Biology subjects

Scott, W. T.

Publications and source records attributed to Scott, W. T..

5 recordsLinked to original sources

bioRxiv2024

Deep sequencing of 16 Ixodes ricinus ticks unveils insights into their interactions with endosymbionts.

BackgroundIxodes ricinus ticks act as vectors for numerous pathogens that present substantial health threats. Additionally, they harbour vertically transmitted symbionts, some of which have been linked to diseases. The difficulty of isolating and cultivating these symbionts has hampered our understanding of their biological role, their potential to cause disease, and their modes of transmission. To expand our understanding on the tick symbiont Midichloria mitochondrii and on Rickettsia helvetica, which has been linked to disease in humans, we utilized deep sequencing on sixteen individual adult female ticks collected from coastal dune and forested areas in the Netherlands. ResultsBy employing a combination of second and third-generation sequencing techniques, we successfully reconstructed the complete genomes of M. mitochondrii from eleven individuals, R. helvetica from eight individuals and the mitochondrial genome from all ticks. Additionally, we visualised the location of R. helvetica in tick organs and constructed genome-scale metabolic models (GEMs) of both symbionts to study their environmental dependencies. Our analysis revealed a strong cophylogeny between M. mitochondrii and mitochondrial genomes, suggesting frequent maternal transmission. In contrast, the absence of cophylogeny between R. helvetica and the mitochondrial genomes, coupled with its presence in the receptaculum seminis of I. ricinus females, raises the possibility of paternal transmission of R. helvetica. Notably, the genetic diversity of R. helvetica was found to be very low, except for the rickA virulence gene, where the presence of up to thirteen insertions of a33nt-long repeat led to significant variability. However, this variation could not account for the differences in infection prevalence observed across eight distinct locations in the Netherlands. ConclusionsBy employing deep sequencing, it becomes feasible to extract complete genomes and genetic data of symbionts directly from their host organisms. This methodology serves as a robust means to gain fresh insights into their interactions. Our observations, which suggest paternal transmission of R. helvetica, a relatively unexplored mode of transmission in ticks, require validation through experimental investigations. The genetic variations identified in the rickA virulence gene of R. helvetica have the potential to influence the infectivity and transmission dynamics of R. helvetica

microbiology↗

bioRxiv2023

Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This have increased the quality and scope of this model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or normal conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through the central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference in nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine-learning models. Based on those findings we anticipate that Yeast9 will empower systems biology studies of yeast metabolism.

systems biology↗

bioRxiv2023

A Structured Evaluation of Genome-Scale Constraint-Based Modeling Tools for Microbial Consortia

Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools. Author summaryConstraint-based modeling employing genome-scale reconstructions of microbial species has become one of the most successful approaches for studying, analyzing, and engineering microbial consortia. Over the past decade, many constraint-based modeling tools have been published to examine an immense variety of microbial consortia spanning from the application areas of bioremediation to food and health biotechnology. However, new potential users lack an overview of the quality and performance of existing metabolic modeling tools that would guide their choice. To tackle this issue, we examined 24 tools for genome-scale metabolic modeling of microbial consortia. After an initial qualitative screening, we quantitatively evaluated 14 adequate tools against published experimental data that included different organisms and conditions. We conducted simulations and evaluated model features such as predictive accuracy, computational time, and tractability in capturing critical physiological properties. We found that, generally, more up-to-date, accessible, and documented tools were superior in many important aspects of model quality and performance. Although, in some cases, we observed tradeoffs in older, less elaborate tools that can be more accurate or flexible. This work has broad implications to help researchers navigate the most suitable tools, and suggests to developers opportunities for improvement of the currently existing capabilities for metabolic modeling of multi-species microbial consortia.

systems biology↗

bioRxiv2022

Dynamic genome-scale modeling of Saccharomyces cerevisiae unravels mechanisms for higher alcohol and ester formation during alcoholic fermentation

