Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

Flux sampling in genome-scale metabolic modeling of microbial communities

BACKGROUND

Microbial communities play a crucial role in ecosystem function through metabolic interactions. Genome-scale modeling is a promising method to understand these interactions and identify strategies to optimize the community. Flux balance analysis (FBA) is most often used to predict the flux through all reactions in a genome-scale model; however, the fluxes predicted by FBA depend on a user-defined cellular objective. Flux sampling is an alternative to FBA, as it provides the range of fluxes possible within a microbial community. Furthermore, flux sampling can capture additional heterogeneity across a population, especially when cells exhibit sub-maximal growth rates.

RESULTS

In this study, we simulate the metabolism of microbial communities and compare the metabolic characteristics found with FBA and flux sampling. With sampling, we find significant differences in the predicted metabolism, including an increase in cooperative interactions and pathway-specific changes in predicted flux.

CONCLUSIONS

Our results suggest the importance of sampling-based approaches to evaluate metabolic interactions. Furthermore, we emphasize the utility of flux sampling in quantitatively studying interactions between cells and organisms.

Dynamic flux balance analysis of 1,3-propanediol production by clostridium butyricum fermentation

To study the relationship between the yield of 1,3-propanediol (1,3-PDO) and the flux change of the Clostridium butyricum metabolic pathway, an optimized calculation method based on dynamic flux balance analysis was used by combining genome-scale flux balance analysis with a kinetic model. A more comprehensive and extensive metabolic pathway was obtained by optimization calculations. The primary extended branches include: the dihydroxyacetone node, which enters the pentose phosphate pathway; the α-oxoglutarate node, which has synthetic metabolic pathways for glutamic acid and amino acids; and the serine and homocysteine nodes, which produce cystathionine before homocysteine enters the methionine cycle pathway. According to the expanded metabolic network, the flux distribution of key nodes in the metabolic pathway and the relationship between the flux distribution ratio of nodes and the yield of 1,3-PDO were analyzed. At the dihydroxyacetone node, the flux of dihydroxyacetone converted to dihydroxyacetone phosphate was positively correlated with the yield of 1,3-PDO. As an important intermediate product, the flux change in the metabolic pathway of α-oxoglutarate reacting with amino acids to produce glutamic acid is positively correlated with the yield. When pyruvate was used as the central node to convert into lactic acid and α-oxoglutarate, the proportion of branch flux was negatively correlated with the yield of 1,3-PDO. These studies provide a theoretical basis for the optimization and further study of the metabolic pathway of C. butyricum.

Trade-offs between the instantaneous growth rate and long-term fitness: Consequences for microbial physiology and predictive computational models

Microbial systems biology has made enormous advances in relating microbial physiology to the underlying biochemistry and molecular biology. By meticulously studying model microorganisms, in particular Escherichia coli and Saccharomyces cerevisiae, increasingly comprehensive computational models predict metabolic fluxes, protein expression, and growth. The modeling rationale is that cells are constrained by a limited pool of resources that they allocate optimally to maximize fitness. As a consequence, the expression of particular proteins is at the expense of others, causing trade-offs between cellular objectives such as instantaneous growth, stress tolerance, and capacity to adapt to new environments. While current computational models are remarkably predictive for E. coli and S. cerevisiae when grown in laboratory environments, this may not hold for other growth conditions and other microorganisms. In this contribution, we therefore discuss the relationship between the instantaneous growth rate, limited resources, and long-term fitness. We discuss uses and limitations of current computational models, in particular for rapidly changing and adverse environments, and propose to classify microbial growth strategies based on Grimes's CSR framework.

Genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer

Colorectal cancer (CRC) shows high incidence and mortality, partly due to the tumor microenvironment (TME), which is viewed as an active promoter of disease progression. Macrophages are among the most abundant cells in the TME. These immune cells are generally categorized as M1, with inflammatory and anti-cancer properties, or M2, which promote tumor proliferation and survival. Although the M1/M2 subclassification scheme is strongly influenced by metabolism, the metabolic divergence between the subtypes remains poorly understood. Therefore, we generated a suite of computational models that characterize the M1- and M2-specific metabolic states. Our models show key differences between the M1 and M2 metabolic networks and capabilities. We leverage the models to identify metabolic perturbations that cause the metabolic state of M2 macrophages to more closely resemble M1 cells. Overall, this work increases understanding of macrophage metabolism in CRC and elucidates strategies to promote the metabolic state of anti-tumor macrophages.

