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Atasoy M, Scott WT, Regueira A, Mauricio-Iglesias M, Schaap PJ, Smidt H. Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches. Biotechnol Adv 2024; 73:108363. [PMID: 38657743 DOI: 10.1016/j.biotechadv.2024.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.
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Affiliation(s)
- Merve Atasoy
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Department of Environmental Technology, Wageningen University & Research, Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
| | - William T Scott
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.
| | - Alberte Regueira
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Center for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium; Center for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, Ghent, Belgium.
| | - Miguel Mauricio-Iglesias
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Peter J Schaap
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.
| | - Hauke Smidt
- UNLOCK, Wageningen University & Research and Delft University of Technology, Wageningen and Delft, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.
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2
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Hsieh YE, Tandon K, Verbruggen H, Nikoloski Z. Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. NPJ Syst Biol Appl 2024; 10:54. [PMID: 38783065 PMCID: PMC11116368 DOI: 10.1038/s41540-024-00384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Genome-scale metabolic models (GEMs) of microbial communities offer valuable insights into the functional capabilities of their members and facilitate the exploration of microbial interactions. These models are generated using different automated reconstruction tools, each relying on different biochemical databases that may affect the conclusions drawn from the in silico analysis. One way to address this problem is to employ a consensus reconstruction method that combines the outcomes of different reconstruction tools. Here, we conducted a comparative analysis of community models reconstructed from three automated tools, i.e. CarveMe, gapseq, and KBase, alongside a consensus approach, utilizing metagenomics data from two marine bacterial communities. Our analysis revealed that these reconstruction approaches, while based on the same genomes, resulted in GEMs with varying numbers of genes and reactions as well as metabolic functionalities, attributed to the different databases employed. Further, our results indicated that the set of exchanged metabolites was more influenced by the reconstruction approach rather than the specific bacterial community investigated. This observation suggests a potential bias in predicting metabolite interactions using community GEMs. We also showed that consensus models encompassed a larger number of reactions and metabolites while concurrently reducing the presence of dead-end metabolites. Therefore, the usage of consensus models allows making full and unbiased use from aggregating genes from the different reconstructions in assessing the functional potential of microbial communities.
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Affiliation(s)
- Yunli Eric Hsieh
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Zoran Nikoloski
- Bioinformatics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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3
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Gelbach PE, Cetin H, Finley SD. Flux sampling in genome-scale metabolic modeling of microbial communities. BMC Bioinformatics 2024; 25:45. [PMID: 38287239 PMCID: PMC10826046 DOI: 10.1186/s12859-024-05655-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
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.
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Affiliation(s)
- Patrick E Gelbach
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Handan Cetin
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Stacey D Finley
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA.
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4
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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5
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Wu P, Yuan Q, Cheng T, Han Y, Zhao W, Liao X, Wang L, Cai J, He Q, Guo Y, Zhang X, Lu F, Wang J, Ma H, Huang Z. Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan. Front Microbiol 2023; 14:1277847. [PMID: 38053556 PMCID: PMC10694236 DOI: 10.3389/fmicb.2023.1277847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
Sulfur-oxidizing bacteria play a crucial role in various processes, including mine bioleaching, biodesulfurization, and treatment of sulfur-containing wastewater. Nevertheless, the pathway involved in sulfur oxidation is highly intricate, making it complete comprehension a formidable and protracted undertaking. The mechanisms of sulfur oxidation within the Acidithiobacillus genus, along with the process of energy production, remain areas that necessitate further research and elucidation. In this study, a novel strain of sulfur-oxidizing bacterium, Acidithiobacillus Ameehan, was isolated. Several physiological characteristics of the strain Ameehan were verified and its complete genome sequence was presented in the study. Besides, the first genome-scale metabolic network model (AMEE_WP1377) was reconstructed for Acidithiobacillus Ameehan to gain a comprehensive understanding of the metabolic capacity of the strain.The characteristics of Acidithiobacillus Ameehan included morphological size and an optimal growth temperature range of 37-45°C, as well as an optimal growth pH range of pH 2.0-8.0. The microbe was found to be capable of growth when sulfur and K2O6S4 were supplied as the energy source and electron donor for CO2 fixation. Conversely, it could not utilize Na2S2O3, FeS2, and FeSO4·7H2O as the energy source or electron donor for CO2 fixation, nor could it grow using glucose or yeast extract as a carbon source. Genome annotation revealed that the strain Ameehan possessed a series of sulfur oxidizing genes that enabled it to oxidize elemental sulfur or various reduced inorganic sulfur compounds (RISCs). In addition, the bacterium also possessed carbon fixing genes involved in the incomplete Calvin-Benson-Bassham (CBB) cycle. However, the bacterium lacked the ability to oxidize iron and fix nitrogen. By implementing a constraint-based flux analysis to predict cellular growth in the presence of 71 carbon sources, 88.7% agreement with experimental Biolog data was observed. Five sulfur oxidation pathways were discovered through model simulations. The optimal sulfur oxidation pathway had the highest ATP production rate of 14.81 mmol/gDW/h, NADH/NADPH production rate of 5.76 mmol/gDW/h, consumed 1.575 mmol/gDW/h of CO2, and 1.5 mmol/gDW/h of sulfur. Our findings provide a comprehensive outlook on the most effective cellular metabolic pathways implicated in sulfur oxidation within Acidithiobacillus Ameehan. It suggests that the OMP (outer-membrane proteins) and SQR enzymes (sulfide: quinone oxidoreductase) have a significant impact on the energy production efficiency of sulfur oxidation, which could have potential biotechnological applications.
