Review
Biochemical Research Methods
Karthik Nagarajan, Congjian Ni, Ting Lu
Summary: This review provides a comprehensive overview of recent advances in agent-based modeling of microbial communities, including algorithms for simulating intracellular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments, as well as applications of agent-based modeling. It also discusses challenges and potential mitigation strategies.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Environmental Sciences
Lvjing Wang, Xiaoyu Wang, Hao Wu, Haixia Wang, Yihan Wang, Zhenmei Lu
Summary: The genome-scale metabolic model (GEM) is a mathematical representation of whole-cell metabolism that allows for in silico simulations of metabolic flux distribution. GEMs have been extensively used in studying microbial interactions and guiding the design of synthetic microbial communities for bioremediation. This review summarizes the various types of microbial interactions, the process of GEM reconstruction, automatic reconstruction programs, and knowledge databases. It also discusses the exciting combination of metabolic models, omics, and machine learning approaches in recent application studies. However, further work is needed to fully understand and utilize GEMs for describing the metabolic interactions of microbial communities and applying them to pollutant biodegradation.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2023)
Review
Biochemical Research Methods
Fangchen Liu, Andrea Giometto, Mingming Wu
Summary: Aquatic microbial communities play a fundamental role in biogeochemical transformations in natural ecosystems, with their composition and function tightly controlled by environmental factors. Microfluidic platforms provide a unique opportunity for quantitative studies and theoretical modeling of microbial communities, which can be applied beyond aquatic ecosystems.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Microbiology
Christian Diener, Sean M. Gibbons
Summary: Microbial consortia play a crucial role in various essential processes, but it is challenging to understand their functional capacities based on their composition alone. Community-scale metabolic models have the potential to simulate complex microbial communities, but there is no consensus on the fitness function and community-wide growth. Transitioning from single-taxon models to multitaxon models poses challenges as well. Dynamic approaches are a solution but are computationally expensive, while two steady-state approaches provide ecologically relevant solutions with improved scalability.
Article
Biochemistry & Molecular Biology
Jia Wang, Dana L. Carper, Leah H. Burdick, Him K. Shrestha, Manasa R. Appidi, Paul E. Abraham, Collin M. Timma, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz
Summary: Microbial communities in plant tissues play a crucial role in host function, but the formation of these communities and the contributions of individual members are not well understood. Synthetic microbial communities are valuable model systems for studying community principles using defined isolates. A study on 10 bacterial strains isolated from Populus deltoides rhizosphere revealed that stable microbial communities formed after several growth cycles, with dominant strains depending on the environment. Understanding metabolic interactions among plant-associated microorganisms provides insights for engineering microbial communities to enhance plant growth and disease resistance.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Mathematical & Computational Biology
Qimin Huang, Martial Ndeffo-Mbah, Anirban Mondal, Sara Lee, David Gurarie
Summary: The ongoing COVID-19 pandemic has posed major challenges to college campuses in the United States. To address the risk and spread of the disease, researchers developed a flexible computational framework to model and control COVID-19 transmission in residential college campuses. The study found that even with a high vaccination coverage, outbreaks can still occur and are influenced by environmental and socio-behavioral risk factors. Combining vaccination with quarantine and mass testing is crucial for preventing or mitigating outbreaks.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2022)
Article
Ecology
Tatyana Zamkovaya, Jamie S. Foster, Valerie de Crecy-Lagard, Ana Conesa
Summary: Microbial dark matter, consisting of unknown microbes, plays essential ecological roles and occupies top hubs within their communities. Excluding unknown taxa results in a reduction in network centrality measures, highlighting the importance of these unknown organisms.
