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Introduction
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Publications (151)
Motivation:
Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of releva...
Metabolic network modeling of microbial communities provides an in-depth understanding of community-wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high-qu...
Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to...
Prediction of possible flux distributions in a metabolic network provides detailed phenotypic information that links metabolism to cellular physiology. To estimate metabolic steady-state fluxes, the most common approach is to solve a set of macroscopic mass balance equations subjected to stoichiometric constraints while attempting to optimize an as...
Metabolic engineering is the field of introducing genetic changes in organisms so as to modify their function towards synthesizing new products of high impact to society. However, engineered cells frequently have impaired growth rates thus seriously limiting the rate at which such products are made. The problem is attributable to inadequate underst...
Dietary fibers play a significant role in shaping the composition and function of microbial communities in the human colon. Our understanding of the specific chemical traits of dietary fibers that influence microbial diversity, interactions, and function remains limited. Toward filling this knowledge gap, we developed a novel measure, termed Chemic...
Integrating genome-scale metabolic networks with reactive transport models (RTMs) provides a detailed description of the dynamic changes in microbial growth and metabolism. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated application of linear...
We developed a new machine learning-based method to optimize dual-shim configurations, aiming to enhance flow uniformity at the die exit in slot coating processes for proton exchange membrane fuel cells (PEMFCs). Initially, we conducted three-dimensional computational fluid dynamics (CFD) simulations to characterize the internal die flows using bot...
Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic matter chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incor...
Dietary fibers play a significant role in shaping the composition and function of microbial communities in the human colon. Our understanding of the specific chemical traits of dietary fibers that influence microbial diversity, interactions, and function remains limited. Towards filling this knowledge gap, we developed a novel measure, termed Chemi...
Microbial priming, characterized by significant changes in organic matter (OM) decomposition rates due to minor external treatments with the addition of labile OM, exerts a significant impact on biogeochemical cycles in ecosystems. Priming can take many forms, including positive priming (increased OM decomposition rates), negative priming (decrease...
Organic matter (OM) composition plays a central role in microbial respiration of dissolved organic matter and subsequent biogeochemical reactions. Here, a direct connection of organic carbon chemistry and thermodynamics to reactive transport simulators has been achieved through the newly developed Lambda-PFLOTRAN workflow tool that succinctly incor...
Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental...
Thermodynamic properties of dissolved organic matter (DOM) influence river biogeochemistry. Using these properties to predict biogeochemical rates across rivers requires knowledge of how they vary. We employed mass spectrometry to quantify three DOM thermodynamic properties mechanistically linked to microbial respiration and biomass growth. We esti...
Since the release of ModelSEED in 2010, the systems biology research community has used the ModelSEED genome-scale metabolic model reconstruction pipeline to build over 200,000 draft metabolic reconstructions that support hundreds of publications. Here we describe the first comprehensive update to this reconstruction tool, with new features such as...
Pyrogenic organic matter (PyOM) from wildfires impacts river corridors globally and is widely regarded as resistant to biological degradation. Though recent work suggests PyOM may be more bioavailable than historically perceived, estimating bioavailability across its chemical spectrum remains elusive. To address this knowledge gap, we assessed pote...
Microbial decomposition of organic matter (OM) in river corridors is a major driver of nutrient and energy cycles in natural ecosystems. Recent advances in omics technologies enabled high-throughput generation of molecular data that could be used to inform biogeochemical models. With ultrahigh-resolution OM data becoming more readily available, in...
Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale micr...
Integration of genome-scale metabolic networks with reactive transport models (RTMs) is an advanced simulation technique that enables predicting the changes of microbial growth and metabolism in space and time. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it re...
Autotroph-heterotroph interactions are ubiquitous in natural environment and play a key role in controlling various essential ecosystem functions, such as production and utilization of organic matter, cycling of nitrogen, sulfur, and other chemical elements. Understanding how these biofilm metabolic interactions are constrained in space and time re...
Prevention of the growth of harmful microorganisms in food products is an important requirement for ensuring food safety and quality. Mathematical models to predict the quantitative changes in microbial populations in food to the variations of environmental conditions are useful tools in this regard. While equations for microbial inactivation have...
Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes, and that can integrate genome-scale mic...
Soil microorganisms provide key ecological functions that often rely on metabolic interactions between individual populations of the soil microbiome. To better understand these interactions and community processes, we used chitin, a major carbon and nitrogen source in soil, as a test substrate to investigate microbial interactions during its decomp...
Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental...
Pyrogenic materials generated by wildfires are negatively impacting many aquatic ecosystems. At least ~10 % of dissolved organic matter (DOM) pools may be comprised of pyrogenic organic matter (PyOM) that is generally considered to be more refractory than DOM from other sources. However, there has been no systematic evaluation of bioavailability ac...
