc is separated from juice immediately after crushing. Both mark and juice are obtained from the same grapes, but they differ strongly for their physical and chemical properties. Marc is mainly composed of solid residues. Its pH is usually higher than that of the juice and Saccharomyces cerevisiae strains are largely present. Therefore, it can be considered as a potential alternative environment for the selection of industrial yeasts. In order to evaluate the effect of different pH and physical state of the two matrices on grapes yeast population composition, the isolation of S. cerevisiae, from both grape juice and marc during simultaneous fermentations, was performed. After yeast identification and genotyping, strains present at high frequencies were tested in fermentation at different pH values. Biofilm production was also tested to evaluate strain ability to develop on a solid matrix. Genotype analysis showed that high-frequency strains were always more abundant in one of the two environments, suggesting the existence of a selective effect. Generally, fermentations at different pH revealed that the best fermentation performance of each strain, in terms of CO2 production, was in the pH range of its original environment. Only one strain, mostly present in grape marc, produced a high biofilm level. Therefore, biofilm production does not seem to favor strain adaptation to grape marc condition. PRACTICAL APPLICATION These results demonstrate that grape juice and marc represent two different environments able to influence yeast strains distribution. The pH level can be included among the selection factors acting on yeast strains distribution. Grape marc can be considered a yeasts reservoir and its fermentation can be used for the development and isolation of new strains, genetically and physiologically different from those present in the grape juice.
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Affiliation(s)
- Barbara Bovo
- Dept. of Agronomy Food Natural resources Animals and Environment (DAFNAE), Univ. of Padova, Viale dell'Università 16, Legnaro, PD, 35020, Italy.,Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), Univ. of Padova, Via XXVIII Aprile 14, Conegliano, TV, 31015, Italy
| | - Chiara Nadai
- Dept. of Agronomy Food Natural resources Animals and Environment (DAFNAE), Univ. of Padova, Viale dell'Università 16, Legnaro, PD, 35020, Italy.,Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), Univ. of Padova, Via XXVIII Aprile 14, Conegliano, TV, 31015, Italy
| | - Wilson Josè Fernandes Lemos Junior
- Dept. of Agronomy Food Natural resources Animals and Environment (DAFNAE), Univ. of Padova, Viale dell'Università 16, Legnaro, PD, 35020, Italy
| | - Milena Carlot
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), Univ. of Padova, Via XXVIII Aprile 14, Conegliano, TV, 31015, Italy
| | - Alessio Giacomini
- Dept. of Agronomy Food Natural resources Animals and Environment (DAFNAE), Univ. of Padova, Viale dell'Università 16, Legnaro, PD, 35020, Italy.,Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), Univ. of Padova, Via XXVIII Aprile 14, Conegliano, TV, 31015, Italy
| | - Viviana Corich
- Dept. of Agronomy Food Natural resources Animals and Environment (DAFNAE), Univ. of Padova, Viale dell'Università 16, Legnaro, PD, 35020, Italy.,Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), Univ. of Padova, Via XXVIII Aprile 14, Conegliano, TV, 31015, Italy
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12
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Lemos Junior WJF, da Silva Duarte V, Treu L, Campanaro S, Nadai C, Giacomini A, Corich V. Whole genome comparison of two Starmerella bacillaris strains with other wine yeasts uncovers genes involved in modulating important winemaking traits. FEMS Yeast Res 2018; 18:5046425. [DOI: 10.1093/femsyr/foy069] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wilson Josè Fernandes Lemos Junior
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, Legnaro, 35020, Italy
| | - Vinicius da Silva Duarte
- Department of Microbiology, Universidade Federal de Viçosa, Av. PH Rolfs s/n, Campus Universitário, 36570 000, Viçosa, Brazil
| | - Laura Treu
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, Legnaro, 35020, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58b, 35121, Padova, Italy
| | - Chiara Nadai
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, Legnaro, 35020, Italy
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Via XXVIII Aprile 14, Conegliano, 31015, Italy
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, Legnaro, 35020, Italy
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Via XXVIII Aprile 14, Conegliano, 31015, Italy
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, Legnaro, 35020, Italy
- Interdepartmental Centre for Research in Viticulture and Enology (CIRVE), University of Padova, Via XXVIII Aprile 14, Conegliano, 31015, Italy