Extracting functionally accurate context-specific models of Atlantic salmon metabolism

Constraint-based models (CBMs) are used to study metabolic network structure and function in organisms ranging from microbes to multicellular eukaryotes. Published CBMs are usually generic rather than context-specific, meaning that they do not capture differences in reaction activities, which, in turn, determine metabolic capabilities, between cell types, tissues, environments, or other conditions. Only a subset of a CBM's metabolic reactions and capabilities are likely to be active in any given context, and several methods have therefore been developed to extract context-specific models from generic CBMs through integration of omics data. We tested the ability of six model extraction methods (MEMs) to create functionally accurate context-specific models of Atlantic salmon using a generic CBM (SALARECON) and liver transcriptomics data from contexts differing in water salinity (life stage) and dietary lipids. Three MEMs (iMAT, INIT, and GIMME) outperformed the others in terms of functional accuracy, which we defined as the extracted models' ability to perform context-specific metabolic tasks inferred directly from the data, and one MEM (GIMME) was faster than the others. Context-specific versions of SALARECON consistently outperformed the generic version, showing that context-specific modeling better captures salmon metabolism. Thus, we demonstrate that results from human studies also hold for a non-mammalian animal and major livestock species.

Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities

Microbial communities play a crucial role in ecosystem function through metabolic interactions. Genome-scale modeling is a promising method to understand these interactions. Flux balance analysis (FBA) is most often used to predict the flux through all reactions in a genome-scale model. However, the fluxes predicted by FBA depend on a user-defined cellular objective. Flux sampling is an alternative to FBA, as it provides the range of fluxes possible within a microbial community. Furthermore, flux sampling may capture additional heterogeneity across cells, especially when cells exhibit sub-maximal growth rates. In this study, we simulate the metabolism of microbial communities and compare the metabolic characteristics found with FBA and flux sampling. We find significant differences in the predicted metabolism with sampling, including increased cooperative interactions and pathway-specific changes in predicted flux. Our results suggest the importance of sampling-based and objective function-independent approaches to evaluate metabolic interactions and emphasize their utility in quantitatively studying interactions between cells and organisms.

Machine learning for metabolic pathway optimization: A review

Optimizing the metabolic pathways of microbial cell factories is essential for establishing viable biotechnological production processes. However, due to the limited understanding of the complex setup of cellular machinery, building efficient microbial cell factories remains tedious and time-consuming. Machine learning (ML), a powerful tool capable of identifying patterns within large datasets, has been used to analyze biological datasets generated using various high-throughput technologies to build data-driven models for complex bioprocesses. In addition, ML can also be integrated with Design-Build-Test-Learn to accelerate development. This review focuses on recent ML applications in genome-scale metabolic model construction, multistep pathway optimization, rate-limiting enzyme engineering, and gene regulatory element designing. In addition, we have discussed some limitations of these methods as well as potential solutions.

Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer

1Colorectal cancer (CRC) shows high incidence and mortality, partly due to the tumor microenvironment, which is viewed as an active promoter of disease progression. Macrophages are among the most abundant cells in the tumor microenvironment. These immune cells are generally categorized as M1, with inflammatory and anti-cancer properties, or M2, which promote tumor proliferation and survival. Although the M1/M2 subclassification scheme is strongly influenced by metabolism, the metabolic divergence between the subtypes remains poorly understood. Therefore, we generated a suite of computational models that characterize the M1- and M2-specific metabolic states. Our models show key differences between the M1 and M2 metabolic networks and capabilities. We leverage the models to identify metabolic perturbations that cause the metabolic state of M2 macrophages to more closely resemble M1 cells. Overall, this work increases understanding of macrophage metabolism in CRC and elucidates strategies to promote the metabolic state of anti-tumor macrophages.

COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions

Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabolite leakage is lacking. Here, we first show that the consensus of automatically generated metabolic reconstructions improves the quality of the draft reconstructions, measured by comparison to reference models. We then devise an approach for gap filling, termed COMMIT, that considers metabolites for secretion based on their permeability and the composition of the community. By applying COMMIT with two soil communities from the Arabidopsis thaliana culture collection, we could significantly reduce the gap-filling solution in comparison to filling gaps in individual reconstructions without affecting the genomic support. Inspection of the metabolic interactions in the soil communities allows us to identify microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile fully automated solution for large-scale modelling of microbial communities for diverse biotechnological applications.

