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Microorganisms, Volume 6, Issue 4 (December 2018)

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Open AccessReview Leaky Gut, Leaky Brain?
Microorganisms 2018, 6(4), 107; https://doi.org/10.3390/microorganisms6040107 (registering DOI)
Received: 28 August 2018 / Revised: 12 October 2018 / Accepted: 15 October 2018 / Published: 18 October 2018
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Abstract
‘Leaky gut’ syndrome, long-associated with celiac disease, has attracted much attention in recent years and for decades, was widely known in complementary/alternative medicine circles. It is often described as an increase in the permeability of the intestinal mucosa, which could allow bacteria, toxic
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‘Leaky gut’ syndrome, long-associated with celiac disease, has attracted much attention in recent years and for decades, was widely known in complementary/alternative medicine circles. It is often described as an increase in the permeability of the intestinal mucosa, which could allow bacteria, toxic digestive metabolites, bacterial toxins, and small molecules to ‘leak’ into the bloodstream. Nervous system involvement with celiac disease is know to occur even at subclinical levels. Gluten and gluten sensitivity are considered to trigger this syndrome in individuals genetically predisposed to celiac disease. However, the incidence of celiac disease in the general population is quite low. Nevertheless, increased public interest in gluten sensitivity has contributed to expanded food labels stating ‘gluten-free’ and the proliferation of gluten-free products, which further drives gluten-free lifestyle changes by individuals without frank celiac disease. Moreover, systemic inflammation is associated with celiac disease, depression, and psychiatric comorbidities. This mini-review focuses on the possible neurophysiological basis of leaky gut; leaky brain disease; and the microbiota’s contribution to inflammation, gastrointestinal, and blood-brain barrier integrity, in order to build a case for possible mechanisms that could foster further ‘leaky’ syndromes. We ask whether a gluten-free diet is important for anyone or only those with celiac disease. Full article
(This article belongs to the Special Issue Gut Microbiota Diversity Relates to Lifestyle)
Open AccessArticle Rational Design and Biotechnological Production of Novel AfpB-PAF26 Chimeric Antifungal Proteins
Microorganisms 2018, 6(4), 106; https://doi.org/10.3390/microorganisms6040106
Received: 6 September 2018 / Revised: 4 October 2018 / Accepted: 11 October 2018 / Published: 15 October 2018
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Abstract
Antimicrobial peptides (AMPs) have been proposed as candidates to develop new antimicrobial compounds for medicine, agriculture, and food preservation. PAF26 is a synthetic antifungal hexapeptide obtained from combinatorial approaches with potent fungicidal activity against filamentous fungi. Other interesting AMPs are the antifungal proteins
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Antimicrobial peptides (AMPs) have been proposed as candidates to develop new antimicrobial compounds for medicine, agriculture, and food preservation. PAF26 is a synthetic antifungal hexapeptide obtained from combinatorial approaches with potent fungicidal activity against filamentous fungi. Other interesting AMPs are the antifungal proteins (AFPs) of fungal origin, which are basic cysteine-rich and small proteins that can be biotechnologically produced in high amounts. A promising AFP is the AfpB identified in the phytopathogen Penicillium digitatum. In this work, we aimed to rationally design, biotechnologically produce and test AfpB::PAF26 chimeric proteins to obtain designed AFPs (dAfpBs) with improved properties. The dAfpB6 and dAfpB9 chimeras could be produced using P. digitatum as biofactory and a previously described Penicillium chrysogenum-based expression cassette, but only dAfpB9 could be purified and characterized. Protein dAfpB9 showed subtle and fungus-dependent differences of fungistatic activity against filamentous fungi compared to native AfpB. Significantly, dAfpB9 lost the fungicidal activity of PAF26 and AfpB, thus disconnecting this activity from the fungistatic activity and mapping fungicidal determinants to the exposed loop L3 of AfpB, wherein modifications are located. This study provides information on the design and development of novel chimeric AFPs. Full article
(This article belongs to the Special Issue Antimicrobial Proteins in Filamentous Fungi)
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Open AccessArticle Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds
Microorganisms 2018, 6(4), 105; https://doi.org/10.3390/microorganisms6040105
Received: 10 September 2018 / Revised: 6 October 2018 / Accepted: 10 October 2018 / Published: 11 October 2018
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Abstract
Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a
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Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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Open AccessReview Role of Natural Volatiles and Essential Oils in Extending Shelf Life and Controlling Postharvest Microorganisms of Small Fruits
Microorganisms 2018, 6(4), 104; https://doi.org/10.3390/microorganisms6040104
Received: 31 August 2018 / Revised: 30 September 2018 / Accepted: 3 October 2018 / Published: 5 October 2018
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Abstract
Small fruits are a multi-billion dollar industry in the US, and are economically important in many other countries. However, they are perishable and susceptible to physiological disorders and biological damage. Food safety and fruit quality are the major concerns of the food chain
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Small fruits are a multi-billion dollar industry in the US, and are economically important in many other countries. However, they are perishable and susceptible to physiological disorders and biological damage. Food safety and fruit quality are the major concerns of the food chain from farm to consumer, especially with increasing regulations in recent years. At present, the industry depends on pesticides and fungicides to control food spoilage organisms. However, due to consumer concerns and increasing demand for safer produce, efforts are being made to identify eco-friendly compounds that can extend the shelf life of small fruits. Most volatiles and essential oils produced by plants are safe for humans and the environment, and lots of research has been conducted to test the in vitro efficacy of single-compound volatiles or multi-compound essential oils on various microorganisms. However, there are not many reports on their in vivo (in storage) and In situ (in the field) applications. In this review, we discuss the efficacy, minimum inhibitory concentrations, and mechanisms of action of volatiles and essential oils that control microorganisms (bacteria and fungi) on small fruits such as strawberries, raspberries, blueberries, blackberries, and grapes under the three conditions. Full article
Open AccessArticle Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities
Microorganisms 2018, 6(4), 103; https://doi.org/10.3390/microorganisms6040103
Received: 28 August 2018 / Revised: 25 September 2018 / Accepted: 29 September 2018 / Published: 4 October 2018
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Abstract
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived
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Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived from engineered algae. The microbial community structure was measured on the single cell level using flow cytometry. Abiotic and operational reactor parameters were analyzed in parallel. The R-based tool flowCyBar facilitated visualization of community dynamics and indicated sub-communities involved in glycolate fermentation and methanogenesis. Cell sorting and amplicon sequencing of 16S rRNA and mcrA genes were used to identify the key organisms involved in the anaerobic conversion process. The microbial community allowed a constant fermentation, although it was sensitive to high glycolate concentrations in the feed. A linear correlation between glycolate loading rate and biogas amount was observed (R2 = 0.99) for glycolate loading rates up to 1.81 g L−1 day−1 with a maximum in biogas amount of 3635 mL day−1 encompassing 45% methane. The cytometric diversity remained high during the whole cultivation period. The dominating bacterial genera were Syntrophobotulus, Clostridia genus B55_F, Aminobacterium, and Petrimonas. Methanogenesis was almost exclusively performed by the hydrogenotrophic genus Methanobacterium. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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Open AccessArticle Synergism of Mild Heat and High-Pressure Pasteurization Against Listeria monocytogenes and Natural Microflora in Phosphate-Buffered Saline and Raw Milk
Microorganisms 2018, 6(4), 102; https://doi.org/10.3390/microorganisms6040102
Received: 10 September 2018 / Revised: 28 September 2018 / Accepted: 1 October 2018 / Published: 3 October 2018
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Abstract
As many as 99% of illnesses caused by Listeria monocytogenes are foodborne in nature, leading to 94% hospitalizations, and are responsible for the collective annual deaths of 266 American adults. The current study is a summary of microbiological hurdle validation studies to investigate
