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Tang J, Jiang Y, Hu Z, Zhou H, You D, Daroch M. Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov. Mol Phylogenet Evol 2024; 197:108094. [PMID: 38723792 DOI: 10.1016/j.ympev.2024.108094] [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: 11/02/2023] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Thermophilic unicellular cyanobacteria of the family Thermosynechococcaceae are essential primary producers and integral components of many microbial mats found in hot springs of Asia and North America. Historically, based on their simple morphology, these organisms, along with members of taxonomically unrelated thermophilic Thermostichaceae have been described with a generic term, "Synechococcus", used for elongated unicellular cyanobacteria. This has created significant misperception in the scientific literature regarding the taxonomic status of these essential thermophilic primary producers and their relationship with Synechococcus sensu stricto. In this manuscript, we attempted a genome-driven taxonomic reevaluation of the family Thermosynechococcaceae. Application of genomic analyses such as GTDB classification, ANI/AAI and phylogenomics support the delineation of eight species within genus Thermosynechococcus. Two subspecies were further identified within T. taiwanensis by dDDH and phylogenomics. Moreover, the results also suggest the presence of two putative new genera phylogenetically alongside genus Thermosynechococcus, a thermophilic genus Parathermosynechococcus represented by PCC 6715 and a non-thermophilic genus represented by PCC 6312. The proposed genospecies and new genera were further integrated with morphological and/or ecological information. Interestingly, the phylogeny of 16S-23S ITS achieved a better taxonomic relationship than that of 16S rRNA and supported the genome-based classification of Thermosynechococcus spp. Finally, the pan-genome analysis indicated a conserved pattern of genomic core among known members of Thermosynechococcus.
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Affiliation(s)
- Jie Tang
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Ying Jiang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Zhe Hu
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Huizhen Zhou
- School of Food and Bioengineering, Chengdu University, Chengdu 610052, Sichuan, China
| | - Dawei You
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China.
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2
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Halary S, Duval C, Marie B, Bernard C, Piquet B, Gros O, Bourguet-Kondracki ML, Duperron S. Genomes of nine biofilm-forming filamentous strains of Cyanobacteria (genera Jaaginema, Scytonema, and Karukerafilum gen. nov.) isolated from mangrove habitats of Guadeloupe (Lesser Antilles). FEMS MICROBES 2023; 5:xtad024. [PMID: 38213393 PMCID: PMC10781437 DOI: 10.1093/femsmc/xtad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024] Open
Abstract
Biofilm-forming cyanobacteria are abundant in mangrove ecosystems, colonizing various niches including sediment surface and periphyton where they can cover large areas, yet have received limited attention. Several filamentous isolates were recently isolated from Guadeloupe, illustrating the diversity and novelty present in these biofilms. In this study, nine strains belonging to three novel lineages found abundantly in Guadeloupe biofilms are characterized by genome sequencing, morphological and ultrastructural examination, metabolome fingerprinting and searched for secondary metabolites biosynthesis pathways. Assignation of two lineages to known genera is confirmed, namely Scytonema and Jaaginema. The third lineage corresponds to a new Coleofasciculales genus herein described as Karukerafilum gen. nov. The four strains belonging to this genus group into two subclades, one of which displays genes necessary for nitrogen fixation as well as the complete pathway for geosmin production. This study gives new insights into the diversity of mangrove biofilm-forming cyanobacteria, including genome-based description of a new genus and the first genome sequence available for the genus Jaaginema.
