High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China

Wu, Yujie; Wu, Yun; Yan, Yinzhuo; Zou, Wan; Xue, Jie; Ma, Wei; Wang, Wei; Tian, Ge; Wang, Liye

doi:10.1371/journal.pone.0193097

Cited by 90 publications

(72 citation statements)

References 56 publications

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“…Similarly, Kaistobacter is also found within the soil, with no reported association with specific disease states. [43] The implications of the presence of these organisms is unknown given the paucity of data within the literature. As this data is from a single mouse, we were not powered to examine the effects of alterations in the baseline microbiome with increased risk of bladder cancer.…”

Section: Discussionmentioning

confidence: 99%

Profiling of urine bacterial DNA to identify an “oncobiome” in a mouse model of bladder cancer

Banskota

et al. 2018

Preprint

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Introduction: Recurrent urinary tract infections have been linked to increased risk of bladder cancer, suggesting a potential role of the urinary microbiome in bladder cancer pathogenesis.Objective: Compare the urinary microbiomes in mice with and without bladder. Methods:Longitudinal study of mice exposed to a dilute bladder-specific carcinogen (0.05% nbutyl-n-(4-hydroxybutyl) nitrosamine, BBN mice, n=10), and control mice (n=10). Urine was sampled monthly from individual mice for 4 months. Microbial DNA was extracted from the urine, and the V4 region of the 16S rRNA gene sequenced. Animals were sacrificed and their bladders harvested for histopathology. Bladder sections were graded by a blinded pathologist. The composition and diversity of the urinary microbiome were compared between the BBN and control mice. Metabolic pathway analysis was completed using PICRUST.Results: Bladder histology in the BBN group showed normal tissue with inflammation (BBNnormal, n=5), precancerous pathologies, (BBN-precancerous, n=3), and invasive cancer (BBNcancer, n=2). Alpha diversity did not differ between the mice exposed to BBN and the control mice at any timepoint. There were no differences in the urinary microbiomes between the BBN and control mice at baseline. At month 4, mice exposed to BBN had higher proportion of both Gardnerella and Bifidobacterium compared to control mice. There were no differences in proportions of specific bacteria between either the BBN-precancer or BBN-cancer and controls at month 4. However, the BBN-normal mice had higher proportions of Gardnerella, Haemophilus, Bifidobacterium, and Ureaplasma Actinobaculum, and lower proportions of Actinomyces, compared to control mice at month 4. Functional pathway analysis demonstrated increases in genes related to purine metabolism, phosphotransferase systems, peptidases, protein folding, and bacterial toxins in the BBN-mice compared to control mice at month 4.Conclusion: Mice exposed to 4 months of BBN, a bladder-specific carcinogen, have distinct urine microbial profiles compared to control mice.

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Section: Discussionmentioning

confidence: 99%

Profiling of urine bacterial DNA to identify an “oncobiome” in a mouse model of bladder cancer

Banskota

et al. 2018

Preprint

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“…During malolactic fermentation Shewanella, Halomonas, and Oenococcus became the dominant genera, whereas at the end of fermentation, Oenococcus, with the species Oenococcus oeni, became the abundant bacterium of the three wines' microbiome. Similarly, HTS analysis of Cabernet Sauvignon samples from three different winery regions in Xinjiang province, China, from Fukang area, identified a common core microbiome composed mostly by the fungal genera Aureobasidium, Pleosporaceae, Cryptococcus, and Dothideales and the bacterial genera Pseudomonas, Acinetobacter, Kaistobacter, Arthrobacter, and Sphingomonas in all grape and grape juice samples analyzed, even though the relative abundances of those genera were different [15]. However, following malolactic fermentation, the microbial biodiversity was gradually reduced and limited mostly to the fungal genera Aspergillus, Penicillium, and Alternaria, while the slowgrowing, necessary for malolactic fermentation, lactic acid bacterium Oenococcus appeared to be the dominant genus in all wine samples.…”

Section: (A) Representation Of the Relative Abundance Of Bacterial Famentioning

confidence: 93%

“…High-throughput sequencing techniques have allowed the discrimination of the microbial diversity as dynamically formed from the initiation of fermentation until wine production, identifying also the non-culturable microorganisms, as well as the limited represented species [12][13][14][15][16] (Figure 2). During the process of fermentation, the microbial community is reshaped and become dominated by the fermentative organisms.…”

