Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

UnlabelledRegionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroirImportanceWine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional microbial biodiversity

Elucidating the prebiotic potential of novel sugar beet oligosaccharides and the mechanism of their degradation by Bifidobacterium pseudocatenulatum MP80

Predicting changes in the human gut microbiome is a primary goal of human nutrition researcher because those changes might be controlled to produce health-promoting metabolites and prevent or reverse dysbiosis. Carbohydrate metabolic networks are a central aspect of gut microbial ecosystems, and so deconvoluting those networks may uncover a causal link between dietary carbohydrates and microbiome function. However, the individual carbohydrate structures that compose those networks are difficult to isolate and purify, limiting mechanistic research to the most easily purifiable carbohydrates. For example, impure, branched arabinan from sugar beet is sold for research, and of pure arabinooligosaccharides, only linear ones are commercially available. In this work, the previously described “Fenton’s initiation toward defined oligosaccharide groups” (FITDOG) reaction was used to transform sugar beet pulp pellets into branched and linear oligosaccharide constituents of sugar beet polysaccharides. Because FITDOG is a non-enzymatic, relatively non-biased reaction, it may simulate the natural production of oligosaccharides from dietary polysaccharides by gut bacteria. Branched and linear sugar beet oligosaccharides derived from FITDOG were used to investigate the mechanism of sugar beet oligosaccharide consumption by human gut bacteria. It was demonstrated that in vitro fecal communities enriched by sugar beet oligosaccharides could not be distinguished from those enriched by sugar beet pulp, which implies that FITDOG products are functionally similar to FITDOG reactants. It was also shown that not all adult human Bifidobacterium species can grow on these sugar beet oligosaccharides. These findings demonstrate the potential of FITDOG as a prebiotic oligosaccharide synthesis method. However, only when it is paired with high throughput glycoanalytical tools can it be used to dissect the glycolytic capabilities of human gut bacteria. Mechanistic investigations of oligosaccharide consumption by gut bacteria have been hampered by low-resolution carbohydrate sequencing technology. However, recent advancements in liquid chromatography/mass spectrometry have enabled the performance of monosaccharide and linkage analysis with unprecedented throughput and breadth. High throughput monitoring of the structural motifs that compose even perfectly defined carbohydrate structures is required to describe the mechanism of those structures’ consumption. This is made especially salient when researching the structural specificity of the glycoside hydrolases. Here we also describe a workflow to find the structural specificity of bacterial glycoside hydrolases that mediate cross-feeding between primary and secondary dietary fiber degraders of arabinan with high throughput monosaccharide, linkage, and oligosaccharide composition analysis. Bifidobacterium pseudocatenulatum was chosen to demonstrate this workflow because it cannot metabolize arabinan, yet it metabolizes sugar beet arabinooligosaccharides and encodes the most predicted arabinosidases in human Bifidobacterium behind Bifidobacterium longum subsp. longum, which can metabolize arabinan. The specificity of arabinofuranosidases from Bifidobacterium pseudocatenulatum suggest that it cleaves arabinan and arabinofuranooligosaccharides with extracellular, substitution-intolerant, endo-arabinofuranosidases. Comparative genomics of Bifidobacterium strains that do and do not grow on sugar beet oligosaccharides and arabinan suggests Bifidobacterium pseudocatenulatum competes with Bifidobacterium longum subsp. longum and Bacteroides species for unsubstituted or lightly substituted arabinofuranooligosaccharides. FITDOG produces diverse oligosaccharides from polysaccharides without highly specific enzymes, meaning this workflow can be used to describe bacterial cross-feeding mechanisms between primary and secondary dietary fiber degraders of any carbohydrate-containing food

Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics

Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir.ISSN:2150-7511ISSN:2161-212

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir Wine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional microbial biodiversity

Bacterial colonization and antimicrobial resistance genes in neonatal enteral feeding tubes.

