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Ghassemi Nedjad C, Bolteau M, Bourneuf L, Paulevé L, Frioux C. Seed2LP: seed inference in metabolic networks for reverse ecology applications. Bioinformatics 2025; 41:btaf140. [PMID: 40163742 PMCID: PMC12007882 DOI: 10.1093/bioinformatics/btaf140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 03/24/2025] [Accepted: 03/27/2025] [Indexed: 04/02/2025] Open
Abstract
MOTIVATION A challenging problem in microbiology is to determine nutritional requirements of microorganisms and culture them, especially for the microbial dark matter detected solely with culture-independent methods. The latter foster an increasing amount of genomic sequences that can be explored with reverse ecology approaches to raise hypotheses on the corresponding populations. Building upon genome-scale metabolic networks (GSMNs) obtained from genome annotations, metabolic models predict contextualized phenotypes using nutrient information. RESULTS We developed the tool Seed2LP, addressing the inverse problem of predicting source nutrients, or seeds, from a GSMN and a metabolic objective. The originality of Seed2LP is its hybrid model, combining a scalable and discrete Boolean approximation of metabolic activity, with the numerically accurate flux balance analysis (FBA). Seed inference is highly customizable, with multiple search and solving modes, exploring the search space of external and internal metabolites combinations. Application to a benchmark of 107 curated GSMNs highlights the usefulness of a logic modelling method over a graph-based approach to predict seeds, and the relevance of hybrid solving to satisfy FBA constraints. Focusing on the dependency between metabolism and environment, Seed2LP is a computational support contributing to address the multifactorial challenge of culturing possibly uncultured microorganisms. AVAILABILITY AND IMPLEMENTATION Seed2LP is available on https://github.com/bioasp/seed2lp.
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Affiliation(s)
- Chabname Ghassemi Nedjad
- University of Bordeaux, CNRS, BordeauxINP, LaBRI, UMR 5800, Talence F-33400, France
- Inria, University of Bordeaux, INRAE, Talence F-33400, France
| | - Mathieu Bolteau
- Inria, University of Bordeaux, INRAE, Talence F-33400, France
- Nantes Université, Ecole Centrale Nantes, CNRS, LS2N, UMR 6004, Nantes F-44000, France
| | - Lucas Bourneuf
- Inria, Université de Rennes, CNRS, IRISA, UMR 6074, Rennes F-35000, France
- CHRU Brest, Université de Bretagne Occidentale, Brest F-29000, France
| | - Loïc Paulevé
- University of Bordeaux, CNRS, BordeauxINP, LaBRI, UMR 5800, Talence F-33400, France
| | - Clémence Frioux
- Inria, University of Bordeaux, INRAE, Talence F-33400, France
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Lu Y, Hui F, Zhou G, Xia J. MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights. Nucleic Acids Res 2025; 53:D789-D796. [PMID: 39441071 PMCID: PMC11701532 DOI: 10.1093/nar/gkae944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/30/2024] [Accepted: 10/08/2024] [Indexed: 10/25/2024] Open
Abstract
The growing volumes of microbiome studies over the past decade have revealed a wide repertoire of microbial associations under diverse conditions. Microbes produce small molecules to interact with each other as well as to modulate their environments. Their metabolic profiles hold the key to understanding these association patterns for translational applications. Based on this concept, we developed MicrobiomeNet, a comprehensive database that integrates microbial associations with their metabolic profiles for mechanistic insights. It currently contains a total of ∼5.8 million known microbial associations, coupled with >12 400 genome-scale metabolic models (GEMs) covering ∼6000 microbial species. Users can intuitively explore microbial associations and compare their corresponding metabolic profiles. Our case studies show that MicrobiomeNet can provide mechanistic insights that are consistent with the literature. MicrobiomeNet is freely available at https://www.microbiomenet.com/.
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Affiliation(s)
- Yao Lu
- Institute of Parasitology, McGill University, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Quebec, Canada
| | - Fiona Hui
- Institute of Parasitology, McGill University, Quebec, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Quebec, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Quebec, Canada
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Tanniche I, Behkam B. New and Notable: Metabolic modeling of microbial communities: Past, present, and future. Biophys J 2024; 123:2966-2968. [PMID: 39192581 PMCID: PMC11427770 DOI: 10.1016/j.bpj.2024.08.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 08/29/2024] Open
Affiliation(s)
- Imen Tanniche
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia; School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia; Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia.
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Jiang F, Ruan Y, Chen XH, Yu HL, Cheng T, Duan XY, Liu YG, Zhang HY, Zhang QY. Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications. Microbiol Spectr 2024; 12:e0234223. [PMID: 38391229 PMCID: PMC10986615 DOI: 10.1128/spectrum.02342-23] [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: 06/05/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Seed metabolites are the combination of essential compounds required by an organism across various potential environmental conditions. The seed metabolites screening framework based on the network topology approach can capture important biological information of species. This study aims to identify comprehensively the relationship between seed metabolites and pathogenic bacteria. A large-scale data set was compiled, describing the seed metabolite sets and metabolite sets of 124,192 pathogenic strains from 34 genera, by constructing genome-scale metabolic models. The enrichment analysis method was used to screen the specific seed metabolites of each species/genus of pathogenic bacteria. The metabolites of pathogenic microorganisms database (MPMdb) (http://qyzhanglab.hzau.edu.cn/MPMdb/) was established for browsing, searching, predicting, or downloading metabolites and seed metabolites of pathogenic microorganisms. Based on the MPMdb, taxonomic and phylogenetic analyses of pathogenic bacteria were performed according to the function of seed metabolites and metabolites. The results showed that the seed metabolites could be used as a feature for microorganism chemotaxonomy, and they could mirror the phylogeny of pathogenic bacteria. In addition, our screened specific seed metabolites of pathogenic bacteria can be used not only for further tapping the nutritional resources and identifying auxotrophies of pathogenic bacteria but also for designing targeted bactericidal compounds by combining with existing antimicrobial agents.IMPORTANCEMetabolites serve as key communication links between pathogenic microorganisms and hosts, with seed metabolites being crucial for microbial growth, reproduction, external communication, and host infection. However, the large-scale screening of metabolites and the identification of seed metabolites have always been the main technical bottleneck due to the low throughput and costly analysis. Genome-scale metabolic models have become a recognized research paradigm to investigate the metabolic characteristics of species. The developed metabolites of pathogenic microorganisms database in this study is committed to systematically predicting and identifying the metabolites and seed metabolites of pathogenic microorganisms, which could provide a powerful resource platform for pathogenic bacteria research.
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Affiliation(s)
- Feng Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yao Ruan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Hui Chen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hai-Long Yu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ting Cheng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xin-Ya Duan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yan-Guang Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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Lyu X, Nuhu M, Candry P, Wolfanger J, Betenbaugh M, Saldivar A, Zuniga C, Wang Y, Shrestha S. Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass. J Ind Microbiol Biotechnol 2024; 51:kuae025. [PMID: 39003244 PMCID: PMC11287213 DOI: 10.1093/jimb/kuae025] [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: 04/11/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
Abstract
Growing environmental concerns and the need to adopt a circular economy have highlighted the importance of waste valorization for resource recovery. Microbial consortia-enabled biotechnologies have made significant developments in the biomanufacturing of valuable resources from waste biomass that serve as suitable alternatives to petrochemical-derived products. These microbial consortia-based processes are designed following a top-down or bottom-up engineering approach. The top-down approach is a classical method that uses environmental variables to selectively steer an existing microbial consortium to achieve a target function. While high-throughput sequencing has enabled microbial community characterization, the major challenge is to disentangle complex microbial interactions and manipulate the structure and function accordingly. The bottom-up approach uses prior knowledge of the metabolic pathway and possible interactions among consortium partners to design and engineer synthetic microbial consortia. This strategy offers some control over the composition and function of the consortium for targeted bioprocesses, but challenges remain in optimal assembly methods and long-term stability. In this review, we present the recent advancements, challenges, and opportunities for further improvement using top-down and bottom-up approaches for microbiome engineering. As the bottom-up approach is relatively a new concept for waste valorization, this review explores the assembly and design of synthetic microbial consortia, ecological engineering principles to optimize microbial consortia, and metabolic engineering approaches for efficient conversion. Integration of top-down and bottom-up approaches along with developments in metabolic modeling to predict and optimize consortia function are also highlighted. ONE-SENTENCE SUMMARY This review highlights the microbial consortia-driven waste valorization for biomanufacturing through top-down and bottom-up design approaches and describes strategies, tools, and unexplored opportunities to optimize the design and stability of such consortia.