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As many as 99% of illnesses caused by Listeria monocytogenes are foodborne in nature, leading to 94% hospitalizations, and are responsible for the collective annual deaths of 266 American adults. The current study is a summary of microbiological hurdle validation studies to investigate synergism of mild heat (up to 55 °C) and elevated hydrostatic pressure (up to 380 MPa) for decontamination of Listeria monocytogenes and natural background microflora in raw milk and phosphate-buffered saline. At 380 MPa, for treatments of 0 to 12 min, d-values of 3.47, 3.15, and 2.94 were observed for inactivation of the pathogen at 4, 25, and 50 °C. Up to 3.73 and >4.26 log CFU/mL reductions (p < 0.05) of habituated Listeria monocytogenes were achieved using pressure at 380 MPa for 3 and 12 min, respectively. Similarly, background microflora counts were reduced (p < 0.05) by 1.3 and >2.4 log CFU/mL after treatments at 380 MPa for 3 and 12 min, respectively. Treatments below three min were less efficacious (p ≥ 0.05) against the pathogen and background microflora, in the vast majority of time and pressure combinations. Results of this study could be incorporated as part of a risk-based food safety management system and risk assessment analyses for mitigating the public health burden of listeriosis. Full article
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Open AccessArticle A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice
Microorganisms 2018, 6(4), 101; https://doi.org/10.3390/microorganisms6040101
Received: 30 June 2018 / Revised: 12 September 2018 / Accepted: 26 September 2018 / Published: 29 September 2018
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Abstract
Commensal microbiota colonize the surface of our bodies. The inside of the gastrointestinal tract is one such surface that provides a habitat for them. The gastrointestinal tract is a long organ system comprising of various parts, and each part possesses various functions. It
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Commensal microbiota colonize the surface of our bodies. The inside of the gastrointestinal tract is one such surface that provides a habitat for them. The gastrointestinal tract is a long organ system comprising of various parts, and each part possesses various functions. It has been reported that the composition of intestinal luminal metabolites between the small and large intestine are different; however, comprehensive metabolomic and commensal microbiota profiles specific to each part of the gastrointestinal lumen remain obscure. In this study, by using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS)-based metabolome and 16S rRNA gene-based microbiome analyses of specific pathogen-free (SPF) and germ-free (GF) murine gastrointestinal luminal profiles, we observed the different roles of commensal microbiota in each part of the gastrointestinal tract involved in carbohydrate metabolism and nutrient production. We found that the concentrations of most amino acids in the SPF small intestine were higher than those in the GF small intestine. Furthermore, sugar alcohols such as mannitol and sorbitol accumulated only in the GF large intestine, but not in the SPF large intestine. On the other hand, pentoses, such as arabinose and xylose, gradually accumulated from the cecum to the colon only in SPF mice, but were undetected in GF mice. Correlation network analysis between the gastrointestinal microbes and metabolites showed that niacin metabolism might be correlated to Methylobacteriaceae. Collectively, commensal microbiota partially affects the gastrointestinal luminal metabolite composition based on their metabolic dynamics, in cooperation with host digestion and absorption. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
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Open AccessBrief Report Antimicrobial Resistance in Class 1 Integron-Positive Shiga Toxin-Producing Escherichia coli Isolated from Cattle, Pigs, Food and Farm Environment
Microorganisms 2018, 6(4), 99; https://doi.org/10.3390/microorganisms6040099
Received: 18 August 2018 / Revised: 24 September 2018 / Accepted: 26 September 2018 / Published: 28 September 2018
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Abstract
The aim of this study was to investigate the presence of class 1 integrons in a collection of Shiga toxin-producing Escherichia coli (STEC) from different origins and to characterize pheno- and genotypically the antimicrobial resistance associated to them. A collection of 649 isolates
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The aim of this study was to investigate the presence of class 1 integrons in a collection of Shiga toxin-producing Escherichia coli (STEC) from different origins and to characterize pheno- and genotypically the antimicrobial resistance associated to them. A collection of 649 isolates were screened for the class 1 integrase gene (intI1) by Polymerase chain reaction The variable region of class 1 integrons was amplified and sequenced. Positive strains were evaluated for the presence of antimicrobial resistance genes with microarray and for antimicrobial susceptibility by the disk diffusion method. Seven out of 649 STEC strains some to serogroups, O26, O103 and O130 isolated from cattle, chicken burger, farm environment and pigs were identified as positive for intl1. Different arrangements of gene cassettes were detected in the variable region of class 1 integron: dfrA16, aadA23 and dfrA1-aadA1. In almost all strains, phenotypic resistance to streptomycin, tetracycline, trimethoprim/sulfamethoxazole, and sulfisoxazole was observed. Microarray analyses showed that most of the isolates carried four or more antimicrobial resistance markers and STEC strains were categorized as Multridrug-resistant. Although antimicrobials are not usually used in the treatment of STEC infections, the presence of Multridrug-resistant in isolates collected from farm and food represents a risk for animal and human health. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