Enteral feeding is a key component of care in neonatal intensive care units (NICUs); however, feeding tubes harbor microbes. These microbes have the potential to cause disease, yet their source remains controversial and clinical recommendations to reduce feeding tube colonization are lacking. This study aims to improve our understanding of the bacteria in neonatal feeding tubes and to evaluate factors that may affect these bacteria. 16S rRNA gene sequencing was used to characterize the bacteria present in pharyngeal, esophageal, and gastric portions of feeding tubes, residual fluid of the tubes, and infant stool using samples from 47 infants. Similar distributions of taxa were observed in all samples, although beta diversity differed by sample type. Feeding tube samples had lower alpha diversity than stool samples, and alpha diversity increased with gestational age, day of life, and tube dwell time. In a subset of samples from 6 infants analyzed by whole metagenome sequencing, there was greater overlap in transferable antimicrobial resistance genes between tube and fecal samples in breast milk fed infants than in formula fed infants. These findings develop our understanding of neonatal feeding tube colonization, laying a foundation for research into methods for minimizing NICU patients' exposure to antimicrobial resistant microbes

Quantifying Gut Microbial Short-Chain Fatty Acids and Their Isotopomers in Mechanistic Studies Using a Rapid, Readily Expandable LC-MS Platform.

Short-chain fatty acids (SCFAs) comprise the largest group of gut microbial fermentation products. While absorption of most nutrients occurs in the small intestine, indigestible dietary components, such as fiber, reach the colon and are processed by the gut microbiome to produce a wide array of metabolites that influence host physiology. Numerous studies have implicated SCFAs as key modulators of host health, such as in regulating irritable bowel syndrome (IBS). However, robust methods are still required for their detection and quantitation to meet the demands of biological studies probing the complex interplay of the gut-host-health paradigm. In this study, a sensitive, rapid-throughput, and readily expandible UHPLC-QqQ-MS platform using 2-PA derivatization was developed for the quantitation of gut-microbially derived SCFAs, related metabolites, and isotopically labeled homologues. The utility of this platform was then demonstrated by investigating the production of SCFAs in cecal contents from mice feeding studies, human fecal bioreactors, and fecal/bacterial fermentations of isotopically labeled dietary carbohydrates. Overall, the workflow proposed in this study serves as an invaluable tool for the rapidly expanding gut-microbiome and precision nutrition research field

A comparison of bacterial colonization between nasogastric and orogastric enteral feeding tubes in infants in the neonatal intensive care unit

ObjectiveFeeding tubes harbor microbial contaminants; studies to date have not explored differences between orogastric (OG) and nasogastric (NG) tube biofilms. We sought to extend a previous analysis by comparing bacterial colonization by location (OG v NG) and by evaluating clinical factors that may affect tube bacterial populations.Study designThe pharyngeal segments of 41 infant feeding tubes (14 OG and 27 NG) from 41 infants were analyzed by next generation 16 S rRNA sequencing on the MiSeq platform.ResultsAt the phylum level, Proteobacteria had the highest relative abundance of both OG and NG tubes. At the genus/species level, nine taxa differed significantly between OG and NG tubes. Alpha and beta diversity analyses showed significant differences between OG and NG tubes with relatively little contribution from clinical factors.ConclusionThe route of feeding tube insertion (oral vs nasal) had a greater impact on bacterial colonization than the assessed clinical factors

Validating bifidobacterial species and subspecies identity in commercial probiotic products.

BackgroundThe ingestion of probiotics to attempt to improve health is increasingly common; however, quality control of some commercial products can be limited. Clinical practice is shifting toward the routine use of probiotics to aid in prevention of necrotizing enterocolitis in premature infants, and probiotic administration to term infants is increasingly common to treat colic and/or prevent atopic disease. Since bifidobacteria dominate the feces of healthy breast-fed infants, they are often included in infant-targeted probiotics.MethodsWe evaluated 16 probiotic products to determine how well their label claims describe the species of detectable bifidobacteria in the product. Recently developed DNA-based methods were used as a primary means of identification, and were confirmed using culture-based techniques.ResultsWe found that the contents of many bifidobacterial probiotic products differ from the ingredient list, sometimes at a subspecies level. Only 1 of the 16 probiotics perfectly matched its bifidobacterial label claims in all samples tested, and both pill-to-pill and lot-to-lot variation were observed.ConclusionGiven the known differences between various bifidobacterial species and subspecies in metabolic capacity and colonization abilities, the prevalence of misidentified bifidobacteria in these products is cause for concern for those involved in clinical trials and consumers of probiotic products