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

Protozoan parasites cause diverse diseases with large global impacts. Research on the pathogenesis and biology of these organisms is limited by economic and experimental constraints. Accordingly, studies of one parasite are frequently extrapolated to infer knowledge about another parasite, across and within genera. Model in vitro or in vivo systems are frequently used to enhance experimental manipulability, but these systems generally use species related to, yet distinct from, the clinically relevant causal pathogen. Characterization of functional differences among parasite species is confined to post hoc or single target studies, limiting the utility of this extrapolation approach. To address this challenge and to accelerate parasitology research broadly, we present a functional comparative analysis of 192 genomes, representing every high-quality, publicly-available protozoan parasite genome including Plasmodium, Toxoplasma, Cryptosporidium, Entamoeba, Trypanosoma, Leishmania, Giardia, and other species. We generated an automated metabolic network reconstruction pipeline optimized for eukaryotic organisms. These metabolic network reconstructions serve as biochemical knowledgebases for each parasite, enabling qualitative and quantitative comparisons of metabolic behavior across parasites. We identified putative differences in gene essentiality and pathway utilization to facilitate the comparison of experimental findings and discovered that phylogeny is not the sole predictor of metabolic similarity. This knowledgebase represents the largest collection of genome-scale metabolic models for both pathogens and eukaryotes; with this resource, we can predict species-specific functions, contextualize experimental results, and optimize selection of experimental systems for fastidious species.

Construction of Environmental Synthetic Microbial Consortia: Based on Engineering and Ecological Principles

In synthetic biology, engineering principles are applied to system design. The development of synthetic microbial consortia represents the intersection of synthetic biology and microbiology. Synthetic community systems are constructed by co-cultivating two or more microorganisms under certain environmental conditions, with broad applications in many fields including ecological restoration and ecological theory. Synthetic microbial consortia tend to have high biological processing efficiencies, because the division of labor reduces the metabolic burden of individual members. In this review, we focus on the environmental applications of synthetic microbial consortia. Although there are many strategies for the construction of synthetic microbial consortia, we mainly introduce the most widely used construction principles based on cross-feeding. Additionally, we propose methods for constructing synthetic microbial consortia based on traits and spatial structure from the perspective of ecology to provide a basis for future work.

Enhancing Microbiome Research through Genome-Scale Metabolic Modeling

Construction and analysis of genome-scale metabolic models (GEMs) is a well-established systems biology approach that can be used to predict metabolic and growth phenotypes. The ability of GEMs to produce mechanistic insight into microbial ecological processes makes them appealing tools that can open a range of exciting opportunities in microbiome research. Here, we briefly outline these opportunities, present current rate-limiting challenges for the trustworthy application of GEMs to microbiome research, and suggest approaches for moving the field forward.

Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis

The pathogen Clostridioides difficile causes toxin-mediated diarrhea and is the leading cause of hospital-acquired infection in the United States. Due to growing antibiotic resistance and recurrent infection, targeting C. difficile metabolism presents a new approach to combat this infection. Genome-scale metabolic network reconstructions (GENREs) have been used to identify therapeutic targets and uncover properties that determine cellular behaviors. Thus, we constructed C. difficile GENREs for a hypervirulent isolate (strain [str.] R20291) and a historic strain (str. 630), validating both with in vitro and in vivo data sets. Growth simulations revealed significant correlations with measured carbon source usage (positive predictive value [PPV] ≥ 92.7%), and single-gene deletion analysis showed >89.0% accuracy. Next, we utilized each GENRE to identify metabolic drivers of both sporulation and biofilm formation. Through contextualization of each model using transcriptomes generated from in vitro and infection conditions, we discovered reliance on the pentose phosphate pathway as well as increased usage of cytidine and N-acetylneuraminate when virulence expression is reduced, which was subsequently supported experimentally. Our results highlight the ability of GENREs to identify novel metabolite signals in higher-order phenotypes like bacterial pathogenesis. IMPORTANCE Clostridioides difficile has become the leading single cause of hospital-acquired infections. Numerous studies have demonstrated the importance of specific metabolic pathways in aspects of C. difficile pathophysiology, from initial colonization to regulation of virulence factors. In the past, genome-scale metabolic network reconstruction (GENRE) analysis of bacteria has enabled systematic investigation of the genetic and metabolic properties that contribute to downstream virulence phenotypes. With this in mind, we generated and extensively curated C. difficile GENREs for both a well-studied laboratory strain (str. 630) and a more recently characterized hypervirulent isolate (str. R20291). In silico validation of both GENREs revealed high degrees of agreement with experimental gene essentiality and carbon source utilization data sets. Subsequent exploration of context-specific metabolism during both in vitro growth and infection revealed consistent patterns of metabolism which corresponded with experimentally measured increases in virulence factor expression. Our results support that differential C. difficile virulence is associated with distinct metabolic programs related to use of carbon sources and provide a platform for identification of novel therapeutic targets.

Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome

A genome-scale metabolic model (GEM) represents metabolic pathways of an organism in a mathematical form and can be built using biochemistry and genome annotation data. GEMs are invaluable for understanding organisms since they analyze the metabolic capabilities and behaviors quantitatively and can predict phenotypes. The development of high-throughput data collection techniques led to an immense increase in omics data such as metagenomics, which expand our knowledge on the human microbiome, but this also created a need for systematic analysis of these data. In recent years, GEMs have also been reconstructed for microbial species, including human gut microbiota, and methods for the analysis of microbial communities have been developed to examine the interaction between the organisms or the host. The purpose of this review is to provide a comprehensive guide for the applications of GEMs in microbial community analysis. Starting with GEM repositories, automatic GEM reconstruction tools, and quality control of models, this review will give insights into microbe-microbe and microbe-host interaction predictions and optimization of microbial community models. Recent studies that utilize microbial GEMs and personalized models to infer the influence of microbiota on human diseases such as inflammatory bowel diseases (IBD) or Parkinson's disease are exemplified. Being powerful system biology tools for both species-level and community-level analysis of microbes, GEMs integrated with omics data and machine learning techniques will be indispensable for studying the microbiome and their effects on human physiology as well as for deciphering the mechanisms behind human diseases.

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quantify. Here we review the major sources of uncertainty and survey existing approaches developed for representing and addressing them. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity.

DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks

The correct identification of metabolic activity in tissues or cells under different conditions can be extremely elusive due to mechanisms such as post-transcriptional modification of enzymes or different rates in protein degradation, making difficult to perform predictions on the basis of gene expression alone. Context-specific metabolic network reconstruction can overcome some of these limitations by leveraging the integration of multi-omics data into genome-scale metabolic networks (GSMN). Using the experimental information, context-specific models are reconstructed by extracting from the generic GSMN the sub-network most consistent with the data, subject to biochemical constraints. One advantage is that these context-specific models have more predictive power since they are tailored to the specific tissue, cell or condition, containing only the reactions predicted to be active in such context. However, an important limitation is that there are usually many different sub-networks that optimally fit the experimental data. This set of optimal networks represent alternative explanations of the possible metabolic state. Ignoring the set of possible solutions reduces the ability to obtain relevant information about the metabolism and may bias the interpretation of the true metabolic states. In this work we formalize the problem of enumerating optimal metabolic networks and we introduce DEXOM, an unified approach for diversity-based enumeration of context-specific metabolic networks. We developed different strategies for this purpose and we performed an exhaustive analysis using simulated and real data. In order to analyze the extent to which these results are biologically meaningful, we used the alternative solutions obtained with the different methods to measure: 1) the improvement of in silico predictions of essential genes in Saccharomyces cerevisiae using ensembles of metabolic network; and 2) the detection of alternative enriched pathways in different human cancer cell lines. We also provide DEXOM as an open-source library compatible with COBRA Toolbox 3.0, available at https://github.com/MetExplore/dexom.