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Affiliation(s)
- Xuejiao Lyu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mujaheed Nuhu
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Pieter Candry
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Jenna Wolfanger
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexis Saldivar
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Cristal Zuniga
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
| | - Ying Wang
- Department of Soil and Crop Sciences, Texas A&M University, TX 77843, USA
| | - Shilva Shrestha
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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Lee MJ, Lee DS. Heterogeneous Popularity of Metabolic Reactions from Evolution. PHYSICAL REVIEW LETTERS 2024; 132:018401. [PMID: 38242656 DOI: 10.1103/physrevlett.132.018401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 08/15/2023] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
The composition of cellular metabolism is different across species. Empirical data reveal that bacterial species contain similar numbers of metabolic reactions but that the cross-species popularity of reactions is so heterogenous that some reactions are found in all the species while others are in just few species, characterized by a power-law distribution with the exponent one. Introducing an evolutionary model concretizing the stochastic recruitment of chemical reactions into the metabolism of different species at different times and their inheritance to descendants, we demonstrate that the exponential growth of the number of species containing a reaction and the saturated recruitment rate of brand-new reactions lead to the empirically identified power-law popularity distribution. Furthermore, the structural characteristics of metabolic networks and the species' phylogeny in our simulations agree well with empirical observations.
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Affiliation(s)
- Mi Jin Lee
- Department of Applied Physics, Hanyang University, Ansan 15588, Korea
| | - Deok-Sun Lee
- School of Computational Sciences and Center for AI and Natural Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea
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Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024; 17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.
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Affiliation(s)
- Klara Cerk
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Chabname Ghassemi Nedjad
- Inria, University of Bordeaux, INRAETalenceFrance
- University of Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800TalenceFrance
| | - Maxime Lecomte
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE STLO¸University of RennesRennesFrance
| | | | | | - Falk Hildebrand
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Simon Labarthe
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE, University of Bordeaux, BIOGECO, UMR 1202CestasFrance
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Seppi M, Pasqualini J, Facchin S, Savarino EV, Suweis S. Emergent Functional Organization of Gut Microbiomes in Health and Diseases. Biomolecules 2023; 14:5. [PMID: 38275746 PMCID: PMC10813293 DOI: 10.3390/biom14010005] [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: 10/07/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.
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Affiliation(s)
- Marcello Seppi
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Jacopo Pasqualini
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Sonia Facchin
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Samir Suweis
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
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Gonçalves OS, Creevey CJ, Santana MF. Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. ENVIRONMENTAL MICROBIOME 2023; 18:81. [PMID: 37974247 PMCID: PMC10655421 DOI: 10.1186/s40793-023-00536-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants. RESULTS We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. CONCLUSION Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.
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Affiliation(s)
- Osiel S Gonçalves
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Mateus F Santana
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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Kumari P, Deepa N, Trivedi PK, Singh BK, Srivastava V, Singh A. Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites. Microb Cell Fact 2023; 22:226. [PMID: 37925404 PMCID: PMC10625306 DOI: 10.1186/s12934-023-02234-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.
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Affiliation(s)
- Poonam Kumari
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Nikky Deepa
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prabodh Kumar Trivedi
- Division of Plant Biotechnology, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2753, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden.
| | - Akanksha Singh
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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11
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Gupta U, Dey P. Rise of the guardians: Gut microbial maneuvers in bacterial infections. Life Sci 2023; 330:121993. [PMID: 37536616 DOI: 10.1016/j.lfs.2023.121993] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
AIMS Bacterial infections are one of the major causes of mortality globally. The gut microbiota, primarily comprised of the commensals, performs an important role in maintaining intestinal immunometabolic homeostasis. The current review aims to provide a comprehensive understanding of how modulation of the gut microbiota influences opportunistic bacterial infections. MATERIALS AND METHODS Primarily centered around mechanisms related to colonization resistance, nutrient, and metabolite-associated factors, mucosal immune response, and commensal-pathogen reciprocal interactions, we discuss how gut microbiota can promote or prevent bacterial infections. KEY FINDINGS Opportunistic infections can occur directly due to obligate pathogens or indirectly due to the overgrowth of opportunistic pathobionts. Gut microbiota-centered mechanisms of altered intestinal immunometabolic and metabolomic homeostasis play a significant role in infection promotion and prevention. Depletion in the population of commensals, increased abundance of pathobionts, and overall decrease in gut microbial diversity and richness caused due to prolonged antibiotic use are risk factors of opportunistic bacterial infections, including infections from multidrug-resistant spp. Gut commensals can limit opportunistic infections by mechanisms including the production of antimicrobials, short-chain fatty acids, bile acid metabolism, promoting mucin formation, and maintaining immunological balance at the mucosa. Gut microbiota-centered strategies, including the administration of probiotics and fecal microbiota transplantation, could help attenuate opportunistic bacterial infections. SIGNIFICANCE The current review discussed the gut microbial population and function-specific aspects contributing to bacterial infection susceptibility and prophylaxis. Collectively, this review provides a comprehensive understanding of the mechanisms related to the dual role of gut microbiota in bacterial infections.
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Affiliation(s)
- Upasana Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India.
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12
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Ramon C, Stelling J. Functional comparison of metabolic networks across species. Nat Commun 2023; 14:1699. [PMID: 36973280 PMCID: PMC10043025 DOI: 10.1038/s41467-023-37429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Metabolic phenotypes are pivotal for many areas, but disentangling how evolutionary history and environmental adaptation shape these phenotypes is an open problem. Especially for microbes, which are metabolically diverse and often interact in complex communities, few phenotypes can be determined directly. Instead, potential phenotypes are commonly inferred from genomic information, and rarely were model-predicted phenotypes employed beyond the species level. Here, we propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and thereby link genotype and environment to phenotype. We show that these correlations provide a consistent functional complement to genomic information by capturing how network context shapes gene function. This enables, for example, phylogenetic inference across all domains of life at the organism level. For 245 bacterial species, we identify conserved and variable metabolic functions, elucidate the quantitative impact of evolutionary history and ecological niche on these functions, and generate hypotheses on associated metabolic phenotypes. We expect our framework for the joint interpretation of metabolic phenotypes, evolution, and environment to help guide future empirical studies.
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Affiliation(s)
- Charlotte Ramon
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058, Basel, Switzerland
- Ph.D. Program Systems Biology, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, 4058, Basel, Switzerland.
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Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome. MICROBIOME 2022; 10:217. [PMID: 36482420 PMCID: PMC9733318 DOI: 10.1186/s40168-022-01383-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND From a theoretical ecology point of view, microbiomes are far more complex than expected. Besides competition and competitive exclusion, cooperative microbe-microbe interactions have to be carefully considered. Metabolic dependencies among microbes likely explain co-existence in microbiota. METHODOLOGY In this in silico study, we explored genome-scale metabolic models (GEMs) of 193 bacteria isolated from Arabidopsis thaliana roots. We analyzed their predicted producible metabolites under simulated nutritional constraints including "root exudate-mimicking growth media" and assessed the potential of putative metabolic exchanges of by- and end-products to avoid those constraints. RESULTS We found that the genome-encoded metabolic potential is quantitatively and qualitatively clustered by phylogeny, highlighting metabolic differentiation between taxonomic groups. Random, synthetic combinations of increasing numbers of strains (SynComs) indicated that the number of producible compounds by GEMs increased with average phylogenetic distance, but that most SynComs were centered around an optimal phylogenetic distance. Moreover, relatively small SynComs could reflect the capacity of the whole community due to metabolic redundancy. Inspection of 30 specific end-product metabolites (i.e., target metabolites: amino acids, vitamins, phytohormones) indicated that the majority of the strains had the genetic potential to produce almost all the targeted compounds. Their production was predicted (1) to depend on external nutritional constraints and (2) to be facilitated by nutritional constraints mimicking root exudates, suggesting nutrient availability and root exudates play a key role in determining the number of producible metabolites. An answer set programming solver enabled the identification of numerous combinations of strains predicted to depend on each other to produce these targeted compounds under severe nutritional constraints thus indicating a putative sub-community level of functional redundancy. CONCLUSIONS This study predicts metabolic restrictions caused by available nutrients in the environment. By extension, it highlights the importance of the environment for niche potential, realization, partitioning, and overlap. Our results also suggest that metabolic dependencies and cooperation among root microbiota members compensate for environmental constraints and help maintain co-existence in complex microbial communities. Video Abstract.