Open AccessReview Recent Advances in Shiga Toxin-Producing Escherichia coli Research in Latin America
Microorganisms 2018, 6(4), 100; https://doi.org/10.3390/microorganisms6040100
Received: 6 August 2018 / Revised: 1 September 2018 / Accepted: 28 September 2018 / Published: 28 September 2018
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Abstract
Pathogenic Escherichia coli are known to be a common cause of diarrheal disease and a frequently occurring bacterial infection in children and adults in Latin America. Despite the effort to combat diarrheal infections, the south of the American continent remains a hot spot
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Pathogenic Escherichia coli are known to be a common cause of diarrheal disease and a frequently occurring bacterial infection in children and adults in Latin America. Despite the effort to combat diarrheal infections, the south of the American continent remains a hot spot for infections and sequelae associated with the acquisition of one category of pathogenic E. coli, the Shiga toxin-producing E. coli (STEC). This review will focus on an overview of the prevalence of different STEC serotypes in human, animals and food products, focusing on recent reports from Latin America outlining the recent research progress achieved in this region to combat disease and endemicity in affected countries and to improve understanding on emerging serotypes and their virulence factors. Furthermore, this review will highlight the progress done in vaccine development and treatment and will also discuss the effort of the Latin American investigators to respond to the thread of STEC infections by establishing a multidisciplinary network of experts that are addressing STEC-associated animal, human and environmental health issues, while trying to reduce human disease. Regardless of the significant scientific contributions to understand and combat STEC infections worldwide, many significant challenges still exist and this review has focus in the Latin American efforts as an example of what can be accomplished when multiple groups have a common goal. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
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Open AccessArticle Gut Microbiota in Patients with Different Metabolic Statuses: Moscow Study
Microorganisms 2018, 6(4), 98; https://doi.org/10.3390/microorganisms6040098
Received: 21 August 2018 / Revised: 17 September 2018 / Accepted: 18 September 2018 / Published: 25 September 2018
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Abstract
The aim of this paper was to study gut microbiota composition in patients with different metabolic statuses. Methods: 92 participants aged 25–76 years (26 of whom were men), with confirmed absence of cardiovascular and other chronic diseases (but with the possible presence of
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The aim of this paper was to study gut microbiota composition in patients with different metabolic statuses. Methods: 92 participants aged 25–76 years (26 of whom were men), with confirmed absence of cardiovascular and other chronic diseases (but with the possible presence of cardiovascular risk factors) were included. Carotid ultrasound examinations, 16S rRNA sequencing of stool samples and diet assessments were performed. Statistical analysis was performed using R programming language, 3.1.0. Results: Enterotyping yielded two clusters differentiated by alpha-diversity. Intima-media thickness was higher in the cluster with lower diversity (adj. p < 0.001). Obesity was associated with higher Serratia (adj. p = 0.003) and Prevotella (adj. p < 0.0003) in relative abundance. Abdominal obesity was associated with higher abundance of Serratia (adj. p = 0.004) and Prevotella (adj. p = 0.0008) and lower levels of Oscillospira (adj. p = 0.0005). Glucose metabolism disturbances were associated with higher Blautia (adj. p = 0.0007) and Serratia (adj. p = 0.003) prevalence. Arterial hypertension was associated with high Blautia levels (adj. p = 0.002). The Blautia genus strongly correlated with low resistant starch consumption (adj. p = 0.007). A combination of high-fat diet and elevated Blautia levels was very common for diabetes mellitus type 2 patients (adj. p = 0.0001). Conclusion: The results show that there is a relationship between metabolic changes and higher representation of opportunistic pathogens and low diversity of gut microbiota even in apparently healthy participants. Full article