Large-scale dynamic social data representation for structure feature learning

The problems caused by network dimension disasters and computational complexity have become an important issue to be solved in the field of social network research. The existing methods for network feature learning are mostly based on static and small-scale assumptions, and there is no modified learning for the unique attributes of social networks. Therefore, existing learning methods cannot adapt to the dynamic and large-scale of current social networks. Even super large scale and other features. This paper mainly studies the feature representation learning of large-scale dynamic social network structure. In this paper, the positive and negative damping sampling of network nodes in different classes is carried out, and the dynamic feature learning method for newly added nodes is constructed, which makes the model feasible for the extraction of structural features of large-scale social networks in the process of dynamic change. The obtained node feature representation has better dynamic robustness. By selecting the real datasets of three large-scale dynamic social networks and the experiments of dynamic link prediction in social networks, it is found that DNPS has achieved a large performance improvement over the benchmark model in terms of prediction accuracy and time efficiency. When the α value is around 0.7, the model effect is optimal.

Systematically gap-filling the genome-scale metabolic model of CHO cells

OBJECTIVE

Chinese hamster ovary (CHO) cells are the leading cell factories for producing recombinant proteins in the biopharmaceutical industry. In this regard, constraint-based metabolic models are useful platforms to perform computational analysis of cell metabolism. These models need to be regularly updated in order to include the latest biochemical data of the cells, and to increase their predictive power. Here, we provide an update to iCHO1766, the metabolic model of CHO cells.

RESULTS

We expanded the existing model of Chinese hamster metabolism with the help of four gap-filling approaches, leading to the addition of 773 new reactions and 335 new genes. We incorporated these into an updated genome-scale metabolic network model of CHO cells, named iCHO2101. In this updated model, the number of reactions and pathways capable of carrying flux is substantially increased.

CONCLUSIONS

The present CHO model is an important step towards more complete metabolic models of CHO cells.

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

Uncertainty in the structure and parameters of networks is ubiquitous across computational biology. In constraint-based reconstruction and analysis of metabolic networks, this uncertainty is present both during the reconstruction of networks and in simulations performed with them. Here, we present Medusa, a Python package for the generation and analysis of ensembles of genome-scale metabolic network reconstructions. Medusa builds on the COBRApy package for constraint-based reconstruction and analysis by compressing a set of models into a compact ensemble object, providing functions for the generation of ensembles using experimental data, and extending constraint-based analyses to ensemble scale. We demonstrate how Medusa can be used to generate ensembles and perform ensemble simulations, and how machine learning can be used in conjunction with Medusa to guide the curation of genome-scale metabolic network reconstructions. Medusa is available under the permissive MIT license from the Python Packaging Index (https://pypi.org) and from github (https://github.com/opencobra/Medusa), and comprehensive documentation is available at https://medusa.readthedocs.io/en/latest.

Nitrogen Substrate Utilization in Three Rhizosphere Bacterial Strains Investigated Using Proteomics

Nitrogen metabolism in the rhizosphere microbiome plays an important role in mediating plant nutrition, particularly under low inputs of mineral fertilizers. However, there is relatively little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to utilize diverse nitrogen substrates. Here we investigate nitrogen substrate utilization in three taxonomically diverse bacterial strains previously isolated from Arabidopsis roots. The three strains represent taxa that are consistently detected as core members of the plant microbiome: Pseudomonas, Streptomyces, and Rhizobium. We use phenotype microarrays to determine the nitrogen substrate preferences of these strains, and compare the experimental results vs. computational simulations of genome-scale metabolic network models obtained with EnsembleFBA. Results show that all three strains exhibit generalistic nitrogen substrate preferences, with substrate utilization being well predicted by EnsembleFBA. Using label-free quantitative proteomics, we document hundreds of proteins in each strain that exhibit differential abundance values following cultivation on five different nitrogen sources: ammonium, glutamate, lysine, serine, and urea. The proteomic response to these nitrogen sources was strongly strain-dependent, with lysine nutrition eliciting widespread protein-level changes in Pseudomonas sp. Root9, whereas Rhizobium sp. Root491 showed relatively stable proteome composition across different nitrogen sources. Our results give new protein-level information about the specific transporters and enzymes induced by diverse rhizosphere bacterial strains to utilize organic nitrogen substrates.

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

Mechanistic models explicitly represent hypothesized biological knowledge. As such, they offer more generalizability than data-driven models. However, identifying model curation efforts that improve performance for mechanistic models is nontrivial. Here, we develop a solution to this problem for genome-scale metabolic models. We generate an ensemble of models, each equally consistent with experimental data, then perform simulations with them. We apply machine learning to the simulation output to identify model structure variation that maximally influences simulations. These variants are high-priority candidates for curation through removal, addition, or reannotation in the model. We apply this approach, automated metabolic model ensemble-driven elimination of uncertainty with statistical learning (AMMEDEUS), to 29 bacterial species to improve gene essentiality predictions. We explore targets for individual species and compile pan-species targets to improve the database used during model construction. AMMEDEUS is an automated and performance-driven recommendation system that complements intuition during curation of biochemical knowledgebases.