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Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35000, Rennes, France
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | - Nathan Vannier
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | | | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany.
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14
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Müller S, Flamm C, Stadler PF. What makes a reaction network "chemical"? J Cheminform 2022; 14:63. [PMID: 36123755 PMCID: PMC9484159 DOI: 10.1186/s13321-022-00621-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reaction networks (RNs) comprise a set X of species and a set [Formula: see text] of reactions [Formula: see text], each converting a multiset of educts [Formula: see text] into a multiset [Formula: see text] of products. RNs are equivalent to directed hypergraphs. However, not all RNs necessarily admit a chemical interpretation. Instead, they might contradict fundamental principles of physics such as the conservation of energy and mass or the reversibility of chemical reactions. The consequences of these necessary conditions for the stoichiometric matrix [Formula: see text] have been discussed extensively in the chemical literature. Here, we provide sufficient conditions for [Formula: see text] that guarantee the interpretation of RNs in terms of balanced sum formulas and structural formulas, respectively. RESULTS Chemically plausible RNs allow neither a perpetuum mobile, i.e., a "futile cycle" of reactions with non-vanishing energy production, nor the creation or annihilation of mass. Such RNs are said to be thermodynamically sound and conservative. For finite RNs, both conditions can be expressed equivalently as properties of the stoichiometric matrix [Formula: see text]. The first condition is vacuous for reversible networks, but it excludes irreversible futile cycles and-in a stricter sense-futile cycles that even contain an irreversible reaction. The second condition is equivalent to the existence of a strictly positive reaction invariant. It is also sufficient for the existence of a realization in terms of sum formulas, obeying conservation of "atoms". In particular, these realizations can be chosen such that any two species have distinct sum formulas, unless [Formula: see text] implies that they are "obligatory isomers". In terms of structural formulas, every compound is a labeled multigraph, in essence a Lewis formula, and reactions comprise only a rearrangement of bonds such that the total bond order is preserved. In particular, for every conservative RN, there exists a Lewis realization, in which any two compounds are realized by pairwisely distinct multigraphs. Finally, we show that, in general, there are infinitely many realizations for a given conservative RN. CONCLUSIONS "Chemical" RNs are directed hypergraphs with a stoichiometric matrix [Formula: see text] whose left kernel contains a strictly positive vector and whose right kernel does not contain a futile cycle involving an irreversible reaction. This simple characterization also provides a concise specification of random models for chemical RNs that additionally constrain [Formula: see text] by rank, sparsity, or distribution of the non-zero entries. Furthermore, it suggests several interesting avenues for future research, in particular, concerning alternative representations of reaction networks and infinite chemical universes.
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Affiliation(s)
- Stefan Müller
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria
| | - Christoph Flamm
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Peter F. Stadler
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, 04107 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases University Leipzig, 04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany
- Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, 111321 Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501 USA
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15
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Silva Gonçalves O, Bonandi Barreiros R, Martins Tupy S, Ferreira Santana M. A reverse-ecology framework to uncover the potential metabolic interplay among 'Candidatus Liberibacter' species, Citrus hosts and psyllid vector. Gene X 2022; 837:146679. [PMID: 35752379 DOI: 10.1016/j.gene.2022.146679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/31/2022] [Accepted: 06/10/2022] [Indexed: 11/04/2022] Open
Abstract
'Candidatus Liberibacter' species have developed a dependency on essential nutrients and metabolites from the host cell, as a result of substantial genome reduction. Still, it is difficult to state which nutrients they acquire and whether or not they are metabolically reliant. We used a reverse-ecology model to investigate the potential metabolic interactions of 'Ca Liberibacter' species, Citrus, and the psyllid Diaphorina citri in the huanglongbing disease pyramid. Our findings show that hosts (citrus and psyllid) tend to support the nutritional needs of 'Ca. Liberibacter' species, implying that the pathogen's metabolism has become tightly linked to hosts, which may reflect in the parasite lifestyle of this important genus.
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Affiliation(s)
- Osiel Silva Gonçalves
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Ralph Bonandi Barreiros
- Departmento de Fitotecnia, Laboratório de Biotecnologia de Plantas Horticulas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Brazil
| | - Sumaya Martins Tupy
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Mateus Ferreira Santana
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Minas Gerais, Brazil.
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16
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Sarkar I, Sen G, Bhattacharyya S, Gtari M, Sen A. Inter-cluster competition and resource partitioning may govern the ecology of Frankia. Arch Microbiol 2022; 204:326. [PMID: 35576077 DOI: 10.1007/s00203-022-02910-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/25/2022]
Abstract
Microbes live in a complex communal ecosystem. The structural complexity of microbial community reflects diversity, functionality, as well as habitat type. Delineation of ecologically important microbial populations along with exploration of their roles in environmental adaptation or host-microbe interaction has a crucial role in modern microbiology. In this scenario, reverse ecology (the use of genomics to study ecology) plays a pivotal role. Since the co-existence of two different genera in one small niche should maintain a strict direct interaction, it will be interesting to utilize the concept of reverse ecology in this scenario. Here, we exploited an 'R' package, the RevEcoR, to resolve the issue of co-existing microbes which are proven to be a crucial tool for identifying the nature of their relationship (competition or complementation) persisting among them. Our target organism here is Frankia, a nitrogen-fixing actinobacterium popular for its genetic and host-specific nature. According to their plant host, Frankia has already been sub-divided into four clusters C-I, C-II, C-III, and C-IV. Our results revealed a strong competing nature of CI Frankia. Among the clusters of Frankia studied, the competition index between C-I and C-III was the largest. The other interesting result was the co-occurrence of C-II and C-IV groups. It was revealed that these two groups follow the theory of resource partitioning in their lifestyle. Metabolic analysis along with their differential transporter machinery validated our hypothesis of resource partitioning among C-II and C-IV groups.
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Affiliation(s)
- I Sarkar
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India
| | - G Sen
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India
| | - S Bhattacharyya
- Biswa Bangla Genome Centre, Univ. of North Bengal, Siliguri, West Bengal, India
| | - M Gtari
- Unité de Bactériologie Moléculaire and Génomique, Département de Génie Biologique and Chimique, Institut National Des Sciences Appliquéeset de Technologie, Université de Carthage, Carthage, Tunisia
| | - A Sen
- Bioinformatics Facility, University of North Bengal, Siliguri, West Bengal, India.
- Biswa Bangla Genome Centre, Univ. of North Bengal, Siliguri, West Bengal, India.
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India.
