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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Thesis
  • Peer Reviewed
UC Davis Electronic Theses and Dissertations (2023)

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.

    Cover page: Elucidating the prebiotic potential of novel sugar beet oligosaccharides and the mechanism of their degradation by Bifidobacterium pseudocatenulatum MP80
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2016)

    Background

    The 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.

    Methods

    We 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.

    Results

    We 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.

    Conclusion

    Given 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.
      Cover page: Validating bifidobacterial species and subspecies identity in commercial probiotic products
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2019)
      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.
        Cover page: Bacterial colonization and antimicrobial resistance genes in neonatal enteral feeding tubes
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2022)

        Objective

        Feeding 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 design

        The 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.

        Results

        At 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.

        Conclusion

        The route of feeding tube insertion (oral vs nasal) had a greater impact on bacterial colonization than the assessed clinical factors.
          Cover page: A comparison of bacterial colonization between nasogastric and orogastric enteral feeding tubes in infants in the neonatal intensive care unit
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2016)

          Unlabelled

          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

          Importance

          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.
            Cover page: Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2024)
            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.
              Cover page: Quantifying Gut Microbial Short-Chain Fatty Acids and Their Isotopomers in Mechanistic Studies Using a Rapid, Readily Expandable LC-MS Platform.
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2024)
              Human milk oligosaccharides (HMOs) are a diverse class of carbohydrates which support the health and development of infants. The vast health benefits of HMOs have made them a commercial target for microbial production; however, producing the approximately 200 structurally diverse HMOs at scale has proved difficult. Here we produce a diversity of HMOs by leveraging the robust carbohydrate anabolism of plants. This diversity includes high-value and complex HMOs, such as lacto-N-fucopentaose I. HMOs produced in transgenic plants provided strong bifidogenic properties, indicating their ability to serve as a prebiotic supplement with potential applications in adult and infant health. Technoeconomic analyses demonstrate that producing HMOs in plants provides a path to the large-scale production of specific HMOs at lower prices than microbial production platforms. Our work demonstrates the promise in leveraging plants for the low-cost and sustainable production of HMOs.
                Cover page: Engineered plants provide a photosynthetic platform for the production of diverse human milk oligosaccharides
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2022)
                The molecular complexity of the carbohydrates consumed by humans has been deceptively oversimplified due to a lack of analytical methods that possess the throughput, sensitivity, and resolution required to provide quantitative structural information. However, such information is becoming an integral part of understanding how specific glycan structures impact health through their interaction with the gut microbiome and host physiology. This work presents a detailed catalogue of the glycans present in complementary foods commonly consumed by toddlers during weaning and foods commonly consumed by American adults. The monosaccharide compositions of over 800 foods from diverse food groups including Fruits, Vegetables, Grain Products, Beans, Peas, Other Legumes, Nuts, Seeds; Sugars, Sweets and Beverages; Animal Products, and more were obtained and used to construct the "Davis Food Glycopedia" (DFG), an open-access database that provides quantitative structural information on the carbohydrates in food. While many foods within the same group possessed similar compositions, hierarchical clustering analysis revealed similarities between different groups as well. Such a Glycopedia can be used to formulate diets rich in specific monosaccharide residues to provide a more targeted modulation of the gut microbiome, thereby opening the door for a new class of prophylactic or therapeutic diets.
                  Cover page: The Development of the Davis Food Glycopedia—A Glycan Encyclopedia of Food
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2022)
                  Human milk enriches members of the genus Bifidobacterium in the infant gut. One species, Bifidobacterium pseudocatenulatum, is found in the gastrointestinal tracts of adults and breastfed infants. In this study, B. pseudocatenulatum strains were isolated and characterized to identify genetic adaptations to the breastfed infant gut. During growth on pooled human milk oligosaccharides (HMOs), we observed two distinct groups of B. pseudocatenulatum, isolates that readily consumed HMOs and those that did not, a difference driven by variable catabolism of fucosylated HMOs. A conserved gene cluster for fucosylated HMO utilization was identified in several sequenced B. pseudocatenulatum strains. One isolate, B. pseudocatenulatum MP80, which uniquely possessed GH95 and GH29 α-fucosidases, consumed the majority of fucosylated HMOs tested. Furthermore, B. pseudocatenulatum SC585, which possesses only a single GH95 α-fucosidase, lacked the ability to consume the complete repertoire of linkages within the fucosylated HMO pool. Analysis of the purified GH29 and GH95 fucosidase activities directly on HMOs revealed complementing enzyme specificities with the GH95 enzyme preferring 1-2 fucosyl linkages and the GH29 enzyme favoring 1-3 and 1-4 linkages. The HMO-binding specificities of the family 1 solute-binding protein component linked to the fucosylated HMO gene cluster in both SC585 and MP80 are similar, suggesting differential transport of fucosylated HMO is not a driving factor in each strain's distinct HMO consumption pattern. Taken together, these data indicate the presence or absence of specific α-fucosidases directs the strain-specific fucosylated HMO utilization pattern among bifidobacteria and likely influences competitive behavior for HMO foraging in situ. IMPORTANCE Often isolated from the human gut, microbes from the bacterial family Bifidobacteriaceae commonly possess genes enabling carbohydrate utilization. Isolates from breastfed infants often grow on and possess genes for the catabolism of human milk oligosaccharides (HMOs), glycans found in human breast milk. However, catabolism of structurally diverse HMOs differs between bifidobacterial strains. This study identifies key gene differences between Bifidobacterium pseudocatenulatum isolates that may impact whether a microbe successfully colonizes an infant gut. In this case, the presence of complementary α-fucosidases may provide an advantage to microbes seeking residence in the infant gut. Such knowledge furthers our understanding of how diet drives bacterial colonization of the infant gut.
                    Cover page: Fucosylated Human Milk Oligosaccharide Foraging within the Species Bifidobacterium pseudocatenulatum Is Driven by Glycosyl Hydrolase Content and Specificity
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2022)
                    Bifidobacterium species are beneficial and dominant members of the breastfed infant gut microbiome; however, their health benefits are partially species-dependent. Here, we characterize the species and subspecies of Bifidobacterium in breastfed infants around the world to consider the potential impact of a historic dietary shift on the disappearance of B. longum subsp. infantis in some populations. Across populations, three distinct patterns of Bifidobacterium colonization emerged: (1) The dominance of Bifidobacterium longum subspecies infantis, (2) prevalent Bifidobacterium of multiple species, and (3) the frequent absence of any Bifidobacterium. These patterns appear related to a country's history of breastfeeding, with infants in countries with historically high rates of long-duration breastfeeding more likely to be colonized by B. longum subspecies infantis compared with infants in countries with histories of shorter-duration breastfeeding. In addition, the timing of infant colonization with B. longum subsp. infantis is consistent with horizontal transmission of this subspecies, rather than the vertical transmission previously reported for other Bifidobacterium species. These findings highlight the need to consider historical and cultural influences on the prevalence of gut commensals and the need to understand epidemiological transmission patterns of Bifidobacterium and other major commensals.
                      Cover page: Bifidobacterium Species Colonization in Infancy: A Global Cross-Sectional Comparison by Population History of Breastfeeding.
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