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Affiliation(s)
- Peng Wu
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qianqian Yuan
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tingting Cheng
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yifan Han
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wei Zhao
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoping Liao
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lu Wang
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jingyi Cai
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian He
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ying Guo
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoxia Zhang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Fuping Lu
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jingjing Wang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Hongwu Ma
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiyong Huang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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6
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Kuppa Baskaran DK, Umale S, Zhou Z, Raman K, Anantharaman K. Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes. ISME COMMUNICATIONS 2023; 3:42. [PMID: 37120693 PMCID: PMC10148797 DOI: 10.1038/s43705-023-00242-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.
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Affiliation(s)
- Dinesh Kumar Kuppa Baskaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India
| | - Shreyansh Umale
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India.
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India.
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.
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7
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Gelbach PE, Finley SD. Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537368. [PMID: 37197028 PMCID: PMC10173371 DOI: 10.1101/2023.04.18.537368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
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.
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Affiliation(s)
- Patrick E. Gelbach
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Stacey D. Finley
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
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8
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Chaos in synthetic microbial communities. PLoS Comput Biol 2022; 18:e1010548. [PMID: 36215322 PMCID: PMC9584520 DOI: 10.1371/journal.pcbi.1010548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/20/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Predictability is a fundamental requirement in biological engineering. As we move to building coordinated multicellular systems, the potential for such systems to display chaotic behaviour becomes a concern. Therefore understanding which systems show chaos is an important design consideration. We developed a methodology to explore the potential for chaotic dynamics in small microbial communities governed by resource competition, intercellular communication and competitive bacteriocin interactions. Our model selection pipeline uses Approximate Bayesian Computation to first identify oscillatory behaviours as a route to finding chaotic behaviour. We have shown that we can expect to find chaotic states in relatively small synthetic microbial systems, understand the governing dynamics and provide insights into how to control such systems. This work is the first to query the existence of chaotic behaviour in synthetic microbial communities and has important ramifications for the fields of biotechnology, bioprocessing and synthetic biology.
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9
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Fornasaro S, Esposito A, Florian F, Pallavicini A, De Leo L, Not T, Lagatolla C, Mezzarobba M, Di Silvestre A, Sergo V, Bonifacio A. Spectroscopic investigation of faeces with surface-enhanced Raman scattering: a case study with coeliac patients on gluten-free diet. Anal Bioanal Chem 2022; 414:3517-3527. [PMID: 35258650 PMCID: PMC9018641 DOI: 10.1007/s00216-022-03975-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 11/06/2022]
Abstract
Surface-enhanced Raman scattering (SERS) spectra of faecal samples can be obtained by adding AuNP to their methanol extracts according to the reported protocol, and display bands that are due to bilirubin-like species but also to xanthine and hypoxanthine, two metabolic products secreted by gut bacteria. A total of 27 faecal samples from three different groups, i.e. coeliac patients (n = 9), coeliac patients on gluten-free diet (n = 10) and a control group (n = 8), were characterized with both SERS spectroscopy and 16S rRNA sequencing analysis. Significant differences are present between SERS spectra of coeliac patients and those on gluten-free diet, with a marked increase in the relative intensity of both xanthine and hypoxanthine for the latter. Interestingly, these differences do not correlate with bacterial composition as derived from 16S rRNA sequencing.