Arsenic, a naturally occurring metalloid derived from the environment, has been studied worldwide for its causative effects in various cancers. However, the effects of arsenic toxicity on the development and progression of metabolic syndrome, including obesity and diabetes, has received less attention. Many studies suggest that metabolic dysfunctio...
This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles in the American Geophysical Union Biogeosciences section, and discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (a) Global collaboration, technology tra...
Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting–drying transitions. Our refined framework includes relationships between cu...
Wildfires are increasing in severity and extent, creating many negative consequences for aquatic ecosystems. Pyrogenic materials generated by wildfires are transported across terrestrial landscapes into inland waters, where ~10% of organic matter pools may be comprised of black carbon (BC), a major component of pyrogenic organic matter (PyOM). Yet,...
Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting/drying transitions. Throughout the system we found threshold-like responses...
Consolidated bioprocessing (CBP) of cellulose is a cost‐effective route to produce valuable biochemicals by integrating saccharification, fermentation and cellulase synthesis in a single step. However, the lack of understanding of governing factors of interdependent saccharification and fermentation in CBP eludes reliable process optimization. Here...
Development of reliable biogeochemical models requires a mechanistic consideration of microbial interactions with hydrology. Microbial response to and its recovery after hydrologic perturbations (i.e., resilience) is a critical component to understand in this regard, but generally difficult to predict because the impacts of future events can be dep...
Proper timely management of various external and internal stresses is critical for metabolic and redox homeostasis in mammals. In particular, dysregulation of mechanistic target of rapamycin complex (mTORC) triggered from metabolic stress and accumulation of reactive oxygen species (ROS) generated from environmental and genotoxic stress are well-kn...
Microbiome engineering aims to manipulate, control, and design community-level properties through targeted interventions of existing microbial communities or the construction of new synthetic consortia. These efforts often lead to unexpected or undesirable outcomes because of highly complex input-output relationships that are primarily ascribable t...
Predictive biogeochemical modeling requires data-model integration that enables explicit representation of the sophisticated roles of microbial processes that transform substrates. Data from high-resolution organic matter (OM) characterization are increasingly available and can serve as a critical resource for this purpose, but their incorporation...
Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting/drying transitions. Throughout the system we found threshold-like responses...
Probiotics are live beneficial microorganisms that can be consumed in the form of dairy and food products as well as dietary supplements to promote a healthy balance of gut bacteria in humans. Practically, the main challenge is to identify and select promising strains and formulate multi-strain probiotic blends with consistent efficacy which is hig...
The soil environment is constantly changing due to shifts in soil moisture, nutrient availability and other conditions. To contend with these changes, soil microorganisms have evolved a variety of ways to adapt to environmental perturbations, including regulation of gene expression. However, it is challenging to untangle the complex phenotypic resp...
Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in global biogeochemical cycles, yet the processes regulating aerobic respiration in aquatic environments remain poorly understood. Aerobic respiration is typically predicted through kinetic controls such as organic carbon and oxygen concentrations, while as...
To study the discrete bond-breaking phenomena of depolymerization, the use of a fully continuous Population Balance Equation (PBE) is inadequate to embody all the inherent characteristics of the process, thus resulting in the need for a discrete-continuous mesh. Here, the performance of the fixed pivot technique (FPT) and the cell average technique...
Microbial communities organize into specific spatial patterns based on their interspecies interactions, but their use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised deep learning as a new tool for network inference. An agent-based model was used to simulate the spatiotemporal evolution of...
Predictive biogeochemical modeling requires data-model integration that enables explicit representation of the sophisticated roles of microbial processes that transform substrates. Data from high-resolution organic matter (OM) characterization are increasingly available and can serve as a critical resource for this purpose, but their incorporation...
Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference met...
Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in global biogeochemical cycles, yet aquatic OM cycling remains poorly understood. Here, we present the first work to explicitly test OM thermodynamics as a key regulator of aerobic respiration, challenging long-held beliefs that organic carbon and oxygen co...
Enzymatic hydrolysis of cellulose offers an attractive biological means to produce biofuels and other high-valued bio-products. Despite considerable efforts to date, the development of the enzymatic hydrolysis of cellulose remains challenging, due to the lack of a mechanistic understanding of the underlying process fundamentals. The inconspicuous f...
Climate change is predicted to result in increased drought extent and intensity in the highly productive, former tallgrass prairie region of the continental United States. These soils store large reserves of carbon. The decrease in soil moisture due to drought has largely unknown consequences on soil carbon cycling and other key biogeochemical cycl...
An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly establis...
Cambridge Core - Bioengineering - Cybernetic Modeling for Bioreaction Engineering - by Doraiswami Ramkrishna
Anthropogenic activities, especially dam operations, often induce larger and more frequent stage fluctuations than those occurring in natural rivers. However, long-term impacts of such flow variations on thermal and biogeochemical dynamics of the associated hyporheic zone (HZ) are poorly understood. In this study, we built a heterogeneous, two-dime...