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Stefanini I, Cavalieri D. Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. Front Microbiol 2018; 9:991. [PMID: 29867889 PMCID: PMC5964215 DOI: 10.3389/fmicb.2018.00991] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/27/2018] [Indexed: 01/08/2023] Open
Abstract
The winemaking is a complex process that begins in the vineyard and ends at consumption moment. Recent reports have shown the relevance of microbial populations in the definition of the regional organoleptic and sensory characteristics of a wine. Metagenomic approaches, allowing the exhaustive identification of microorganisms present in complex samples, have recently played a fundamental role in the dissection of the contribution of the vineyard environment to wine fermentation. Systematic approaches have explored the impact of agronomical techniques, vineyard topologies, and climatic changes on bacterial and fungal populations found in the vineyard and in fermentations, also trying to predict or extrapolate the effects on the sensorial characteristics of the resulting wine. This review is aimed at highlighting the major technical and experimental challenges in dissecting the contribution of the vineyard and native environments microbiota to the wine fermentation process, and how metagenomic approaches can help in understanding microbial fluxes and selections across the environments and specimens related to wine fermentation.
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Affiliation(s)
- Irene Stefanini
- Division of Biomedical Sciences, University of Warwick, Coventry, United Kingdom
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14
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Fontana A, Campanaro S, Treu L, Kougias PG, Cappa F, Morelli L, Angelidaki I. Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes. WATER RESEARCH 2018; 134:181-191. [PMID: 29427960 DOI: 10.1016/j.watres.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 05/25/2023]
Abstract
The present research is the first comprehensive study regarding the thermophilic anaerobic degradation of cheese wastewater, which combines the evaluation of different reactor configurations (i.e. single and two-stage continuous stirred tank reactors) on the process efficiency and the in-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design reached a methane yield equal to 95% of the theoretical value, in contrast with the single stage configuration, which reached a maximum of 33% of the theoretical methane yield. The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration. In fact, the acidogenic reactor of the serial configuration was almost solely composed by the lactose degrader Bifidobacterium crudilactis UC0001. The predictive functional analyses of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer Tepidanaerobacter acetatoxydans UC0018 and to the absence of aceticlastic methanogens.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy; Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Fabrizio Cappa
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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15
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Nakano M. 16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products. J Food Prot 2018; 81:848-859. [PMID: 29664320 DOI: 10.4315/0362-028x.jfp-17-346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.
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Affiliation(s)
- Miyo Nakano
- Division of Food Science, Toyo Institute of Food Technology, 23-2, 4-chome, Minami-hanayashiki, Kawanishi-shi, Hyogo, 666-0026 Japan
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16
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De Filippis F, Parente E, Ercolini D. Recent Past, Present, and Future of the Food Microbiome. Annu Rev Food Sci Technol 2018; 9:589-608. [DOI: 10.1146/annurev-food-030117-012312] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80131 Naples, Italy
| | - Eugenio Parente
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, 80131 Naples, Italy
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17
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Abstract
In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.
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18
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Tinello F, Vendramin V, Barros Divino V, Treu L, Corich V, Lante A, Giacomini A. Co-fermentation of onion and whey: A promising synbiotic combination. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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19
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Morgan HH, du Toit M, Setati ME. The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing. Front Microbiol 2017; 8:820. [PMID: 28553266 PMCID: PMC5425579 DOI: 10.3389/fmicb.2017.00820] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.