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.

Designing Metabolic Division of Labor in Microbial Communities

Microbes face a trade-off between being metabolically independent and relying on neighboring organisms for the supply of some essential metabolites. This balance of conflicting strategies affects microbial community structure and dynamics, with important implications for microbiome research and synthetic ecology. A "gedanken" (thought) experiment to investigate this trade-off would involve monitoring the rise of mutual dependence as the number of metabolic reactions allowed in an organism is increasingly constrained. The expectation is that below a certain number of reactions, no individual organism would be able to grow in isolation and cross-feeding partnerships and division of labor would emerge. We implemented this idealized experiment using in silico genome-scale models. In particular, we used mixed-integer linear programming to identify trade-off solutions in communities of Escherichia coli strains. The strategies that we found revealed a large space of opportunities in nuanced and nonintuitive metabolic division of labor, including, for example, splitting the tricarboxylic acid (TCA) cycle into two separate halves. The systematic computation of possible solutions in division of labor for 1-, 2-, and 3-strain consortia resulted in a rich and complex landscape. This landscape displayed a nonlinear boundary, indicating that the loss of an intracellular reaction was not necessarily compensated for by a single imported metabolite. Different regions in this landscape were associated with specific solutions and patterns of exchanged metabolites. Our approach also predicts the existence of regions in this landscape where independent bacteria are viable but are outcompeted by cross-feeding pairs, providing a possible incentive for the rise of division of labor. IMPORTANCE Understanding how microbes assemble into communities is a fundamental open issue in biology, relevant to human health, metabolic engineering, and environmental sustainability. A possible mechanism for interactions of microbes is through cross-feeding, i.e., the exchange of small molecules. These metabolic exchanges may allow different microbes to specialize in distinct tasks and evolve division of labor. To systematically explore the space of possible strategies for division of labor, we applied advanced optimization algorithms to computational models of cellular metabolism. Specifically, we searched for communities able to survive under constraints (such as a limited number of reactions) that would not be sustainable by individual species. We found that predicted consortia partition metabolic pathways in ways that would be difficult to identify manually, possibly providing a competitive advantage over individual organisms. In addition to helping understand diversity in natural microbial communities, our approach could assist in the design of synthetic consortia.

Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations

Understanding genotype-phenotype dependency is a universal aim for all life sciences. While the complete genotype-phenotype relations remain challenging to resolve, metabolic phenotypes are moving within the reach through genome-scale metabolic model simulations. Genome-scale metabolic models are available for commonly investigated yeasts, such as model eukaryote and domesticated fermentation species Saccharomyces cerevisiae, and automatic reconstruction methods facilitate obtaining models for any sequenced species. The models allow for investigating genotype-phenotype relations through simulations simultaneously considering the effects of nutrient availability, and redox and energy homeostasis in cells. Genome-scale models also offer frameworks for omics data integration to help to uncover how the translation of genotypes to the apparent phenotypes is regulated at different levels. In this chapter, we provide an overview of the yeast genome-scale metabolic models and the simulation approaches for using these models to interrogate genotype-phenotype relations. We review the methodological approaches according to the underlying biological reasoning in order to inspire formulating novel questions and applications that the genome-scale metabolic models could contribute to. Finally, we discuss current challenges and opportunities in the genome-scale metabolic model simulations.

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Genome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in microbial communities. Yet, the application of genome-scale models, especially to microbial communities, is lagging behind the availability of sequenced genomes. This is largely due to the time-consuming steps of manual curation required to obtain good quality models. Here, we present an automated tool, CarveMe, for reconstruction of species and community level metabolic models. We introduce the concept of a universal model, which is manually curated and simulation ready. Starting with this universal model and annotated genome sequences, CarveMe uses a top-down approach to build single-species and community models in a fast and scalable manner. We show that CarveMe models perform closely to manually curated models in reproducing experimental phenotypes (substrate utilization and gene essentiality). Additionally, we build a collection of 74 models for human gut bacteria and test their ability to reproduce growth on a set of experimentally defined media. Finally, we create a database of 5587 bacterial models and demonstrate its potential for fast generation of microbial community models. Overall, CarveMe provides an open-source and user-friendly tool towards broadening the use of metabolic modeling in studying microbial species and communities.