Article
Engineering, Environmental
Valeria Alvarado, Shu-Chien Hsu, Zhuoying Wu, Huichuan Zhuang, Po-Heng Lee, Jeremy S. Guest
Summary: Biological models of anaerobic digestion have been used to test control strategies. This study developed a novel microbial individuality model that identified the importance of homoacetogenesis in anaerobic digestion.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Review
Biochemical Research Methods
Elie Desmond-Le Quemener, Roman Moscoviz, Nicolas Bernet, Andrew Marcus
Summary: The study of mathematical modeling of DIET and MIET in anaerobic ecosystems offers new strategies for improving biotechnologies. While the modeling of DIET kinetics is still in its early stages, recent concepts introduced for modeling electroactive biofilms should be further developed. DIET shows potential to increase IET rates compared to H 2 -MIET, but additional characterizations of biological components supporting IET are needed to enhance predictions.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Oncology
Angelina De Martin, Mechthild Lutge, Yves Stanossek, Celine Engetschwiler, Jovana Cupovic, Kirsty Brown, Izadora Demmer, Martina A. Broglie, Markus B. Geuking, Wolfram Jochum, Kathy D. McCoy, Sandro J. Stoeckli, Burkhard Ludewig
Summary: Squamous cell carcinoma of the tonsil, associated with high risk-human papilloma virus (HR-HPV) infections, has been found to have a distinct microbiome composition in the tonsillar crypts compared to sleep apnea patients. Specific bacterial species abundance such as Filifactor alocis and Prevotella melaninogenica are identified as traits of tonsil cancer.
Article
Automation & Control Systems
Xiaobo Zhang, Zhanxue Wang, Li Zhou
Summary: The present study aims to address the issue of accuracy degradation in the traditional zero-dimensional variable cycle engine (VCE) model due to the multi-angle characteristics in the core-driven fan stage (CDFS). A two-dimensional model was established using the streamline curvature method, and a multi-level VCE model was developed to integrate the CDFS characteristics. The simulation results show that the proposed multi-level modeling approach is time-efficient and significantly improves optimal thrust and specific fuel consumption compared to the traditional zero-dimensional VCE model.
JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS
(2023)
Article
Chemistry, Applied
Siyu Wei, Cheng Wang, Qifan Zhang, Hui Yang, Edward C. Deehan, Xin Zong, Yizhen Wang, Mingliang Jin
Summary: This study investigated the short-term dynamics of gut microbiota and metabolic function during inulin fermentation with distinct microbiota from two swine breeds. It found that different gut microbiota displayed a similar response to inulin intervention and that inulin-induced bacterial succession and metabolic changes were determined by the original microbial compositions.
CARBOHYDRATE POLYMERS
(2022)
Article
Engineering, Civil
Xin Liu, Annan Zhou, Shui-long Shen, Jie Li
Summary: The pore morphology method (PMM) is commonly used to simulate the drainage process of porous media. A new enhanced method called Lvca-PMM is proposed, which takes into account locally variable contact angles and can reproduce the primary drainage process under different wettability conditions.
JOURNAL OF HYDROLOGY
(2022)
Article
Multidisciplinary Sciences
Chandana Gopalakrishnappa, Karna Gowda, Kaumudi H. Prabhakara, Seppe Kuehn
Summary: This article introduces the quantitative and mapping methods of community metabolic fluxes to reveal the relationship between community structure and metabolic activity, and discusses the application prospects of this method in different types of communities.
Article
Multidisciplinary Sciences
Yi Yang, Xinjun Mao, Shuo Yang, Menghan Wu
Summary: Incentive mechanisms are important for guiding users in Q&A communities to achieve community goals, but they need careful review and revision before actual industrial application. Simulating these mechanisms is significant for predicting how changes will affect community emergence. However, the complexity of Q&A communities makes it challenging to establish connections and simulate their emergence. This paper proposes a Normative Multi-Agent System based Simulation (NorMASS) approach to fill this gap and provides an effective solution for simulating incentive mechanisms of Q&A communities, with a similarity of 80% or above demonstrated through evaluation.
