Showing papers by "Bas Teusink published in 2011"

Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

Abstract: The genomes of four Lactobacillus reuteri strains isolated from human breast milk and the gastrointestinal tract have been recently sequenced as part of the Human Microbiome Project. Preliminary genome comparisons suggested that these strains belong to two different clades, previously shown to differ with respect to antimicrobial production, biofilm formation, and immunomodulation. To explain possible mechanisms of survival in the host and probiosis, we completed a detailed genomic comparison of two breast milk–derived isolates representative of each group: an established probiotic strain (L. reuteri ATCC 55730) and a strain with promising probiotic features (L. reuteri ATCC PTA 6475). Transcriptomes of L. reuteri strains in different growth phases were monitored using strain-specific microarrays, and compared using a panmetabolic model representing all known metabolic reactions present in these strains. Both strains contained candidate genes involved in the survival and persistence in the gut such as mucus-binding proteins and enzymes scavenging reactive oxygen species. A large operon predicted to encode the synthesis of an exopolysaccharide was identified in strain 55730. Both strains were predicted to produce health-promoting factors, including antimicrobial agents and vitamins (folate, vitamin B12). Additionally, a complete pathway for thiamine biosynthesis was predicted in strain 55730 for the first time in this species. Candidate genes responsible for immunomodulatory properties of each strain were identified by transcriptomic comparisons. The production of bioactive metabolites by human-derived probiotics may be predicted using metabolic modeling and transcriptomics. Such strategies may facilitate selection and optimization of probiotics for health promotion, disease prevention and amelioration.

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

Abstract: A standard approach to estimate intracellular fluxes on a genome-wide scale is flux-balance analysis (FBA), which optimizes an objective function subject to constraints on (relations between) fluxes. The performance of FBA models heavily depends on the relevance of the formulated objective function and the completeness of the defined constraints. Previous studies indicated that FBA predictions can be improved by adding regulatory on/off constraints. These constraints were imposed based on either absolute or relative gene expression values. We provide a new algorithm that directly uses regulatory up/down constraints based on gene expression data in FBA optimization (tFBA). Our assumption is that if the activity of a gene drastically changes from one condition to the other, the flux through the reaction controlled by that gene will change accordingly. We allow these constraints to be violated, to account for posttranscriptional control and noise in the data. These up/down constraints are less stringent than the on/off constraints as previously proposed. Nevertheless, we obtain promising predictions, since many up/down constraints can be enforced. The potential of the proposed method, tFBA, is demonstrated through the analysis of fluxes in yeast under nine different cultivation conditions, between which approximately 5,000 regulatory up/down constraints can be defined. We show that changes in gene expression are predictive for changes in fluxes. Additionally, we illustrate that flux distributions obtained with tFBA better fit transcriptomics data than previous methods. Finally, we compare tFBA and FBA predictions to show that our approach yields more biologically relevant results.

Systems Biology of lactic acid bacteria: a critical review.

Abstract: Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute. There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them. We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future.

A practical guide to genome-scale metabolic models and their analysis.

Abstract: Genome-scale metabolic reconstructions and their analysis with constraint-based modeling techniques have gained enormous momentum. It is a natural next step after sequencing of a genome, as a technique that links top-down systems biology analyses at genome scale with bottom-up systems biology modeling scrutiny. This chapter aims at (systems) biologists that have an interest in, but no extensive knowledge of, applying genome-scale metabolic reconstruction and modeling to their organism. Rather than being comprehensive--excellent and extensive reviews exist on every aspect of this field--we give a rather personal account on our experience with the process of reconstruction and modeling. First, we place genome-scale metabolic models in the spectrum of modeling approaches, and rather extensively discuss, for nonexperts, the central concept in constraint-based modeling: the solution space that is bounded through constraints on fluxes. We subsequently provide an overview of the different steps involved in metabolic reconstruction and modeling, pointing to aspects that we found difficult, important, not well enough addressed in the current reviews, or any combination thereof. In this way, we hope that this chapter serves as a practical guide through the field.

Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis

Abstract: Background Lactobacillus reuteri harbors the genes responsible for glycerol utilization and vitamin B12 synthesis within a genetic island phylogenetically related to gamma-Proteobacteria. Within this island, resides a gene (lreu_1750) that based on its genomic context has been suggested to encode the regulatory protein PocR and presumably control the expression of the neighboring loci. However, this functional assignment is not fully supported by sequence homology, and hitherto, completely lacks experimental confirmation.

Systems biology of lactic acid bacteria: a critical

Abstract: Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute. There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them. We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future.