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Affiliation(s)
- Stefano Fornasaro
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Alessandro Esposito
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Fiorella Florian
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Luigina De Leo
- Institute for Maternal Child Health-IRCCS "Burlo Garofolo" Trieste, via dell'Istria 65/1, 34100, Trieste, Italy
| | - Tarcisio Not
- Institute for Maternal Child Health-IRCCS "Burlo Garofolo" Trieste, via dell'Istria 65/1, 34100, Trieste, Italy
| | - Cristina Lagatolla
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Marica Mezzarobba
- Department of Life Sciences, University of Trieste, Via Edoardo Weiss 2, 34128, Trieste, TS, Italy
| | - Alessia Di Silvestre
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Valter Sergo
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy
| | - Alois Bonifacio
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, P.le Europa 1, 34100, Trieste, Italy.
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10
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Kim M, Sung J, Chia N. Resource-allocation constraint governs structure and function of microbial communities in metabolic modeling. Metab Eng 2022; 70:12-22. [PMID: 34990848 DOI: 10.1016/j.ymben.2021.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/01/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Predictive modeling tools for assessing microbial communities are important for realizing transformative capabilities of microbiomes in agriculture, ecology, and medicine. Constraint-based community-scale metabolic modeling is unique in its potential for making mechanistic predictions regarding both the structure and function of microbial communities. However, accessing this potential requires an understanding of key physicochemical constraints, which are typically considered on a per-species basis. What is needed is a means of incorporating global constraints relevant to microbial ecology into community models. Resource-allocation constraint, which describes how limited resources should be distributed to different cellular processes, sets limits on the efficiency of metabolic and ecological processes. In this study, we investigate the implications of resource-allocation constraints in community-scale metabolic modeling through a simple mechanism-agnostic implementation of resource-allocation constraints directly at the flux level. By systematically performing single-, two-, and multi-species growth simulations, we show that resource-allocation constraints are indispensable for predicting the structure and function of microbial communities. Our findings call for a scalable workflow for implementing a mechanistic version of resource-allocation constraints to ultimately harness the full potential of community-scale metabolic modeling tools.
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Affiliation(s)
- Minsuk Kim
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jaeyun Sung
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA; Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA; Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA.
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11
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Reprogramming microbial populations using a programmed lysis system to improve chemical production. Nat Commun 2021; 12:6886. [PMID: 34824227 PMCID: PMC8617184 DOI: 10.1038/s41467-021-27226-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.
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12
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Giannari D, Ho CH, Mahadevan R. A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PLoS Comput Biol 2021; 17:e1009060. [PMID: 34723959 PMCID: PMC8584699 DOI: 10.1371/journal.pcbi.1009060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/11/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
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Affiliation(s)
- Dafni Giannari
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- The Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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13
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Patel A, Carlson RP, Henson MA. In silico analysis of synthetic multispecies biofilms for cellobiose-to-isobutanol conversion reveals design principles for stable and productive communities. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Nazem-Bokaee H, Hom EFY, Warden AC, Mathews S, Gueidan C. Towards a Systems Biology Approach to Understanding the Lichen Symbiosis: Opportunities and Challenges of Implementing Network Modelling. Front Microbiol 2021; 12:667864. [PMID: 34012428 PMCID: PMC8126723 DOI: 10.3389/fmicb.2021.667864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Lichen associations, a classic model for successful and sustainable interactions between micro-organisms, have been studied for many years. However, there are significant gaps in our understanding about how the lichen symbiosis operates at the molecular level. This review addresses opportunities for expanding current knowledge on signalling and metabolic interplays in the lichen symbiosis using the tools and approaches of systems biology, particularly network modelling. The largely unexplored nature of symbiont recognition and metabolic interdependency in lichens could benefit from applying a holistic approach to understand underlying molecular mechanisms and processes. Together with ‘omics’ approaches, the application of signalling and metabolic network modelling could provide predictive means to gain insights into lichen signalling and metabolic pathways. First, we review the major signalling and recognition modalities in the lichen symbioses studied to date, and then describe how modelling signalling networks could enhance our understanding of symbiont recognition, particularly leveraging omics techniques. Next, we highlight the current state of knowledge on lichen metabolism. We also discuss metabolic network modelling as a tool to simulate flux distribution in lichen metabolic pathways and to analyse the co-dependence between symbionts. This is especially important given the growing number of lichen genomes now available and improved computational tools for reconstructing such models. We highlight the benefits and possible bottlenecks for implementing different types of network models as applied to the study of lichens.
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Affiliation(s)
- Hadi Nazem-Bokaee
- CSIRO Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, NCMI, Canberra, ACT, Australia.,CSIRO Land and Water, Canberra, ACT, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Erik F Y Hom
- Department of Biology and Center for Biodiversity and Conservation Research, The University of Mississippi, University City, MS, United States
| | | | - Sarah Mathews
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Cécile Gueidan
- CSIRO Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, NCMI, Canberra, ACT, Australia
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15
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The sum is greater than the parts: exploiting microbial communities to achieve complex functions. Curr Opin Biotechnol 2021; 67:149-157. [PMID: 33561703 DOI: 10.1016/j.copbio.2021.01.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.