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Affiliation(s)
- Sébastien Halary
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Charlotte Duval
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Benjamin Marie
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Cécile Bernard
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Bérénice Piquet
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 97110 Pointe-à-Pitre, France
| | - Marie-Lise Bourguet-Kondracki
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Sébastien Duperron
- Molécules de Communication et Adaptation des Microorganismes, UMR 7245 CNRS, Muséum National d'Histoire Naturelle, 75005 Paris, France
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3
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Teikari J, Baunach M, Dittmann E. Cyanobacterial Genome Sequencing, Annotation, and Bioinformatics. Methods Mol Biol 2022; 2489:269-287. [PMID: 35524055 DOI: 10.1007/978-1-0716-2273-5_14] [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] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are collectively a globally important monophyletic phylum of bacteria. They have attracted a lot of attention, not only because they are rich sources of natural bioactive products, including toxic substances, but also because they play an important role in global nitrogen and carbon cycles, and are capable of maintaining versatile environmental niche adaptations. A vast number of cyanobacterial genomes have become available due to fast development of sequencing technologies, but effort is still needed to comprehensively understand the molecular basis of their diversity. Here, we introduce a basic pipeline for the cyanobacterial genome sequencing project that can be employed to complete the whole cyanobacterial genome. The pipeline includes DNA extraction from the cyanobacterial culture of interest, hybrid genome sequencing, and genome assembly and annotation. At the end of the chapter, we briefly introduce genome mining tools and one successful genome mining example from our laboratory. This chapter provides general guidance regarding the sequencing project and thus includes several references for alternative methods and tools so that the reader can easily modify the pipeline according to the needs of the laboratory.
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Affiliation(s)
- Jonna Teikari
- Environmental Soil Science, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki, Finland.
- University of Potsdam, Potsdam, Germany.
| | - Martin Baunach
- University of Potsdam, Karl-Liebknecht-Straße 24-25, Potsdam, Germany
| | - Elke Dittmann
- University of Potsdam, Karl-Liebknecht-Straße 24-25, Potsdam, Germany
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4
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Prondzinsky P, Berkemer SJ, Ward LM, McGlynn SE. The Thermosynechococcus Genus: Wide Environmental Distribution, but a Highly Conserved Genomic Core. Microbes Environ 2021; 36. [PMID: 33952861 PMCID: PMC8209445 DOI: 10.1264/jsme2.me20138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyanobacteria thrive in diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain as well as few genes that are unique to the genus. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle-or reduced genetic complexity of hot spring habitats relative to other environments.
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Affiliation(s)
- Paula Prondzinsky
- Department of Chemical Science and Engineering, Tokyo Institute of Technology.,Earth-Life Science Institute, Tokyo Institute of Technology
| | - Sarah J Berkemer
- Bioinformatics Group, Department of Computer Science, University Leipzig.,Competence Center for Scalable Data Services and Solutions
| | - Lewis M Ward
- Earth-Life Science Institute, Tokyo Institute of Technology.,Department of Earth and Planetary Sciences, Harvard University
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5
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MacCready JS, Basalla JL, Vecchiarelli AG. Origin and Evolution of Carboxysome Positioning Systems in Cyanobacteria. Mol Biol Evol 2021; 37:1434-1451. [PMID: 31899489 PMCID: PMC7182216 DOI: 10.1093/molbev/msz308] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Carboxysomes are protein-based organelles that are essential for allowing cyanobacteria to fix CO2. Previously, we identified a two-component system, McdAB, responsible for equidistantly positioning carboxysomes in the model cyanobacterium Synechococcus elongatus PCC 7942 (MacCready JS, Hakim P, Young EJ, Hu L, Liu J, Osteryoung KW, Vecchiarelli AG, Ducat DC. 2018. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. eLife 7:pii:e39723). McdA, a ParA-type ATPase, nonspecifically binds the nucleoid in the presence of ATP. McdB, a novel factor that directly binds carboxysomes, displaces McdA from the nucleoid. Removal of McdA from the nucleoid in the vicinity of carboxysomes by McdB causes a global break in McdA symmetry, and carboxysome motion occurs via a Brownian-ratchet-based mechanism toward the highest concentration of McdA. Despite the importance for cyanobacteria to properly position their carboxysomes, whether the McdAB system is widespread among cyanobacteria remains an open question. Here, we show that the McdAB system is widespread among β-cyanobacteria, often clustering with carboxysome-related components, and is absent in α-cyanobacteria. Moreover, we show that two distinct McdAB systems exist in β-cyanobacteria, with Type 2 systems being the most ancestral and abundant, and Type 1 systems, like that of S. elongatus, possibly being acquired more recently. Lastly, all McdB proteins share the sequence signatures of a protein capable of undergoing liquid–liquid phase separation. Indeed, we find that representatives of both McdB types undergo liquid–liquid phase separation in vitro, the first example of a ParA-type ATPase partner protein to exhibit this behavior. Our results have broader implications for understanding carboxysome evolution, biogenesis, homeostasis, and positioning in cyanobacteria.