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17
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Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications. Mar Drugs 2022; 20:md20020108. [PMID: 35200637 PMCID: PMC8874374 DOI: 10.3390/md20020108] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
Environmental microbes living in communities engage in complex interspecies interactions that are challenging to decipher. Nevertheless, the interactions provide the basis for shaping community structure and functioning, which is crucial for ecosystem service. In addition, microbial interactions facilitate specific adaptation and ecological evolution processes particularly essential for microbial communities dwelling in resource-limiting habitats, such as the deep oceans. Recent technological and knowledge advancements provide an opportunity for the study of interactions within complex microbial communities, such as those inhabiting deep-sea waters and sediments. The microbial interaction studies provide insights into developing new strategies for biotechnical applications. For example, cooperative microbial interactions drive the degradation of complex organic matter such as chitins and celluloses. Such microbiologically-driven biogeochemical processes stimulate creative designs in many applied sciences. Understanding the interaction processes and mechanisms provides the basis for the development of synthetic communities and consequently the achievement of specific community functions. Microbial community engineering has many application potentials, including the production of novel antibiotics, biofuels, and other valuable chemicals and biomaterials. It can also be developed into biotechniques for waste processing and environmental contaminant bioremediation. This review summarizes our current understanding of the microbial interaction mechanisms and emerging techniques for inferring interactions in deep-sea microbial communities, aiding in future biotechnological and therapeutic applications.
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18
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Cao MH, Tang BH, Ruan Y, Liang XL, Chu XY, Liang ZM, Zhang QY, Zhang HY. Development of specific and selective bactericide by introducing exogenous metabolite of pathogenic bacteria. Eur J Med Chem 2021; 225:113808. [PMID: 34461506 DOI: 10.1016/j.ejmech.2021.113808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/16/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
The widespread and repeated use of broad-spectrum bactericides has led to an increase in resistance. Developing novel broad-spectrum bactericides cannot solve the resistance problem, and may even aggravate it. The design of specific and selective bactericides has become urgent. A specific bactericidal design strategy was proposed by introducing exogenous metabolites in this study. This strategy was used to optimize two known antibacterial agents, luteolin (M) and Isoprothiolane (D), against Xoo. Based on the prodrug principles, target compound MB and DB were synthesized by combing M or D with exogenous metabolites, respectively. Bactericidal activity test results demonstrated that while the antibacterial ability of target compounds was significantly improved, their selectivity was also well enhanced by the introducing of exogenous metabolites. Comparing with the original compound, the antibacterial activity of target compound was significantly increased 92.0% and 74.5%, respectively. The optimized target compounds were more easily absorbed, and the drug application concentrations were much lower than those of the original agents, which would greatly reduce environmental pollution and relieve resistance risk. Our proposed strategy is of great significance for exploring the specific and selective bactericides against other pathogens.
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Affiliation(s)
- Min-Hui Cao
- College of Science, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China
| | - Bao-He Tang
- College of Science, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, PR China
| | - Yao Ruan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xiao-Long Liang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhan-Min Liang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, PR China
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19
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Tal O, Bartuv R, Vetcos M, Medina S, Jiang J, Freilich S. NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data. Microorganisms 2021; 9:microorganisms9091838. [PMID: 34576734 PMCID: PMC8468097 DOI: 10.3390/microorganisms9091838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/08/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online.
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Affiliation(s)
- Ofir Tal
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Rotem Bartuv
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 7628604, Israel
| | - Maria Vetcos
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Shlomit Medina
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Shiri Freilich
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- Correspondence:
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20
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Lara EG, van der Windt I, Molenaar D, de Vos MGJ, Melkonian C. Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. Genes (Basel) 2021; 12:genes12081221. [PMID: 34440394 PMCID: PMC8393552 DOI: 10.3390/genes12081221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 02/01/2023] Open
Abstract
The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities.
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Affiliation(s)
- Elena G. Lara
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
| | | | - Douwe Molenaar
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
| | - Marjon G. J. de Vos
- GELIFES, Universtity of Groningen, 9747 AG Groningen, The Netherlands;
- Correspondence: (M.G.J.d.V.); (C.M.)
| | - Chrats Melkonian
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
- Correspondence: (M.G.J.d.V.); (C.M.)
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21
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Moyer D, Pacheco AR, Bernstein DB, Segrè D. Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure. J Mol Evol 2021; 89:472-483. [PMID: 34230992 PMCID: PMC8318951 DOI: 10.1007/s00239-021-10018-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/12/2021] [Indexed: 11/15/2022]
Abstract
Uncovering the general principles that govern the structure of metabolic networks is key to understanding the emergence and evolution of living systems. Artificial chemistries can help illuminate this problem by enabling the exploration of chemical reaction universes that are constrained by general mathematical rules. Here, we focus on artificial chemistries in which strings of characters represent simplified molecules, and string concatenation and splitting represent possible chemical reactions. We developed a novel Python package, ARtificial CHemistry NEtwork Toolbox (ARCHNET), to study string chemistries using tools from the field of stoichiometric constraint-based modeling. In addition to exploring the topological characteristics of different string chemistry networks, we developed a network-pruning algorithm that can generate minimal metabolic networks capable of producing a specified set of biomass precursors from a given assortment of environmental nutrients. We found that the composition of these minimal metabolic networks was influenced more strongly by the metabolites in the biomass reaction than the identities of the environmental nutrients. This finding has important implications for the reconstruction of organismal metabolic networks and could help us better understand the rise and evolution of biochemical organization. More generally, our work provides a bridge between artificial chemistries and stoichiometric modeling, which can help address a broad range of open questions, from the spontaneous emergence of an organized metabolism to the structure of microbial communities.
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Affiliation(s)
- Devlin Moyer
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Alan R Pacheco
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA
- Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - David B Bernstein
- Biological Design Center, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, 02215, USA.
- Department of Biology, Boston University, Boston, MA, 02215, USA.
- Biological Design Center, Boston University, Boston, MA, 02215, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Department of Physics, Boston University, Boston, MA, 02215, USA.
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22
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Abstract
Global warming and the increase in organic waste from agro-industries create a major problem for the environment. In this sense, microbial fuel cells (MFC) have great potential for the generation of bioelectricity by using organic waste as fuel. This research produced low-cost MFC by using zinc and copper electrodes and taking blueberry waste as fuel. A peak current and voltage of 1.130 ± 0.018 mA and 1.127 ± 0.096 V, respectively, were generated. The pH levels were acid, with peak conductivity values of 233. 94 ± 0.345 mS/cm and the degrees Brix were descending from the first day. The maximum power density was 3.155 ± 0.24 W/cm2 at 374.4 mA/cm2 current density, and Cándida boidinii was identified by means of molecular biology and bioinformatics techniques. This research gives a new way to generate electricity with this type of waste, generating added value for the companies in this area and helping to reduce global warming.
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23
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Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL. A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Nature 2021; 595:415-420. [PMID: 34262212 PMCID: PMC8939302 DOI: 10.1038/s41586-021-03707-9] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023]
Abstract
Gut microorganisms modulate host phenotypes and are associated with numerous health effects in humans, ranging from host responses to cancer immunotherapy to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microorganisms has hindered efforts to define mechanistic connections between individual microbial strains and host phenotypes. One key way in which the gut microbiome influences host physiology is through the production of small molecules1-3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect the products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites in diverse sample types. We report the metabolic profiles of 178 gut microorganism strains using our library of 833 metabolites. Using this metabolomics resource, we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover a previously undescribed type of metabolism in Bacteroides, and reveal candidate biochemical pathways using comparative genomics. Microbiota-dependent metabolites can be detected in diverse biological fluids from gnotobiotic and conventionally colonized mice and traced back to the corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microorganisms and interactions between microorganisms and their host.
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Affiliation(s)
- Shuo Han
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Will Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Microbiology and Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt R. Fischer
- ChEM-H, Stanford University, Stanford, CA, USA,Chan-Zuckerburg Biohub, San Francisco, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Microbiology and Immunology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Leah Guthrie
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lalla A. Fall
- ChEM-H, Stanford University, Stanford, CA, USA,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA,Address correspondence to: , ,
| | - Michael A. Fischbach
- Chan-Zuckerburg Biohub, San Francisco, CA, USA,Department of Bioengineering, Stanford University, Stanford, CA, USA,Address correspondence to: , ,
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA,Chan-Zuckerburg Biohub, San Francisco, CA, USA,Center for Human Microbiome Studies, Stanford, CA, USA,Address correspondence to: , ,
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24
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Twining CW, Bernhardt JR, Derry AM, Hudson CM, Ishikawa A, Kabeya N, Kainz MJ, Kitano J, Kowarik C, Ladd SN, Leal MC, Scharnweber K, Shipley JR, Matthews B. The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification. Ecol Lett 2021; 24:1709-1731. [PMID: 34114320 DOI: 10.1111/ele.13771] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/20/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022]
Abstract
The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.