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16
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Biohydrogen production beyond the Thauer limit by precision design of artificial microbial consortia. Commun Biol 2020; 3:443. [PMID: 32796915 PMCID: PMC7429504 DOI: 10.1038/s42003-020-01159-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/23/2020] [Indexed: 01/25/2023] Open
Abstract
Dark fermentative biohydrogen (H2) production could become a key technology for providing renewable energy. Until now, the H2 yield is restricted to 4 moles of H2 per mole of glucose, referred to as the "Thauer limit". Here we show, that precision design of artificial microbial consortia increased the H2 yield to 5.6 mol mol-1 glucose, 40% higher than the Thauer limit. In addition, the volumetric H2 production rates of our defined artificial consortia are superior compared to any mono-, co- or multi-culture system reported to date. We hope this study to be a major leap forward in the engineering of artificial microbial consortia through precision design and provide a breakthrough in energy science, biotechnology and ecology. Constructing artificial consortia with this drawing-board approach could in future increase volumetric production rates and yields of other bioprocesses. Our artificial consortia engineering blueprint might pave the way for the development of a H2 production bioindustry.
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17
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Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation. Sci Rep 2020; 10:13019. [PMID: 32747737 PMCID: PMC7398907 DOI: 10.1038/s41598-020-69509-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 06/25/2020] [Indexed: 01/06/2023] Open
Abstract
Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based flux balance analysis and time dependent simulations were used to explore the organism’s phenotypic landscape. Simulations aimed at designing media optimized for supporting growth and enhancing degradation, by passing the need in strain design via genetic modifications. Growth and degradation simulations were carried with more than 100 compounds consumed by P. aurescens TC1. In vitro validation confirmed the predicted classification of different compounds as efficient, moderate or poor stimulators of growth. Simulations successfully captured previous reports on the use of glucose and phosphate as bio-stimulators of atrazine degradation, supported by in vitro validation. Model predictions can go beyond supplementing the medium with a single compound and can predict the growth outcomes for higher complexity combinations. Hence, the analysis demonstrates that the exhaustive power of the genome scale metabolic reconstruction allows capturing complexities that are beyond common biochemical expertise and knowledge and further support the importance of computational platforms for the educated design of complex media. The model presented here can potentially serve as a predictive tool towards achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation.
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Frioux C, Singh D, Korcsmaros T, Hildebrand F. From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. Comput Struct Biotechnol J 2020; 18:1722-1734. [PMID: 32670511 PMCID: PMC7347713 DOI: 10.1016/j.csbj.2020.06.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Metagenomic sequencing of complete microbial communities has greatly enhanced our understanding of the taxonomic composition of microbiotas. This has led to breakthrough developments in bioinformatic disciplines such as assembly, gene clustering, metagenomic binning of species genomes and the discovery of an incredible, so far undiscovered, taxonomic diversity. However, functional annotations and estimating metabolic processes from single species - or communities - is still challenging. Earlier approaches relied mostly on inferring the presence of key enzymes for metabolic pathways in the whole metagenome, ignoring the genomic context of such enzymes, resulting in the 'bag-of-genes' approach to estimate functional capacities of microbiotas. Here, we review recent developments in metagenomic bioinformatics, with a special focus on emerging technologies to simulate and estimate metabolic information, that can be derived from metagenomic assembled genomes. Genome-scale metabolic models can be used to model the emergent properties of microbial consortia and whole communities, and the progress in this area is reviewed. While this subfield of metagenomics is still in its infancy, it is becoming evident that there is a dire need for further bioinformatic tools to address the complex combinatorial problems in modelling the metabolism of large communities as a 'bag-of-genomes'.