Fermentation employing Saccharomyces cerevisiae has produced alcoholic beverages and bread for millennia. More recently, S. cerevisiae has been used to manufacture specific metabolites for the food, pharmaceutical, and cosmetic industries. Among the most important of these metabolites are compounds associated with desirable aromas and flavors, including higher alcohols and esters. Although the physiology of yeast has been well-studied, its metabolic modulation leading to aroma production in relevant industrial scenarios such as winemaking is still unclear. Here we ask what are the underlying metabolic mechanisms that explain the conserved and varying behavior of different yeasts regarding aroma formation under enological conditions? We employed dynamic flux balance analysis (dFBA) to answer this key question using the latest genome-scale metabolic model (GEM) of S. cerevisiae. The model revealed several conserved mechanisms among wine yeasts, e.g., acetate ester formation is dependent on intracellular metabolic acetyl-CoA/CoA levels, and the formation of ethyl esters facilitates the removal of toxic fatty acids from cells using CoA. Species-specific mechanisms were also found, such as a preference for the shikimate pathway leading to more 2-phenylethanol production in the Opale strain as well as strain behavior varying notably during the carbohydrate accumulation phase and carbohydrate accumulation inducing redox restrictions during a later cell growth phase for strain Uvaferm. In conclusion, our new metabolic model of yeast under enological conditions revealed key metabolic mechanisms in wine yeasts, which will aid future research strategies to optimize their behavior in industrial settings.

systems biology↗

bioRxiv2021

Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity

Strain and environmental nutrient concentrations can affect the production of sensory impact compounds during yeast fermentation. Despite reports on the impact of nutrient conditions on kinetics of cellular growth, it is uncertain to what extent nitrogen utilization by commercial Saccharomyces cerevisiae wine strains affects the production of volatile organic (aroma) compounds (VOCs). Here we ask whether i) consumption of amino acids contribute to VOCs (fusel alcohols, acetate esters, and fatty acid esters) in commercial S. cerevisiae yeast strains, ii) there is inter-strain variation in VOC production, and iii) there is a correlation between the production of aroma compounds and nitrogen utilization. We analyzed the consumption of nutrients as well as the production of major VOCs during fermentation of a chemically defined grape juice medium with four commercial S. cerevisiae yeast strains: Elixir, Opale, R2, and Uvaferm. The production of VOCs was variable among the strains where Uvaferm correlated with ethyl acetate and ethyl hexanoate production, R2 negatively correlated with the acetate esters, and Opale positively correlated with fusel alcohols. The four strains total biomass formation was similar, pointing to metabolic differences in the utilization of nutrients to form secondary metabolites such as VOCs. To understand the strain-dependent differences in VOC production, partial least-squares linear regression coupled with genome-scale metabolic modeling was performed with the objective to correlate nitrogen utilization with fermentation biomass and volatile formation. Total aroma production was found to be a strong function of nitrogen utilization (R2 = 0.87). We found that glycine, tyrosine, leucine, and lysine utilization were positively correlated with fusel alcohols and acetate esters concentrations e.g., 2-phenyl acetate during wine fermentation. Parsimonious flux balance analysis and flux enrichment analysis confirmed the usage of these nitrogen utilization pathways based on the strains VOC production phenotype. IMPORTANCESaccharomyces cerevisiae is widely used in grape juice fermentation to produce wines. Along with the genetic background, the nitrogen in the environment in which S. cerevisiae grows impacts its regulation of metabolism. Also, commercial S. cerevisiae strains exhibit immense diversity in their formation of aromas, and a desirable aroma bouquet is an essential characteristic for wines. Since nitrogen affects aroma formation in wines, it is essential to know the extent of this connection and how it leads to strain-dependent aroma profiles in wines. We evaluated the differences in the production of key aroma compounds among four commercial wine strains. Moreover, we analyzed the role of nitrogen utilization on the formation of various aroma compounds. This work illustrates the unique aroma producing differences among industrial yeast strains and suggests more intricate, nitrogen associated routes influencing those aroma producing differences.

microbiology↗