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Affiliation(s)
- Cornelia W Twining
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Limnological Institute, University of Konstanz, Konstanz-Egg, Germany
| | - Joey R Bernhardt
- Department of Biology, McGill University, Montréal, QC, Canada.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Cameron M Hudson
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology (TUMSAT, Tokyo, Japan
| | - Martin J Kainz
- WasserCluster Lunz-Inter-university Center for Aquatic Ecosystems Research, Lunz am See, Austria
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Carmen Kowarik
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Nemiah Ladd
- Ecosystem Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Miguel C Leal
- ECOMARE and CESAM - Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Kristin Scharnweber
- Department of Ecology and Genetics; Limnology, Uppsala University, Uppsala, Sweden.,University of Potsdam, Plant Ecology and Nature Conservation, Potsdam-Golm, Germany
| | - Jeremy R Shipley
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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25
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Functional prediction of environmental variables using metabolic networks. Sci Rep 2021; 11:12192. [PMID: 34108539 PMCID: PMC8190111 DOI: 10.1038/s41598-021-91486-8] [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: 09/21/2020] [Accepted: 05/05/2021] [Indexed: 11/23/2022] Open
Abstract
In this manuscript, we propose a novel approach to assess relationships between environment and metabolic networks. We used a comprehensive dataset of more than 5000 prokaryotic species from which we derived the metabolic networks. We compute the scope from the reconstructed graphs, which is the set of all metabolites and reactions that can potentially be synthesized when provided with external metabolites. We show using machine learning techniques that the scope is an excellent predictor of taxonomic and environmental variables, namely growth temperature, oxygen tolerance, and habitat. In the literature, metabolites and pathways are rarely used to discriminate species. We make use of the scope underlying structure—metabolites and pathways—to construct the predictive models, giving additional information on the important metabolic pathways needed to discriminate the species, which is often absent in other metabolic network properties. For example, in the particular case of growth temperature, glutathione biosynthesis pathways are specific to species growing in cold environments, whereas tungsten metabolism is specific to species in warm environments, as was hinted in current literature. From a machine learning perspective, the scope is able to reduce the dimension of our data, and can thus be considered as an interpretable graph embedding.
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26
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Assessment of phylo-functional coherence along the bacterial phylogeny and taxonomy. Sci Rep 2021; 11:8299. [PMID: 33859339 PMCID: PMC8050241 DOI: 10.1038/s41598-021-87909-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/06/2021] [Indexed: 11/25/2022] Open
Abstract
In this report we use available curated phylogenies, taxonomy, and genome annotations to assess the phylogenetic and gene content similarity associated with each different taxon and taxonomic rank. Subsequently, we employ the same data to assess the frontiers of functional coherence along the bacterial phylogeny. Our results show that within-group phylogenetic and gene content similarity of taxa in the same rank are not homogenous, and that these values show extensive overlap between ranks. Functional coherence along the 16S rRNA gene-based phylogeny was limited to 44 particular nodes presenting large variations in phylogenetic depth. For instance, the deep subtree affiliated to class Actinobacteria presented functional coherence, while the shallower family Enterobacteriaceae-affiliated subtree did not. On the other hand, functional coherence along the genome-based phylogeny delimited deep subtrees affiliated to phyla Actinobacteriota, Deinococcota, Chloroflexota, Firmicutes, and a subtree containing the rest of the bacterial phyla. The results presented here can be used to guide the exploration of results in many microbial ecology and evolution research scenarios. Moreover, we provide dedicated scripts and files that can be used to continue the exploration of functional coherence along the bacterial phylogeny employing different parameters or input data (https://git.io/Jec5U).
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27
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LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. Signatures of optimal codon usage in metabolic genes inform budding yeast ecology. PLoS Biol 2021; 19:e3001185. [PMID: 33872297 PMCID: PMC8084343 DOI: 10.1371/journal.pbio.3001185] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 04/29/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023] Open
Abstract
Reverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism (GAL) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in the GAL pathway is positively correlated with quantitative growth on galactose, suggesting that GAL codon optimization reflects increased capacity to grow on galactose. Optimal codon usage in the GAL pathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage of GAL genes is greater than 85% of all genes in the genome of the major human pathogen Candida albicans (CUG-Ser1 clade) and greater than 75% of genes in the genome of the dairy yeast Kluyveromyces lactis (family Saccharomycetaceae). We further find a correlation between optimization in the GALactose pathway genes and several genes associated with nutrient sensing and metabolism. This work suggests that codon optimization harbors information about the metabolic ecology of microbial eukaryotes. This information may be particularly useful for studying fungal dark matter-species that have yet to be cultured in the lab or have only been identified by genomic material.
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Affiliation(s)
- Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Dana A. Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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28
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Liu Z, Ma A, Mathé E, Merling M, Ma Q, Liu B. Network analyses in microbiome based on high-throughput multi-omics data. Brief Bioinform 2021; 22:1639-1655. [PMID: 32047891 PMCID: PMC7986608 DOI: 10.1093/bib/bbaa005] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Together with various hosts and environments, ubiquitous microbes interact closely with each other forming an intertwined system or community. Of interest, shifts of the relationships between microbes and their hosts or environments are associated with critical diseases and ecological changes. While advances in high-throughput Omics technologies offer a great opportunity for understanding the structures and functions of microbiome, it is still challenging to analyse and interpret the omics data. Specifically, the heterogeneity and diversity of microbial communities, compounded with the large size of the datasets, impose a tremendous challenge to mechanistically elucidate the complex communities. Fortunately, network analyses provide an efficient way to tackle this problem, and several network approaches have been proposed to improve this understanding recently. Here, we systemically illustrate these network theories that have been used in biological and biomedical research. Then, we review existing network modelling methods of microbial studies at multiple layers from metagenomics to metabolomics and further to multi-omics. Lastly, we discuss the limitations of present studies and provide a perspective for further directions in support of the understanding of microbial communities.
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Affiliation(s)
- Zhaoqian Liu
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Marlena Merling
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Bingqiang Liu
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
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29
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Bernstein DB, Sulheim S, Almaas E, Segrè D. Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. Genome Biol 2021; 22:64. [PMID: 33602294 PMCID: PMC7890832 DOI: 10.1186/s13059-021-02289-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quantify. Here we review the major sources of uncertainty and survey existing approaches developed for representing and addressing them. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity.
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Affiliation(s)
- David B Bernstein
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Snorre Sulheim
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Daniel Segrè
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA.
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Biology and Department of Physics, Boston University, Boston, MA, USA.
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30
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Smith HB, Drew A, Malloy JF, Walker SI. Seeding Biochemistry on Other Worlds: Enceladus as a Case Study. ASTROBIOLOGY 2021; 21:177-190. [PMID: 33064954 PMCID: PMC7876360 DOI: 10.1089/ast.2019.2197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
The Solar System is becoming increasingly accessible to exploration by robotic missions to search for life. However, astrobiologists currently lack well-defined frameworks to quantitatively assess the chemical space accessible to life in these alien environments. Such frameworks will be critical for developing concrete predictions needed for future mission planning, both to determine the potential viability of life on other worlds and to anticipate the molecular biosignatures that life could produce. Here, we describe how uniting existing methods provides a framework to study the accessibility of biochemical space across diverse planetary environments. Our approach combines observational data from planetary missions with genomic data catalogued from across Earth and analyzed using computational methods from network theory. To demonstrate this, we use 307 biochemical networks generated from genomic data collected across Earth and "seed" these networks with molecules confirmed to be present on Saturn's moon Enceladus. By expanding through known biochemical reaction space starting from these seed compounds, we are able to determine which products of Earth's biochemistry are, in principle, reachable from compounds available in the environment on Enceladus, and how this varies across different examples of life from Earth (organisms, ecosystems, planetary-scale biochemistry). While we find that none of the 307 prokaryotes analyzed meet the threshold for viability, the reaction space covered by this process can provide a map of possible targets for detection of Earth-like life on Enceladus, as well as targets for synthetic biology approaches to seed life on Enceladus. In cases where biochemistry is not viable because key compounds are missing, we identify the environmental precursors required to make it viable, thus providing a set of compounds to prioritize for detection in future planetary exploration missions aimed at assessing the ability of Enceladus to sustain Earth-like life or directed panspermia.