Article
Biotechnology & Applied Microbiology
Jamin C. Wood, Esteban Marcellin, Manuel R. Plan, Bernardino Virdis
Summary: This study presents the growth of Eubacterium limosum ATCC8486 using methanol and formate as substrates, showing evidence of native butanol production for the first time. The research found that both methanol and formate are required for high growth rates and cell densities, with formate being the preferred substrate. Additionally, the study suggests that butanol production in E. limosum may be due to overflow metabolism, similar to the production of 2,3-butanediol in other acetogens. Further research is needed to confirm the pathway of butanol production in E. limosum.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Engineering, Environmental
Xueqin Zhang, Hesamoddin Rabiee, Gaofeng Ni, Joshua Frank, Jing Zhao, Chen Cai, Bernardino Virdis, Zhiguo Yuan, Shihu Hu
Summary: Bioelectrochemical methane oxidation can be improved by using a special methanotrophic consortium to assemble conductive reduced graphene oxide on hollow fibers, resulting in enhanced current output. This strategy can be applied to other bioelectrochemical systems with low solubility issues.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Engineering, Environmental
Gabriel Capson-Tojo, Damien J. Batstone, Maria Grassino, Tim Hulsen
Summary: This study evaluated the light attenuation in enriched purple phototrophic bacteria (PPB) cultures. The results showed that increased biomass concentrations led to higher light attenuation, and pigment concentration had a strong effect on attenuation. A proposed mathematical model allowed effective prediction of the kinetics of photoheterotrophic growth.
Article
Engineering, Environmental
Xueqin Zhang, Simon J. McIlroy, Igor Vassilev, Hesamoddin Rabiee, Manuel Plan, Chen Cai, Bernardino Virdis, Gene W. Tyson, Zhiguo Yuan, Shihu Hu
Summary: Anaerobic oxidation of methane (AOM) is an important microbial process that reduces methane emissions from natural sediments. In this study, a microbial consortium in a methane-fed microbial electrolysis cell (MEC) was investigated, and acetate was identified as a likely intermediate for methane oxidation. The oxidation of intracellular polyhydroxybutyrate (PHB) and breakdown of extracellular polymeric substances (EPSs) were found to contribute to current generation in the absence of methane.
Article
Engineering, Environmental
Tanmoy Das, Shane P. Usher, Damien J. Batstone, Catherine A. Rees, Anthony D. Stickland, Nicky Eshtiaghi
Summary: Due to the non-homogeneous and multiphase nature of anaerobic lagoon constituents, continuous functions are required to describe shear and solid-liquid separation properties in CFD modelling for process optimization. However, the measurement of existing material properties of anaerobic sludges is limited to certain aspects and concentrations. This study measured the shear properties and solid-liquid separation properties of an anaerobic sludge across a wide range of concentrations, enabling CFD modeling of the hydrodynamics and performance of anaerobic lagoons.
Article
Agricultural Engineering
Y. Segura, R. Molina, I. Rodriguez, T. Hulsen, D. Batstone, V. Monsalvo, F. Martinez, J. A. Melero, D. Puyol
Summary: Purple phototrophic bacteria (PPB) are used to recover organics and nutrients from wastewater through assimilative growth. Thermal hydrolysis (TH) as a pretreatment method before anaerobic digestion (AD) improves digestibility and recovery potentials. The study found that continuous TH pretreatment resulted in enhanced recovery potentials, with methane production reaching up to 380 LCH4/kgVS and 73% nitrogen release over 165 days. Although TH pretreatment is energy-intensive, a combined configuration with heat recovery and increased methane production in AD can make it energy positive.
BIORESOURCE TECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Bernardino Virdis, Robert D. Hoelzle, Angela Marchetti, Santiago T. Boto, Miriam A. Rosenbaum, Ramiro Blasco-Gomez, Sebastia Puig, Stefano Freguia, Marianna Villano
Summary: The market of biobased products obtained through fermentation processes has been growing steadily due to the demand for a decarbonized economy. However, the economic viability of industrial fermentation is hindered by low product titers and selectivity. Electrofermentation, as an innovative approach, can address these challenges by altering the yield, titer, concentration, or product distribution in traditional fermentation processes. Yet, the molecular and biochemical basis of electrofermentation is still largely unknown.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Engineering, Environmental
Vicente Monje, Helena Junicke, Damien J. Batstone, Kasper Kjellberg, Krist Gernaey, Xavier Flores-Alsina
Summary: This paper develops and combines a set of mathematical tools to assess and predict mass and volumetric flows in waste treatment systems. By testing it on a large industrial waste treatment system, the proposed approach successfully balances and predicts the behavior of different compounds, providing valuable tools for waste treatment.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Green & Sustainable Science & Technology
Christopher H. Buhlmann, Bede S. Mickan, Stephan Tait, Damien J. Batstone, George D. Mercer, Parisa A. Bahri
Summary: Environmental conditions significantly affect microbial community composition, product spectrum, and fermentation yield in mixed-culture food waste fermentation. pH and temperature regulation can improve lactic acid production, but may also lead to the production of competitive metabolites. The use of adapted fermentation inoculum and environmental control are effective strategies to promote lactic acid production.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Engineering, Environmental
Gabriel Capson-Tojo, Damien J. Batstone, Tim Hulsen
Summary: This work presents an extended Photo-Anaerobic Model (ePAnM) that considers the metabolic capabilities of purple phototrophic bacteria (PPB), microbial clades interacting with PPB, and varying environmental conditions. The model was calibrated and validated using different datasets and was able to predict key compound concentrations and microbial communities.