Section: Microbial Evolution Of Must During Spontaneous Fermentation mentioning

confidence: 99%

“…The high detection sensitivities of HTS technologies have allowed the identification of the rich bacterial biodiversity implicated in Cabernet, Negroamaro, and Stefanini et al [16], Marzano et al [14], Wei et al [15], and Pinto et al [13].…”

Section: Microbial Evolution Of Must During Spontaneous Fermentation mentioning

confidence: 99%

“…The development of high-throughput sequencing technologies has allowed the evaluation of the microbial consortium comprising grapes' microbiome in terms of revealing the concept of the microbial terroir [12][13][14][15][16]. The contribution of originassociated factors of grape varieties, including climate and microclimate, region site, as well as grape cultivar, in the microbial community formation and the final metabolic profiles, has been recently investigated [12,[17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%

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Contribution of the Microbiome as a Tool for Estimating Wine’s Fermentation Output and Authentication

Anagnostopoulos¹,

Kamilari²,

Tsaltas³

2019

Advances in Grape and Wine Biotechnology

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Wine is the alcoholic beverage which is the product of alcoholic fermentation, usually, of fresh grape must. Grape microbiome is the source of a vastly diverse pool of filamentous fungi, yeast, and bacteria, the combination of which plays a crucial role for the quality of the final product of any grape must fermentation. In recent times, the significance of this pool of microorganisms has been acknowledged by several studies analyzing the microbial ecology of grape berries of different geographical origins, cultural practices, grape varieties, and climatic conditions. Furthermore, the microbial evolution of must during fermentation process has been overstudied. The combination of the microbial evolution along with metabolic and sensorial characterizations of the produced wines could lead to the suggestion of the microbial terroir. These aspects are today leading to open a new horizon for products such as wines, especially in the case of PDO-PGI products. The aims of this review is to describe (a) how the microbiome communities are dynamically differentiated during the process of fermentation from grape to ready-to-drink wine, in order to finalize each wine's unique sensorial characteristics, and (b) whether the microbiome could be used as a fingerprinting tool for geographical indication, based on high-throughput sequencing (HTS) technologies. Nowadays, it has been strongly indicated that microbiome analysis of grapes and fermenting musts using next-generation sequencing (NGS) could open a new horizon for wine, in the case of protected designation of origin (PDO) and protected geographical indication (PGI) determination.

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Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard

Mandl

Cantelmo

Gruber

et al. 2018

Bull Environ Contam Toxicol

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In a vineyard we examined the effects of broad-spectrum herbicides with three different active ingredients (glyphosate, glufosinate, flazasulfuron) on soil microorganisms. Mechanical weeding served as control treatment. Treatments were applied within grapevine rows and soil samples taken from there in 10–20 cm depth 77 days after application. Fungi were analyzed using classical sequencing technology and bacteria using next-generation sequencing. The number of colony-forming units (CFU) comprising bacteria, yeasts and molds was higher under flazasulfuron compared to all other treatments which had similar CFU levels. Abundance of the fungus Mucor was higher under flazasulfuron than glufosinate and mechanical weeding; Mucor was absent under glyphosate. Several other fungi taxa were exclusively found under a specific treatment. Up to 160 different bacteria species were found – some of them for the first time in vineyard soils. Total bacterial counts under herbicides were on average 260% higher than under mechanical weeding; however due to high variability this was not statistically significant. We suggest that herbicide-induced alterations of soil microorganisms could have knock-on effects on other parts of the grapevine system.

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High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China

Cited by 90 publications

References 56 publications

Profiling of urine bacterial DNA to identify an “oncobiome” in a mouse model of bladder cancer

Profiling of urine bacterial DNA to identify an “oncobiome” in a mouse model of bladder cancer

Contribution of the Microbiome as a Tool for Estimating Wine’s Fermentation Output and Authentication

Effects of Glyphosate-, Glufosinate- and Flazasulfuron-Based Herbicides on Soil Microorganisms in a Vineyard

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