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Affiliation(s)
- Joshua S MacCready
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Joseph L Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI
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6
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A network approach to elucidate and prioritize microbial dark matter in microbial communities. ISME JOURNAL 2020; 15:228-244. [PMID: 32963345 PMCID: PMC7852563 DOI: 10.1038/s41396-020-00777-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/18/2020] [Accepted: 09/10/2020] [Indexed: 01/13/2023]
Abstract
Microbes compose most of the biomass on the planet, yet the majority of taxa remain uncharacterized. These unknown microbes, often referred to as “microbial dark matter,” represent a major challenge for biology. To understand the ecological contributions of these Unknown taxa, it is essential to first understand the relationship between unknown species, neighboring microbes, and their respective environment. Here, we establish a method to study the ecological significance of “microbial dark matter” by building microbial co-occurrence networks from publicly available 16S rRNA gene sequencing data of four extreme aquatic habitats. For each environment, we constructed networks including and excluding unknown organisms at multiple taxonomic levels and used network centrality measures to quantitatively compare networks. When the Unknown taxa were excluded from the networks, a significant reduction in degree and betweenness was observed for all environments. Strikingly, Unknown taxa occurred as top hubs in all environments, suggesting that “microbial dark matter” play necessary ecological roles within their respective communities. In addition, novel adaptation-related genes were detected after using 16S rRNA gene sequences from top-scoring hub taxa as probes to blast metagenome databases. This work demonstrates the broad applicability of network metrics to identify and prioritize key Unknown taxa and improve understanding of ecosystem structure across diverse habitats.
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7
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Schober AF, Mathis AD, Ingle C, Park JO, Chen L, Rabinowitz JD, Junier I, Rivoire O, Reynolds KA. A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism. Cell Rep 2020; 27:3359-3370.e7. [PMID: 31189117 DOI: 10.1016/j.celrep.2019.05.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 04/05/2019] [Accepted: 05/09/2019] [Indexed: 11/29/2022] Open
Abstract
Enzyme function and evolution are influenced by the larger context of a metabolic pathway. Deleterious mutations or perturbations in one enzyme can often be compensated by mutations to others. We used comparative genomics and experiments to examine evolutionary interactions with the essential metabolic enzyme dihydrofolate reductase (DHFR). Analyses of synteny and co-occurrence across bacterial species indicate that DHFR is coupled to thymidylate synthase (TYMS) but relatively independent from the rest of folate metabolism. Using quantitative growth rate measurements and forward evolution in Escherichia coli, we demonstrate that the two enzymes adapt as a relatively independent unit in response to antibiotic stress. Metabolomic profiling revealed that TYMS activity must not exceed DHFR activity to prevent the depletion of reduced folates and the accumulation of the intermediate dihydrofolate. Comparative genomics analyses identified >200 gene pairs with similar statistical signatures of modular co-evolution, suggesting that cellular pathways may be decomposable into small adaptive units.
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Affiliation(s)
- Andrew F Schober
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andrew D Mathis
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christine Ingle
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Junyoung O Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Li Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ivan Junier
- Centre National de la Recherche Scientifique, Université Grenoble Alpes, TIMC-IMAG, F-38000 Grenoble, France
| | - Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, F-75005 Paris, France
| | - Kimberly A Reynolds
- The Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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8
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Labella JI, Llop A, Contreras A. The default cyanobacterial linked genome: an interactive platform based on cyanobacterial linkage networks to assist functional genomics. FEBS Lett 2020; 594:1661-1674. [PMID: 32233038 DOI: 10.1002/1873-3468.13775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/14/2020] [Accepted: 03/12/2020] [Indexed: 01/01/2023]
Abstract
A database of cyanobacterial linked genomes that can be accessed through an interactive platform (https://dfgm.ua.es/genetica/investigacion/cyanobacterial_genetics/Resources.html) was generated on the bases of conservation of gene neighborhood across 124 cyanobacterial species. It allows flexible generation of gene networks at different threshold values. The default cyanobacterial linked genome, whose global properties are analyzed here, connects most of the cyanobacterial core genes. The potential of the web tool is discussed in relation to other bioinformatics approaches based on guilty-by-association principles, with selected examples of networks illustrating its usefulness for genes found exclusively in cyanobacteria or in cyanobacteria and chloroplasts. We believe that this tool will provide useful predictions that are readily testable in Synechococcus elongatus PCC7942 and other model organisms performing oxygenic photosynthesis.