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Affiliation(s)
- Harrison B. Smith
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Alexa Drew
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - John F. Malloy
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Sara Imari Walker
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
- ASU-SFI Center for Biosocial Complex Systems, Arizona State University, Tempe, Arizona, USA
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, Arizona, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
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31
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García-Jiménez B, Torres-Bacete J, Nogales J. Metabolic modelling approaches for describing and engineering microbial communities. Comput Struct Biotechnol J 2020; 19:226-246. [PMID: 33425254 PMCID: PMC7773532 DOI: 10.1016/j.csbj.2020.12.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to growing awareness of their influence on a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications involving microorganisms, both in vivo and in silico, have been developed in the context of isolated microbes. In vivo microbial consortia development is extremely difficult and costly because it implies replicating suitable environments in the wet-lab. Computational approaches are thus a good, cost-effective alternative to study microbial communities, mainly via descriptive modelling, but also via engineering modelling. In this review we provide a detailed compilation of examples of engineered microbial communities and a comprehensive, historical revision of available computational metabolic modelling methods to better understand, and rationally engineer wild and synthetic microbial communities.
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Affiliation(s)
- Beatriz García-Jiménez
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
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32
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Huang C, Liu Q, Chen X, Nan J, Li Z, Wang A. Bioaugmentation with Thiobacillus sp. H1 in an autotrophic denitrification desulfurization microbial reactor: Microbial community changes and relationship. ENVIRONMENTAL RESEARCH 2020; 189:109927. [PMID: 32678744 DOI: 10.1016/j.envres.2020.109927] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Thiobacillus sp. H1 was isolated and made into solid bacterial agent. The Thiobacillus sp. H1 agent was dosed into two reactor (all the agent dosed one-time, and multi-dosing bacteria evenly) and run for 40 days, a start-up with no microbial agent bioreactor as control. We found that the operational performance of multi-dosing inoculum reactor was stable, and the amount of elemental sulfur produced remained stable at 143.2-152.3 mg/L. The amount of elemental sulfur generated in the reactor without the addition of the inoculum was gradually increased, and the amount of elemental sulfur generated in the reactor with the inoculum added at one-time was decreased. Two kinds of Thiobacillus gen. and unclassified betaproteobacteria that coordinated the overall community function in the autotrophic denitrification desulfurization system with high-throughput sequencing. The trend of FccAB gene in each bioreactor was similar with the trend of elemental sulfur in the effluent. On the 5th day, the copy number of FccAB in bioreactor II was the highest among the three bioreactors, reaching 11.8 log copies L/g. This study explores the possibility of artificially synthesized denitrifying desulfurization flora in the future.
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Affiliation(s)
- Cong Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Xueqi Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China.
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33
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Lam TJ, Stamboulian M, Han W, Ye Y. Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PLoS Comput Biol 2020; 16:e1007951. [PMID: 33125363 PMCID: PMC7657538 DOI: 10.1371/journal.pcbi.1007951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/11/2020] [Accepted: 09/10/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of cooperative and competitive metabolic interactions between bacterial species. By nature, phylogenetically similar microbial species are more likely to share common functional profiles or biological pathways due to their genomic similarity. Without properly factoring out the phylogenetic relationship, any estimation of the competition and cooperation between species based on functional/pathway profiles may bias downstream applications. To address these challenges, we developed a novel approach for estimating the competition and complementarity indices for a pair of microbial species, adjusted by their phylogenetic distance. An automated pipeline, PhyloMint, was implemented to construct competition and complementarity indices from genome scale metabolic models derived from microbial genomes. Application of our pipeline to 2,815 human-gut associated bacteria showed high correlation between phylogenetic distance and metabolic competition/cooperation indices among bacteria. Using a discretization approach, we were able to detect pairs of bacterial species with cooperation scores significantly higher than the average pairs of bacterial species with similar phylogenetic distances. A network community analysis of high metabolic cooperation but low competition reveals distinct modules of bacterial interactions. Our results suggest that niche differentiation plays a dominant role in microbial interactions, while habitat filtering also plays a role among certain clades of bacterial species.
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Affiliation(s)
- Tony J. Lam
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Moses Stamboulian
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Wontack Han
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
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34
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Abstract
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population's persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.
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Affiliation(s)
- Ashkaan K Fahimipour
- University of California Davis, Department of Computer Science, 1 Shields Ave, Davis, CA, 95616, USA.
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, 110 McAllister Way, Santa Cruz, CA, 95060, USA.
| | - Thilo Gross
- University of California Davis, Department of Computer Science, 1 Shields Ave, Davis, CA, 95616, USA
- Alfred-Wegener-Institut Helmholtz-Centre for Marine and Polar Research, AM Handelshafen 12, Bremerhaven, 27570, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Ammerländer Heerstrasse 231, 26129, Oldenburg, Germany
- University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky Str. 9 - 11, 26129, Oldenburg, Germany
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35
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Hussan JR, Hunter PJ. Our natural "makeup" reveals more than it hides: Modeling the skin and its microbiome. WIREs Mech Dis 2020; 13:e1497. [PMID: 32539232 DOI: 10.1002/wsbm.1497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 01/23/2023]
Abstract
Skin is our primary interface with the environment. A structurally and functionally complex organ that hosts a dynamic ecosystem of microbes, and synthesizes many compounds that affect our well-being and psychosocial interactions. It is a natural platform of signal exchange between internal organs, skin resident microbes, and the environment. These interactions have gained a great deal of attention due to the increased prevalence of atopic diseases, and the co-occurrence of multiple allergic diseases related to allergic sensitization in early life. Despite significant advances in experimentally characterizing the skin, its microbial ecology, and disease phenotypes, high-levels of variability in these characteristics even for the same clinical phenotype are observed. Addressing this variability and resolving the relevant biological processes requires a systems approach. This review presents some of our current understanding of the skin, skin-immune, skin-neuroendocrine, skin-microbiome interactions, and computer-based modeling approaches to simulate this ecosystem in the context of health and disease. The review highlights the need for a systems-based understanding of this sophisticated ecosystem. This article is categorized under: Infectious Diseases > Computational Models.
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Affiliation(s)
- Jagir R Hussan
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Peter J Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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36
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Gysi DM, Nowick K. Construction, comparison and evolution of networks in life sciences and other disciplines. J R Soc Interface 2020; 17:20190610. [PMID: 32370689 PMCID: PMC7276545 DOI: 10.1098/rsif.2019.0610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Network approaches have become pervasive in many research fields. They allow for a more comprehensive understanding of complex relationships between entities as well as their group-level properties and dynamics. Many networks change over time, be it within seconds or millions of years, depending on the nature of the network. Our focus will be on comparative network analyses in life sciences, where deciphering temporal network changes is a core interest of molecular, ecological, neuropsychological and evolutionary biologists. Further, we will take a journey through different disciplines, such as social sciences, finance and computational gastronomy, to present commonalities and differences in how networks change and can be analysed. Finally, we envision how borrowing ideas from these disciplines could enrich the future of life science research.