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Affiliation(s)
- Horatio H Morgan
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Maret du Toit
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Mathabatha E Setati
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
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20
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Genome comparison and physiological characterization of eight Streptococcus thermophilus strains isolated from Italian dairy products. Food Microbiol 2017; 63:47-57. [DOI: 10.1016/j.fm.2016.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/27/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
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21
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Şimşek Ö, Özel S, Çon AH. Comparison of lactic acid bacteria diversity during the fermentation of Tarhana produced at home and on a commercial scale. Food Sci Biotechnol 2017; 26:181-187. [PMID: 30263526 DOI: 10.1007/s10068-017-0024-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
In this study, lactic acid bacteria diversity during the fermentation of homemade and commercially prepared Tarhana, a traditional fermented cereal food from Anatolia, was determined and compared. The isolates collected from Tarhana dough were differentiated according to their (GTG)5 profiles and then identified using 16S rDNA and pheS gene sequences. The variation of lactic acid bacteria during fermentation was also screened using PCR-DGGE. Commercially prepared Tarhana dough was fermented with higher Lactobacillus spp. diversity than homemade Tarhana dough. Lactobacillus casei, L. alimentarius, L. fabifermentas, and L. paralimentarius were identified differently from the fermentation of commercially prepared Tarhana dough. PCR-DGGE analysis revealed that L. plantarum was the main strain for homemade Tarhana, whereas L. brevis and L. alimentarius were observed in commercially prepared Tarhana dough fermentation. In conclusion, L. plantarum, L. brevis and L. alimentarius can be useful as a potential starter culture for the industrial production of Tarhana.
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Affiliation(s)
- Ömer Şimşek
- 1Department of Food Engineering, University of Pamukkale, Faculty of Engineering, Denizli, Turkey
| | - Serap Özel
- 1Department of Food Engineering, University of Pamukkale, Faculty of Engineering, Denizli, Turkey
| | - Ahmet Hilmi Çon
- 2Department of Food Engineering, University of Ondokuz Mayıs, Faculty of Engineering, Samsun, Turkey
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22
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Bergsveinson J, Kajala I, Ziola B. Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages. AIMS Microbiol 2017; 3:8-24. [PMID: 31294146 PMCID: PMC6604971 DOI: 10.3934/microbiol.2017.1.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/12/2017] [Indexed: 12/31/2022] Open
Abstract
Plant-based beverages and milk alternatives produced from cereals and legumes have grown in popularity in recent years due to a range of consumer concerns over dairy products. These plant-based products can often have undesirable physiochemical properties related to flavour, texture, and nutrient availability and/or deficiencies. Lactic acid bacteria (LAB) fermentation offers potential remediation for many of these issues, and allows consumers to retain their perception of the resultant products as natural and additive-free. Using next-generation sequencing (NGS) or omics approaches to characterize LAB isolates to find those that will improve properties of plant-based beverages is the most direct way to product improvement. Although NGS/omics approaches have been extensively used for selection of LAB for use in the dairy industry, a comparable effort has not occurred for selecting LAB for fermenting plant raw substrates, save those used in producing wine and certain types of beer. Here we review the few and recent applications of NGS/omics to profile and improve LAB fermentation of various plant-based substrates for beverage production. We also identify specific issues in the production of various LAB fermented plant-based beverages that such NGS/omics applications have the power to resolve.
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Affiliation(s)
- Jordyn Bergsveinson
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
| | - Ilkka Kajala
- VTT Technical Research Centre of Finland Ltd., PL1000, 02044VTT, Espoo, Finland
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
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23
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Bora SS, Keot J, Das S, Sarma K, Barooah M. Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India. 3 Biotech 2016; 6:153. [PMID: 28330225 PMCID: PMC4947050 DOI: 10.1007/s13205-016-0471-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/05/2016] [Indexed: 12/11/2022] Open
Abstract
This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq® System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method. The microbial community revealed the existence of amylase producers, such as Rhizopus delemar, Mucor circinelloides, and Aspergillus sp. Ethanol producers viz., Meyerozyma guilliermondii, Wickerhamomyces ciferrii, Saccharomyces cerevisiae, Candida glabrata, Debaryomyces hansenii, Ogataea parapolymorpha, and Dekkera bruxellensis, were found associated with the starter culture along with a diverse range of opportunistic contaminants. The bacterial microflora was dominated by lactic acid bacteria (LAB). The most frequent occurring LAB was Lactobacillus plantarum, Lactobacillus brevis, Leuconostoc lactis, Weissella cibaria, Lactococcus lactis, Weissella para mesenteroides, Leuconostoc pseudomesenteroides, etc. Our study provided a comprehensive picture of microbial diversity associated with rice wine fermentation starter and indicated the superiority of metagenomic sequencing over previously used techniques.