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Affiliation(s)
- Clémence Frioux
- Inria, CNRS, INRAE Bordeaux, France
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
| | - Dipali Singh
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk, UK
| | - Tamas Korcsmaros
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
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19
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Naizabekov S, Lee EY. Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b. Microorganisms 2020; 8:microorganisms8030437. [PMID: 32244934 PMCID: PMC7144005 DOI: 10.3390/microorganisms8030437] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 01/09/2023] Open
Abstract
Methylosinus trichosporium OB3b is an obligate aerobic methane-utilizing alpha-proteobacterium. Since its isolation, M. trichosporium OB3b has been established as a model organism to study methane metabolism in type II methanotrophs. M. trichosporium OB3b utilizes soluble and particulate methane monooxygenase (sMMO and pMMO respectively) for methane oxidation. While the source of electrons is known for sMMO, there is less consensus regarding electron donor to pMMO. To investigate this and other questions regarding methane metabolism, the genome-scale metabolic model for M. trichosporium OB3b (model ID: iMsOB3b) was reconstructed. The model accurately predicted oxygen: methane molar uptake ratios and specific growth rates on nitrate-supplemented medium with methane as carbon and energy source. The redox-arm mechanism which links methane oxidation with complex I of electron transport chain has been found to be the most optimal mode of electron transfer. The model was also qualitatively validated on ammonium-supplemented medium indicating its potential to accurately predict methane metabolism in different environmental conditions. Finally, in silico investigations regarding flux distribution in central carbon metabolism of M. trichosporium OB3b were performed. Overall, iMsOB3b can be used as an organism-specific knowledgebase and a platform for hypothesis-driven theoretical investigations of methane metabolism.
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20
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Ehsan A, Mahmood MK, Khan YD, Barukab OM, Khan SA, Chou KC. iHyd-PseAAC (EPSV): Identifying Hydroxylation Sites in Proteins by Extracting Enhanced Position and Sequence Variant Feature via Chou's 5-Step Rule and General Pseudo Amino Acid Composition. Curr Genomics 2019; 20:124-133. [PMID: 31555063 PMCID: PMC6728902 DOI: 10.2174/1389202920666190325162307] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 01/13/2023] Open
Abstract
Background In various biological processes and cell functions, Post Translational Modifications (PTMs) bear critical significance. Hydroxylation of proline residue is one kind of PTM, which occurs following protein synthesis. The experimental determination of hydroxyproline sites in an uncharacterized protein sequence requires extensive, time-consuming and expensive tests. Methods With the torrential slide of protein sequences produced in the post-genomic age, certain remarkable computational strategies are desired to overwhelm the issue. Keeping in view the composition and sequence order effect within polypeptide chains, an innovative in-silico> predictor via a mathematical model is proposed. Results Later, it was stringently verified using self-consistency, cross-validation and jackknife tests on benchmark datasets. It was established after a rigorous jackknife test that the new predictor values are superior to the values predicted by previous methodologies. Conclusion This new mathematical technique is the most appropriate and encouraging as compared with the existing models.
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Affiliation(s)
- Asma Ehsan
- 1Department of Mathematics, University of the Punjab, Lahore, Pakistan; 2Faculty of Information Technology, University of Management and Technology, Lahore, Pakistan; 3King Abdul Aziz University, Faculty of Computing and Information Technology in Rabigh, Jeddah, KSA; 4Gordon Life Science Institute, Boston, MA 02478, USA
| | - Muhammad K Mahmood
- 1Department of Mathematics, University of the Punjab, Lahore, Pakistan; 2Faculty of Information Technology, University of Management and Technology, Lahore, Pakistan; 3King Abdul Aziz University, Faculty of Computing and Information Technology in Rabigh, Jeddah, KSA; 4Gordon Life Science Institute, Boston, MA 02478, USA
| | - Yaser D Khan
- 1Department of Mathematics, University of the Punjab, Lahore, Pakistan; 2Faculty of Information Technology, University of Management and Technology, Lahore, Pakistan; 3King Abdul Aziz University, Faculty of Computing and Information Technology in Rabigh, Jeddah, KSA; 4Gordon Life Science Institute, Boston, MA 02478, USA
| | - Omar M Barukab
- 1Department of Mathematics, University of the Punjab, Lahore, Pakistan; 2Faculty of Information Technology, University of Management and Technology, Lahore, Pakistan; 3King Abdul Aziz University, Faculty of Computing and Information Technology in Rabigh, Jeddah, KSA; 4Gordon Life Science Institute, Boston, MA 02478, USA
| | - Sher A Khan
- 1Department of Mathematics, University of the Punjab, Lahore, Pakistan; 2Faculty of Information Technology, University of Management and Technology, Lahore, Pakistan; 3King Abdul Aziz University, Faculty of Computing and Information Technology in Rabigh, Jeddah, KSA; 4Gordon Life Science Institute, Boston, MA 02478, USA
| | - Kuo-Chen Chou
- 1Department of Mathematics, University of the Punjab, Lahore, Pakistan; 2Faculty of Information Technology, University of Management and Technology, Lahore, Pakistan; 3King Abdul Aziz University, Faculty of Computing and Information Technology in Rabigh, Jeddah, KSA; 4Gordon Life Science Institute, Boston, MA 02478, USA
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