Investigating the microbiome is on the frontier of science. It has the potential to resolve many issues in the realms of energy, food, human health, the environment, and biotechnology. Scientists are trying to understand, in a fundamental way, how microbes influence each other and how they organize into interaction networks. These are the keys to p...
The advent of high-throughput ‘omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for species-resolved functional studies. Here, a mutual information approach was applied to build a gene association network of a commensal consortium, in which a unicellular cyanobacterium Thermosy...
Microbial communities are networks of species, the interaction structure of which dynamically reorganizes in a varying environment. Even in a static condition, community dynamics are often difficult to predict due to highly nonlinear interspecies interactions. Understanding the fundamental principles of microbial interactions is therefore key for p...
Bile acids are metabolic links between hosts and their gut microbiomes, yet little is known about the roles they play in microbe-to-microbe interactions. Here we present a study designed to investigate the effect that a common probiotic, Lactobacillus acidophilus , has on microbial interactions that lead to formation of secondary bile acids. A mode...
Anthropogenic activities, especially dam operations, often induce larger and more frequent stage fluctuations than those occurring in natural rivers. However, long-term impacts of such flow variations on thermal and biogeochemical dynamics of the associated hyporheic zone (HZ) are poorly understood. In this study, we built a heterogeneous, two-dime...
The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacter...
Interest in applying microbial communities to biotechnology continues to increase. Successful engineering of microbial communities requires a fundamental shift in focus from enhancing metabolic capabilities in individual organisms to promoting synergistic interspecies interactions. This goal necessitates in silico tools that provide a predictive un...
In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates...
Microbial communities exert a significant impact on our environment, human health and industry. A mechanistic understanding of complex interplay between member species is essential for engineering microbial communities. Metabolic network models that provide comprehensive community-wide predictions on cross-species metabolite exchanges can serve as...
Bioprocesses are contingent on the metabolic activity of microorganisms which is subject to dynamic variations as environmental changes occur concurrently. It is well known that such changes in the environment evoke regulatory response from the organismsto drive metabolism in specific ways but mathematical models have either neglected this feature...
Microbial communities exert a significant impact on our environment, human health and industry. A mechanistic understanding of complex interplay between member species is essential for engineering microbial communities. Metabolic network models that provide comprehensive community-wide predictions on cross-species metabolite exchanges can serve as...
The cover image, by Hyun-Seob Song et al., is based on the Article Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction, DOI: 10.1002/jcp.25428. Confocal micrograph depicting a metabolically coupled microbial consortium composed of cyanobacterium Thermosynechococcus elongatus (red) supporting heterotrophic bacteriu...
Productivity is a major determinant of ecosystem diversity. Microbial ecosystems are the most diverse on the planet yet very few relationships between diversity and productivity have been reported as compared with macro-ecological studies. Here we evaluated the spatial relationships of productivity and microbiome diversity in a laboratory-cultivate...
Table S1. Network reconstruction protocol for individual genomes.
Heterotrophic partnership alters and regulates the transcriptional profile of the cyanobacterial primary-producer to coordinate resource exchange (i.e., reduced-C, -N, vitamins and O2) and protection from oxidative stress.
As a complex adaptive system, microbial communities change their composition and functions in response to environmental variation in ways that are difficult to predict. A mechanistic understanding of the interplay among member species is key to prediction and control of a community’s dynamics and emergent properties. To predict microbial interactio...
The emergent property of resilience is the ability of a system to return to an original state after a disturbance. Resilience may be used as an early warning system for significant or irreversible community transition; that is, a community with diminishing or low resilience may be close to catastrophic shift in function or an irreversible collapse....
Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into r...
We developed a novel approach that combines 1) data-driven inference and 2) genome analysis for predicting microbial interactions in complex consortia. In the analysis of our model consortium, we identified nitrogen source-dependent interactions of member species that exhibit a significant change in population and protein production.
We developed a novel approach that combines 1) data-driven inference and 2) genome analysis for predicting microbial interactions in complex consortia. In the analysis of our model consortium, we identified nitrogen source-dependent interactions of member species that exhibit a significant change in population and protein production.
We developed a novel approach that combines 1) data-driven inference and 2) genome analysis for predicting microbial interactions in complex consortia. In the analysis of our model consortium, we identified nitrogen source-dependent interactions of member species that exhibit a significant change in population and protein production.
Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex na...
Biological networks often show remarkable robustness by preserving their functionalities against perturbations. Robust networks are known to possess specific topological characteristics such as being scale-free, meaning that they can tolerate random disruption of genes (nodes), but are vulnerable to targeted removal of highly connected genes (hubs)...
Knowledge of interspecies interactions in microbial communities is the key not only to predict and modify their dynamics and properties, but also to design novel consortia for desirable outputs. Thanks to the advancement of high-throughput sequencing technology, time-series analysis of species abundance data is increasingly common, offering a valua...