COL1A1: A potential therapeutic target for colorectal cancer expressing wild-type or mutant KRAS

Colorectal cancer (CRC) treatment primarily relies on chemotherapy along with surgery, radiotherapy and, more recently, targeted therapy at the late stages. However, chemotherapeutic drugs have high cytotoxicity, and the similarity between the effects of these drugs on cancerous and healthy cells limits their wider use in clinical settings. Targeted monoclonal antibody treatment may compensate for this deficiency. Epidermal growth factor receptor (EGFR)-targeted drugs have a positive effect on CRC with intact KRAS proto-oncogene GTPase (KRAS or KRAS^WT), but may be ineffective or harmful in patients with KRAS mutations (KRAS^MUT). Therefore, it is important to identify drug target genes that are uniformly effective with regards to KRAS^WT and KRAS^MUT CRC. The present study performed gene expression analysis, and identified 294 genes upregulated in KRAS^WT and KRAS^MUT CRC samples. Collagen type I α 1 (COL1A1) was identified as the hub gene through STRING and Cytoscape analyses. Consistent with results obtained from Oncomine, a cancer microarray database and web-based data-mining platform, it was demonstrated that the expression of COL1A1 was significantly upregulated in CRC tissues and cell lines regardless of KRAS status. Inhibition of COL1A1 in KRAS^WT and KRAS^MUT CRC cell lines significantly decreased cell proliferation and invasion. In addition, increased COL1A1 expression in CRC was significantly associated with serosal invasion, lymph metastases and hematogenous metastases. Taken together, the findings of the present study indicated that COL1A1 may serve as a candidate diagnostic biomarker and a promising therapeutic target for CRC.

Advances in gap-filling genome-scale metabolic models and model-driven experiments lead to novel metabolic discoveries

With rapid improvements in next-generation sequencing technologies, our knowledge about metabolism of many organisms is rapidly increasing. However, gaps in metabolic networks exist due to incomplete knowledge (e.g., missing reactions, unknown pathways, unannotated and misannotated genes, promiscuous enzymes, and underground metabolic pathways). In this review, we discuss recent advances in gap-filling algorithms based on genome-scale metabolic models and the importance of both high-throughput experiments and detailed biochemical characterization, which work in concert with in silico methods, to allow a more accurate and comprehensive understanding of metabolism.

Modeling metabolism of the human gut microbiome

The human gut microbiome plays an important part in human health. The complexity of the microbiome makes it difficult to determine the detailed metabolic functions and cross-talk occurs between the individual species. In silico systems biology studies of the microbiome can help to identify metabolite exchanges among gut microbes. Constraint-based reconstruction and analysis methods use biochemically accurate genome-scale metabolic networks of microorganisms to simulate metabolism between species in a given microbiome and help generate novel hypotheses on microbial interactions. Here, we review metabolic modeling studies that have investigated metabolic functions of the gut microbiome.

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore

For decades, microbiologists have considered uncertainties as an undesired side effect of experimental protocols. As a consequence, standard microbial system modeling strives to hide uncertainties for the sake of deterministic understanding.

For decades, microbiologists have considered uncertainties as an undesired side effect of experimental protocols. As a consequence, standard microbial system modeling strives to hide uncertainties for the sake of deterministic understanding. However, recent studies have highlighted greater experimental variability than expected and emphasized uncertainties not as a weakness but as a necessary feature of complex microbial systems. We therefore advocate that biological uncertainties need to be considered foundational facets that must be incorporated in models. Not only will understanding these uncertainties improve our understanding and identification of microbial traits, it will also provide fundamental insights on microbial systems as a whole. Taking into account uncertainties within microbial models calls for new validation techniques. Formal verification already overcomes this shortcoming by proposing modeling frameworks and validation techniques dedicated to probabilistic models. However, further work remains to extract the full potential of such techniques in the context of microbial models. Herein, we demonstrate how statistical model checking can enhance the development of microbial models by building confidence in the estimation of critical parameters and through improved sensitivity analyses.