Microbial diversity present on grapes in wineries, and throughout fermentation has been associated with important metabolites for final wine quality. Although microbiome-metabolome associations have been well characterized and could be used as indicators of wine quality, the impact of regionality on the microbiome and metabolome is not well known. Additionally, studies between microbiome and metabolome have been conducted on single species grape such as Vitis vinifera instead of other species and interspecific hybrids. Although the Pennsylvania wine industry is relatively young compared to California, the industry has been experiencing rapid growth over the past decade and is expected to continue to grow in the future. Pennsylvania’s climate of cold winters and high levels of rainfall throughout the growing season favors cultivation of interspecific hybrid grapes such as Vitis ssp. Chambourcin, one of the most commonly grown hybrid varieties in the state. Chambourcin is a prime candidate for studying the impact of regionality on microbiome-metabolome interactions as interspecific hybrid varieties could shape the future of winemaking. Here, we identify for the first time the regional distribution of microbial communities and their interactions with volatile metabolome during fermentation (0–20 days) by integrating high throughput Illumina sequencing (16S and ITS) and headspace-solid phase microextraction-gas chromatography-mass spectrometry. Analyzing 88 samples from nine wineries in the Central and East Pennsylvania regions, we observed high microbial diversity during early stages of fermentation (1–4 days) where non-Saccharomyces yeasts such as Starmerella and Aureobasidium and non-Oenococcus bacteria, Sphingomonas, likely contribute to microbial terroir to the resulting wines. Furthermore, key differentiators between two regions in Pennsylvania, as identified by LEfSe analysis, include the fungal genera Cladosporium and Kazachstania and the bacterial genera Lactococcus and Microbacterium. Moreover, 29 volatile fermentation metabolites were discriminated significantly (variable importance in projection > 1) between the two regions as shown by Partial Least Squares-Discriminant Analysis. Finally, Spearman’s correlation identified regional differences of microbial-metabolite associations throughout fermentation that could be used for targeted microbiome manipulation to improve wine quality and preserve regionality. In summary, these results demonstrate the microbial signatures during fermentation and differential microorganisms and metabolites further support impact of regionality on Chambourcin wines in Pennsylvania.
Objectives Inhalation of crystalline silica (Si) has been linked to the pathogenesis of human autoimmunity such as lupus. Dietary lipid intervention can delay progression of Si-induced autoimmunity in the lupus-prone female NZBWF1 mice. However, the role of gut microbiome relative to dietary lipids and Si-induced autoimmunity is unknown. We seek to ask whether Si-induced pathogenicity and supplementation of a Western diet with DHA can alter gut microbial populations. Methods Four experimental diets were used in this study: modified Total Western Diet (MTWD), MTWD supplemented with DHA (↑DHA), MTWD with reduced saturated and ω-6 fatty acids (↓SFω6), and MTWD with ↓SFω6 and ↑DHA (↓SFω6/↑DHA). Groups of mice (n = 8/gp) were fed one of the four isocaloric experimental diets beginning at 6 wks of age. After 2 wks, mice were anesthetized and intranasally instilled with phosphate-buffered saline (PBS) or Si in PBS. DNA obtained from fecal pellets for gut microbiome analysis was collected from an individual mouse at 13 (early-phase) and 22 (late-phase) wks of age. DNA was extracted and sequenced on the Illumina MiSeq platform. The relative abundance of microbial taxa was differentiated by pairwise comparisons using ANalysis of COmposition of Microbiomes (ANCOM), Linear Mixed model (LM), and LDA Effect Size (LEfSe). Results Lupus triggering by Si with dietary lipid intervention caused a significant difference in Lachnospiraceae bacterium 609 (Lb609) abundance depending on the stringency of analysis frameworks. Under early-phase data, Lb609 was significantly found to be higher in the group of Si-exposed MTWD (MTWD/Si) than all other groups in LefSe analysis (LDA score >3). LM showed the same results except the comparison between MTWD/Si and ↓SFω6 (FDR-adjust P > 0.05). In the results of ANCOM, Lb609 in MTWD/Si was only significantly different from the groups of PBS-exposed MTWD (MTWD/PBS) and ↓SFω6+↑DHA. Although Lb609 was identified discriminatively between MTWD/Si and MTWD/PBS in all analyses from late-phase data, it was not differential in other comparisons. Conclusions Lupus triggering altered microbial composition reflected in increased Lb609 and decreased when supplementation was applied. Further, the studies revealed that interventions on microbial populations were dependent on time. Funding Sources The USDA National Institute of Food and Federal Appropriations.
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