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Affiliation(s)
- Deisy Morselli Gysi
- Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, 04109 Leipzig, Germany
- Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, 04109 Leipzig, Germany
- Center for Complex Networks Research, Northeastern University, 177 Huntington Avenue, Boston, MA 02115, USA
| | - Katja Nowick
- Human Biology Group, Institute for Biology, Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Königin-Luise-Straβe 1-3, 14195 Berlin, Germany
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Derakhshani H, Plaizier JC, De Buck J, Barkema HW, Khafipour E. Composition and co-occurrence patterns of the microbiota of different niches of the bovine mammary gland: potential associations with mastitis susceptibility, udder inflammation, and teat-end hyperkeratosis. Anim Microbiome 2020; 2:11. [PMID: 33499931 PMCID: PMC7807822 DOI: 10.1186/s42523-020-00028-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022] Open
Abstract
Background Within complex microbial ecosystems, microbe-microbe interrelationships play crucial roles in determining functional properties such as metabolic potential, stability and colonization resistance. In dairy cows, microbes inhabiting different ecological niches of the udder may have the potential to interact with mastitis pathogens and therefore modulate susceptibility to intramammary infection. In the present study, we investigated the co-occurrence patterns of bacterial communities within and between different niches of the bovine mammary gland (teat canal vs. milk) in order to identify key bacterial taxa and evaluate their associations with udder health parameters and mastitis susceptibility. Results Overall, teat canal microbiota was more diverse, phylogenetically less dispersed, and compositionally distinct from milk microbiota. This, coupled with identification of a large number of bacterial taxa that were exclusive to the teat canal microbiota suggested that the intramammary ecosystem, represented by the milk microbiota, acts as a selective medium that disfavors the growth of certain environmental bacterial lineages. We further observed that the diversity of milk microbiota was negatively correlated with udder inflammation. By performing correlation network analysis, we identified two groups of phylogenetically distinct hub species that were either positively (unclassified Bacteroidaceae and Phascolarctobacterium) or negatively (Sphingobacterium) correlated with biodiversity metrics of the mammary gland (MG). The latter group of bacteria also showed positive associations with the future incidence of clinical mastitis. Conclusions Our results provide novel insights into the composition and structure of bacterial communities inhabiting different niches of the bovine MG. In particular, we identified hub species and candidate foundation taxa that were associated with the inflammatory status of the MG and/or future incidences of clinical mastitis. Further in vitro and in vivo interrogations of MG microbiota can shed light on different mechanisms by which commensal microbiota interact with mastitis pathogens and modulate udder homeostasis.
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Affiliation(s)
- Hooman Derakhshani
- Present Address: McMaster University, Faculty of Medicine, Hamilton, ON, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Jan C Plaizier
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada. .,Present Address: Cargill, Animal Nutrition and Health Division, Cargill Health Technologies, Diamond V brand, Cedar Rapids, IA, USA.
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Lawson CE, Harcombe WR, Hatzenpichler R, Lindemann SR, Löffler FE, O'Malley MA, García Martín H, Pfleger BF, Raskin L, Venturelli OS, Weissbrodt DG, Noguera DR, McMahon KD. Common principles and best practices for engineering microbiomes. Nat Rev Microbiol 2019; 17:725-741. [PMID: 31548653 PMCID: PMC8323346 DOI: 10.1038/s41579-019-0255-9] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 12/16/2022]
Abstract
Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.
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Affiliation(s)
- Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | | | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbra, CA, USA
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
| | - Héctor García Martín
- DOE Joint Bioenergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- DOE Agile BioFoundry, Emeryville, CA, USA
- Basque Center for Applied Mathematics, Bilbao, Spain
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ophelia S Venturelli
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Daniel R Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, Madison, WI, USA
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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Aguirre de Cárcer D. A conceptual framework for the phylogenetically constrained assembly of microbial communities. MICROBIOME 2019; 7:142. [PMID: 31666129 PMCID: PMC6822436 DOI: 10.1186/s40168-019-0754-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/24/2019] [Indexed: 05/17/2023]
Abstract
Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs' identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.
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40
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Robust structure measures of metabolic networks that predict prokaryotic optimal growth temperature. BMC Bioinformatics 2019; 20:499. [PMID: 31615420 PMCID: PMC6794987 DOI: 10.1186/s12859-019-3112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 09/20/2019] [Indexed: 01/24/2023] Open
Abstract
Background Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to study fluxes through the reactions, or to relate the graph structure to environmental characteristics and phenotypes. About ten years ago, Takemoto et al. (2007) stated that the structure of prokaryotic metabolic networks represented as undirected graphs, is correlated to their living environment. Although metabolic networks are naturally directed graphs, they are still usually analysed as undirected graphs. Results We implemented a pipeline to reconstruct metabolic networks from genome data and confirmed some of the results of Takemoto et al. (2007) with today data using up-to-date databases. However, Takemoto et al. (2007) used only a fraction of all available enzymes from the genome and taking into account all the enzymes we fail to reproduce the main results. Therefore, we introduce three robust measures on directed representations of graphs, which lead to similar results regardless of the method of network reconstruction. We show that the size of the largest strongly connected component, the flow hierarchy and the Laplacian spectrum are strongly correlated to the environmental conditions. Conclusions We found a significant negative correlation between the size of the largest strongly connected component (a cycle) and the optimal growth temperature of the considered prokaryotes. This relationship holds true for the spectrum, high temperature being associated with lower eigenvalues. The hierarchy flow shows a negative correlation with optimal growth temperature. This suggests that the dynamical properties of the network are dependant on environmental factors.
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41
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Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ. Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection. Microbiol Mol Biol Rev 2019; 83:e00007-19. [PMID: 31167904 PMCID: PMC6710460 DOI: 10.1128/mmbr.00007-19] [Citation(s) in RCA: 310] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gut microbiome is critical in providing resistance against colonization by exogenous microorganisms. The mechanisms via which the gut microbiota provide colonization resistance (CR) have not been fully elucidated, but they include secretion of antimicrobial products, nutrient competition, support of gut barrier integrity, and bacteriophage deployment. However, bacterial enteric infections are an important cause of disease globally, indicating that microbiota-mediated CR can be disturbed and become ineffective. Changes in microbiota composition, and potential subsequent disruption of CR, can be caused by various drugs, such as antibiotics, proton pump inhibitors, antidiabetics, and antipsychotics, thereby providing opportunities for exogenous pathogens to colonize the gut and ultimately cause infection. In addition, the most prevalent bacterial enteropathogens, including Clostridioides difficile, Salmonella enterica serovar Typhimurium, enterohemorrhagic Escherichia coli, Shigella flexneri, Campylobacter jejuni, Vibrio cholerae, Yersinia enterocolitica, and Listeria monocytogenes, can employ a wide array of mechanisms to overcome colonization resistance. This review aims to summarize current knowledge on how the gut microbiota can mediate colonization resistance against bacterial enteric infection and on how bacterial enteropathogens can overcome this resistance.
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Affiliation(s)
- Q R Ducarmon
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - R D Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - B V H Hornung
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - W van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - V B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine/Infectious Diseases Division, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - E J Kuijper
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- Netherlands Donor Feces Bank, Leiden, Netherlands
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42
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Bernstein DB, Dewhirst FE, Segrè D. Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. eLife 2019; 8:39733. [PMID: 31194675 PMCID: PMC6609349 DOI: 10.7554/elife.39733] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.