(This article belongs to the Special Issue Gut Microbiota Diversity Relates to Lifestyle)
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Open AccessReview Thermophilic Proteins as Versatile Scaffolds for Protein Engineering
Microorganisms 2018, 6(4), 97; https://doi.org/10.3390/microorganisms6040097
Received: 2 September 2018 / Revised: 23 September 2018 / Accepted: 23 September 2018 / Published: 25 September 2018
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Abstract
Literature from the past two decades has outlined the existence of a trade-off between protein stability and function. This trade-off creates a unique challenge for protein engineers who seek to introduce new functionality to proteins. These engineers must carefully balance the mutation-mediated creation
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Literature from the past two decades has outlined the existence of a trade-off between protein stability and function. This trade-off creates a unique challenge for protein engineers who seek to introduce new functionality to proteins. These engineers must carefully balance the mutation-mediated creation and/or optimization of function with the destabilizing effect of those mutations. Subsequent research has shown that protein stability is positively correlated with “evolvability” or the ability to support mutations which bestow new functionality on the protein. Since the ultimate goal of protein engineering is to create and/or optimize a protein’s function, highly stable proteins are preferred as potential scaffolds for protein engineering. This review focuses on the application potential for thermophilic proteins as scaffolds for protein engineering. The relatively high inherent thermostability of these proteins grants them a great deal of mutational robustness, making them promising scaffolds for various protein engineering applications. Comparative studies on the evolvability of thermophilic and mesophilic proteins have strongly supported the argument that thermophilic proteins are more evolvable than mesophilic proteins. These findings indicate that thermophilic proteins may represent the scaffold of choice for protein engineering in the future. Full article
(This article belongs to the Special Issue Thermophiles and Thermozymes)
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Open AccessArticle Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach
Microorganisms 2018, 6(4), 96; https://doi.org/10.3390/microorganisms6040096
Received: 6 July 2018 / Revised: 10 September 2018 / Accepted: 19 September 2018 / Published: 21 September 2018
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Abstract
Plant surface or phyllosphere is the habitat of hyperdiverse microbial communities and it is always exposed to the fluctuating environmental factors, which is thought to be one of the potential drivers of microbial community structuring. Impact of grapevine genotypes in variable environmental factors
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Plant surface or phyllosphere is the habitat of hyperdiverse microbial communities and it is always exposed to the fluctuating environmental factors, which is thought to be one of the potential drivers of microbial community structuring. Impact of grapevine genotypes in variable environmental factors (i.e., at different geographic locations) on the phyllosphere has never been studied and is the main objective of this report. Using high throughput short amplicon sequencing of 16S rRNA genes and internal transcribed spacer (ITS), we analyzed the impacts of genotypes of Vitis Vinifera (coming from three genetic pool), on the microbial (bacterial and fungal) assemblage in the phyllosphere. First, we performed the analysis of the phyllosphere microbiome while using fifteen genotypes that were chosen to maximize intra-specific diversity and grown in two Mediterranean vineyards. Then, the same analysis was performed on five commercially important varieties of Vitis vinifera that were sampled from three different French agro-climatic zones (or terroir: a combination of climate, soils, and human practices). Our study revealed that, at a particular geographic location, genotypes have an impact on microbial assemblage in the phyllosphere and carposphere of leaf and fruit (or berries), respectively, which is more prominent on the carposphere but the effect of terroir was much stronger than the genotype when the leaf phyllosphere of five grapevine varieties grown in different agro-climatic zones was compared. Impacts of the season and exterior plant organs (leaf and berries) on microbial taxa structuring in the phyllosphere was also assessed and presented in this report. Full article
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