Review
Microbiology
Christian Krohn, Leadin Khudur, Daniel Anthony Dias, Ben van den Akker, Catherine A. A. Rees, Nicholas D. D. Crosbie, Aravind Surapaneni, Denis M. M. O'Carroll, Richard M. M. Stuetz, Damien J. J. Batstone, Andrew S. S. Ball
Summary: The use of next-generation diagnostic tools to optimize anaerobic digestion has the potential to improve renewable natural gas recovery, biosolid fertilizer reuse, and circular economies. This review highlights the importance of microbial ecology in improving digester performance, and the need for a systems biology approach to monitor anaerobic sewage sludge in continuously stirred reactor tanks. Further research on sludge ecology and the development of biomarkers will be crucial for addressing operational issues and improving the overall function of anaerobic digestion.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Chemistry, Physical
Jamin C. Wood, Zhiguo Yuan, Bernardino Virdis
Summary: A circular carbon economy can decouple production from fossil fuels, but strategies are needed to maximize decarbonization in the short term. Electrochemical processes offer opportunities to link renewable electricity with chemical production, but currently only a few chemical products have reached commercialization stages. By using commercialized electro-chemical products, such as hydrogen and carbon monoxide, as feedstocks, higher overall energy efficiencies can be achieved in producing other platform chemicals. This approach is being recognized in the industry, with several companies leading the way.
CURRENT OPINION IN ELECTROCHEMISTRY
(2023)
Article
Agricultural Engineering
Gabriel Capson-Tojo, Albie Zuo Meng Gan, Pablo Ledezma, Damien J. Batstone, Tim Hulsen
Summary: Purple phototrophic bacteria (PPB) can produce single-cell protein at high yields from wastewater. Growing in a biofilm versus suspended state improves product quality and consistency. This study compared the performance of enriched PPB cultures in an outdoor photobioreactor using suspended and attached growths, and found similar treatment performances and productivities, although attached growth had lower VFA removal efficiencies and higher biomass quality.
BIORESOURCE TECHNOLOGY
(2023)
Article
Engineering, Environmental
Felix Egger, Tim Hulsen, Damien J. Batstone
Summary: Anaerobic digestion produces biogas that requires desulfurization before use due to its corrosive nature. A continuous desulfurization process using purple phototrophic bacteria, powered by light, was developed as an alternative to traditional methods. This caustic-free process can integrate with anaerobic digestion using centrate as a nutrient source, but may be limited by the availability of light for nighttime operation in a scaled process.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Physical
Jamin C. Wood, R. Axayacatl Gonzalez-Garcia, Dara Daygon, Gert Talbo, Manuel R. Plan, Esteban Marcellin, Bernardino Virdis
Summary: Methanol is a promising renewable energy carrier due to its high energy efficiency conversion and ease of integration within existing infrastructure. Some acetogenic bacteria have the ability to utilize methanol and other C-1 substrates to produce valuable chemicals. This study investigates the metabolism of Eubacterium limosum under methanol growth conditions and highlights key aspects of methanol metabolism and bottleneck conditions preventing the formation of valuable products.
SUSTAINABLE ENERGY & FUELS
(2023)