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Affiliation(s)
- David B Bernstein
- Department of Biomedical Engineering, Boston University, Boston, United States.,Biological Design Center, Boston University, Boston, United States
| | - Floyd E Dewhirst
- The Forsyth Institute, Cambridge, United States.,Harvard School of Dental Medicine, Boston, United States
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, United States.,Biological Design Center, Boston University, Boston, United States.,Bioinformatics Program, Boston University, Boston, United States.,Department of Biology, Boston University, Boston, United States.,Department of Physics, Boston University, Boston, United States
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43
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Wang Z, Qi Q. Gut microbial metabolites associated with HIV infection. Future Virol 2019; 14:335-347. [PMID: 31263508 PMCID: PMC6595475 DOI: 10.2217/fvl-2019-0002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023]
Abstract
HIV infection has been associated with alterations in gut microbiota and related microbial metabolite production. However, the mechanisms of how these functional microbial metabolites may affect HIV immunopathogenesis and comorbidities, such as cardiovascular disease and other metabolic diseases, remain largely unknown. Here we review the current understanding of gut microbiota and related metabolites in the context of HIV infection. We focus on several bacteria-produced metabolites, including tryptophan catabolites, short-chain fatty acids and trimethylamine-N-oxide (TMAO), and discuss their implications in HIV infection and comorbidities. We also prospect future studies using integrative multiomics approaches to better understand host-microbiota-metabolites interactions in HIV infection, and facilitate integrative medicine utilizing the microbiota in HIV infection.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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44
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Badyaev AV, Posner AB, Morrison ES, Higginson DM. Cycles of external dependency drive evolution of avian carotenoid networks. Nat Commun 2019; 10:1596. [PMID: 30962432 PMCID: PMC6453931 DOI: 10.1038/s41467-019-09579-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/19/2019] [Indexed: 01/01/2023] Open
Abstract
All organisms depend on input of exogenous compounds that cannot be internally produced. Gain and loss of such dependencies structure ecological communities and drive species' evolution, yet the evolution of mechanisms that accommodate these variable dependencies remain elusive. Here, we show that historical cycles of gains and losses of external dependencies in avian carotenoid-producing networks are linked to their evolutionary diversification. This occurs because internalization of metabolic controls-produced when gains in redundancy of dietary inputs coincide with increased branching of their derived products-enables rapid and sustainable exploration of an existing network by shielding it from environmental fluctuations in inputs. Correspondingly, loss of internal controls constrains evolution to the rate of the gains and losses of dietary precursors. Because internalization of a network's controls necessarily bridges diet-specific enzymatic modules within a network, it structurally links local adaptation and continuous evolution even for traits fully dependent on contingent external inputs.
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Affiliation(s)
- Alexander V Badyaev
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
| | - Alexander B Posner
- Department of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Erin S Morrison
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Dawn M Higginson
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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45
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Evolutionary transitions in controls reconcile adaptation with continuity of evolution. Semin Cell Dev Biol 2019; 88:36-45. [DOI: 10.1016/j.semcdb.2018.05.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/19/2018] [Accepted: 05/15/2018] [Indexed: 12/14/2022]
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46
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Goodman AJ, Feldman MW. Evolution of hierarchy in bacterial metabolic networks. Biosystems 2019; 180:71-78. [PMID: 30878498 DOI: 10.1016/j.biosystems.2019.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/08/2019] [Accepted: 02/26/2019] [Indexed: 11/26/2022]
Abstract
Flow hierarchy is a useful way to characterize the movement of information and matter throughout a network. Hierarchical network organizations are shown to arise when there is a cost of maintaining links in the network. A similar constraint exists in metabolic networks, where costs come from reduced efficiency of nonspecific enzymes or from producing unnecessary enzymes. Previous analyses of bacterial metabolic networks have been used to predict the minimal nutrients that a bacterium needs to grow, its mutualistic relationships with other bacteria, and its major ecological niche. We use metabolic network inference to obtain metabolite flow graphs of 2935 bacterial metabolic networks and find that flow hierarchy evolves independently of modularity and other network properties. By inferring the ancestral metabolic networks and estimating the hierarchical character of the inferred network, we show that hierarchical structure first increased and later decreased over evolutionary history. Furthermore, hierarchical structure in the network is associated with slower growth rates; bacteria with hierarchy scores above the median grow on average 2.25 times faster than those with hierarchy scores below the median.
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Affiliation(s)
- Aaron J Goodman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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47
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Eveillard D, Bouskill NJ, Vintache D, Gras J, Ward BB, Bourdon J. Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle. Front Microbiol 2019; 9:3298. [PMID: 30745899 PMCID: PMC6360161 DOI: 10.3389/fmicb.2018.03298] [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: 06/11/2018] [Accepted: 12/18/2018] [Indexed: 11/15/2022] Open
Abstract
Understanding the interactions between microbial communities and their environment sufficiently to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is problematic, because (i) communities are complex, (ii) most descriptions are qualitative, and (iii) quantitative understanding of the way communities interact with their surroundings remains incomplete. One approach to overcoming such complications is the integration of partial qualitative and quantitative descriptions into more complex networks. Here we outline the development of a probabilistic framework, based on Event Transition Graph (ETG) theory, to predict microbial community structure across observed chemical data. Using reverse engineering, we derive probabilities from the ETG that accurately represent observations from experiments and predict putative constraints on communities within dynamic environments. These predictions can feedback into the future development of field experiments by emphasizing the most important functional reactions, and associated microbial strains, required to characterize microbial ecosystems.
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Affiliation(s)
- Damien Eveillard
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France.,Research Federation (FR2022) Tara Oceans GO-SEE, Paris, France
| | - Nicholas J Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Damien Vintache
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France.,Research Federation (FR2022) Tara Oceans GO-SEE, Paris, France
| | - Julien Gras
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France
| | - Bess B Ward
- Geoscience Department, Princeton University, Princeton, NJ, United States
| | - Jérémie Bourdon
- LS2N, UMR6004 CNRS, Université de Nantes, Centrale Nantes, IMTA, Nantes, France
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48
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Modelling the complexity of plankton communities exploiting omics potential: From present challenges to an integrative pipeline. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2018.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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49
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Sloan TJ, Turton JC, Tyson J, Musgrove A, Fleming VM, Lister MM, Loose MW, Sockett RE, Diggle M, Game FL, Jeffcoate W. Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection. J Med Microbiol 2019; 68:230-240. [DOI: 10.1099/jmm.0.000907] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Tim J. Sloan
- 2Department of Clinical Microbiology, Queen’s Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- 1School of Life Sciences, University of Nottingham, Nottingham, UK
- 3Path Links Pathology, Northern Lincolnshire and Goole NHS Foundation Trust, Lincolnshire, UK
| | - James C. Turton
- 1School of Life Sciences, University of Nottingham, Nottingham, UK
- 2Department of Clinical Microbiology, Queen’s Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jess Tyson
- 1School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Alison Musgrove
- 4Foot Ulcer Trials Unit, Department of Diabetes and Endocrinology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Vicki M. Fleming
- 2Department of Clinical Microbiology, Queen’s Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Michelle M. Lister
- 2Department of Clinical Microbiology, Queen’s Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Matthew W. Loose
- 1School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Mathew Diggle
- 2Department of Clinical Microbiology, Queen’s Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Frances L. Game
- 4Foot Ulcer Trials Unit, Department of Diabetes and Endocrinology, Nottingham University Hospitals NHS Trust, Nottingham, UK
- 5Department of Diabetes and Endocrinology, Derby Teaching Hospitals NHS Foundation Trust, Derby, UK
| | - William Jeffcoate
- 4Foot Ulcer Trials Unit, Department of Diabetes and Endocrinology, Nottingham University Hospitals NHS Trust, Nottingham, UK
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50
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Topological assessment of metabolic networks reveals evolutionary information. Sci Rep 2018; 8:15918. [PMID: 30374088 PMCID: PMC6206017 DOI: 10.1038/s41598-018-34163-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 10/07/2018] [Indexed: 12/03/2022] Open
Abstract
Evolutionary information was inferred from the topology of metabolic networks corresponding to 17 plant species belonging to major plant lineages Chlorophytes, Bryophytes, Lycophytes and Angiosperms. The plant metabolic networks were built using the substrate-product network modeling based on the metabolic reactions available on the PlantCyc database (version 9.5), from which their local topological properties such as degree, in-degree, out-degree, clustering coefficient, hub-score, authority-score, local efficiency, betweenness and eigencentrality were measured. The topological measurements corresponding to each metabolite within the networks were considered as a set of metabolic characters to compound a feature vector representing each plant. Our results revealed that some local topological characters are able to discern among plant kinships, since similar phylogenies were found when comparing dendrograms obtained by topological metrics to the one obtained by DNA sequences of chloroplast genes. Furthermore, we also found that even a smaller number of metabolic characters is able to separate among major clades with high bootstrap support (BS > 95), while for some suborders a bigger content has been required.
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