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Affiliation(s)
- Sudipta Sankar Bora
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Jyotshna Keot
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Saurav Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Kishore Sarma
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India.
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24
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Formation of In Vitro Mixed-Species Biofilms by Lactobacillus pentosus and Yeasts Isolated from Spanish-Style Green Table Olive Fermentations. Appl Environ Microbiol 2015; 82:689-95. [PMID: 26567305 DOI: 10.1128/aem.02727-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/09/2015] [Indexed: 01/10/2023] Open
Abstract
The present work details the in vitro interactions between Lactobacillus pentosus and yeast strains isolated from table olive processing to form mixed biofilms. Among the different pairs assayed, the strongest biofilms were obtained from L. pentosus and Candida boidinii strain cocultures. However, biofilm formation was inhibited in the presence of d-(+)-mannose. In addition, biofilm formation by C. boidinii monoculture was stimulated in the absence of cell-cell contact with L. pentosus. Scanning electron microscopy revealed that a sort of "sticky" material formed by the yeasts contributed to substrate adherence. Hence, the data obtained in this work suggest that yeast-lactobacilli biofilms may be favored by the presence of a specific mate of yeast and L. pentosus, and that more than one mechanism might be implicated in the biofilm formation. This knowledge will help in the design of appropriate mixed starter cultures of L. pentosus-yeast species pairs that are able to improve the quality and safety of Spanish-style green table olive processing.
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25
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Zepeda Mendoza ML, Sicheritz-Pontén T, Gilbert MTP. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform 2015; 16:745-58. [PMID: 25673291 PMCID: PMC4570204 DOI: 10.1093/bib/bbv001] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Indexed: 01/19/2023] Open
Abstract
DNA-based taxonomic and functional profiling is widely used for the characterization of organismal communities across a rapidly increasing array of research areas that include the role of microbiomes in health and disease, biomonitoring, and estimation of both microbial and metazoan species richness. Two principal approaches are currently used to assign taxonomy to DNA sequences: DNA metabarcoding and metagenomics. When initially developed, each of these approaches mandated their own particular methods for data analysis; however, with the development of high-throughput sequencing (HTS) techniques they have begun to share many aspects in data set generation and processing. In this review we aim to define the current characteristics, goals and boundaries of each field, and describe the different software used for their analysis. We argue that an appreciation of the potential and limitations of each method can help underscore the improvements required by each field so as to better exploit the richness of current HTS-based data sets.
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26
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De Francisci D, Kougias PG, Treu L, Campanaro S, Angelidaki I. Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition. BIORESOURCE TECHNOLOGY 2015; 176:56-64. [PMID: 25460984 DOI: 10.1016/j.biortech.2014.10.126] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 05/07/2023]
Abstract
The anaerobic digestion process is often inhibited by alteration of substrates and/or organic overload. This study aimed to elucidate changes of microbial ecology in biogas reactors upon radical changes of substrates and to determine their importance to process imbalance. For this reason, continuously fed reactors were disturbed with pulses of proteins, lipids and carbohydrates and the microbial ecology of the reactors were characterized by 16S rRNA gene sequencing before and after the imposed changes. The microbial composition of the three reactors, initially similar, diverged greatly after substrate change. The greatest increase in diversity was observed in the reactor supplemented with carbohydrates and the microbial community became dominated by lactobacilli, while the lowest corresponded to the reactor overfed with proteins, where only Desulfotomaculum showed significant increase. The overall results suggest that feed composition has a decisive impact on the microbial composition of the reactors, and thereby on their performance.
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Affiliation(s)
- Davide De Francisci
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK 2800, Denmark
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK 2800, Denmark
| | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK 2800, Denmark
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK 2800, Denmark.
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