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Affiliation(s)
- Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Antonio Llop
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Asuncion Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
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9
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New Benthic Cyanobacteria from Guadeloupe Mangroves as Producers of Antimicrobials. Mar Drugs 2019; 18:md18010016. [PMID: 31878034 PMCID: PMC7024286 DOI: 10.3390/md18010016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 02/03/2023] Open
Abstract
Benthic cyanobacteria strains from Guadeloupe have been investigated for the first time by combining phylogenetic, chemical and biological studies in order to better understand the taxonomic and chemical diversity as well as the biological activities of these cyanobacteria through the effect of their specialized metabolites. Therefore, in addition to the construction of the phylogenetic tree, indicating the presence of 12 potentially new species, an LC-MS/MS data analysis workflow was applied to provide an overview on chemical diversity of 20 cyanobacterial extracts, which was linked to antimicrobial activities evaluation against human pathogenic and ichtyopathogenic environmental strains.
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10
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Sharma S, Steuer R. Modelling microbial communities using biochemical resource allocation analysis. J R Soc Interface 2019; 16:20190474. [PMID: 31690234 PMCID: PMC6893496 DOI: 10.1098/rsif.2019.0474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 10/15/2019] [Indexed: 01/08/2023] Open
Abstract
To understand the functioning and dynamics of microbial communities is a fundamental challenge in current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. There is, however, a large chasm between ecologically motivated descriptions of microbial growth used in many current ecosystems simulations, and detailed metabolic pathway and genome-based descriptions developed in the context of systems and synthetic biology. Here, we seek to demonstrate how resource allocation models of microbial growth offer the potential to advance ecosystem simulations and their parametrization. In particular, recent work on quantitative resource allocation allow us to formulate mechanistic models of microbial growth that are physiologically meaningful while remaining computationally tractable. These models go beyond Michaelis-Menten and Monod-type growth models, and are capable of accounting for emergent properties that underlie the remarkable plasticity of microbial growth. We outline the utility and advantages of using biochemical resource allocation models by considering a coarse-grained model of cyanobacterial growth and demonstrate how the model allows us to address specific questions of relevance for the simulation of marine microbial ecosystems, including the physiological acclimation of protein expression to different environments, the description of co-limitation by several nutrients and the differential use of alternative nutrient sources, as well as the description of metabolic diversity based on our increasing knowledge about quantitative cell physiology.
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Affiliation(s)
| | - Ralf Steuer
- Humboldt-Universität zu Berlin, Institut für Biologie, FachInstitut für Theoretische Biologie (ITB), Invalidenstr. 110, 10115 Berlin, Germany
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11
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Han W, Ye Y. A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2019; 24:236-247. [PMID: 30864326 PMCID: PMC6417824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The microbiome research is going through an evolutionary transition from focusing on the characterization of reference microbiomes associated with different environments/hosts to the translational applications, including using microbiome for disease diagnosis, improving the effcacy of cancer treatments, and prevention of diseases (e.g., using probiotics). Microbial markers have been identified from microbiome data derived from cohorts of patients with different diseases, treatment responsiveness, etc, and often predictors based on these markers were built for predicting host phenotype given a microbiome dataset (e.g., to predict if a person has type 2 diabetes given his or her microbiome data). Unfortunately, these microbial markers and predictors are often not published so are not reusable by others. In this paper, we report the curation of a repository of microbial marker genes and predictors built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline called Mi2P (from Microbiome to Phenotype) for using the repository. As an initial effort, we focus on microbial marker genes related to two diseases, type 2 diabetes and liver cirrhosis, and immunotherapy efficacy for two types of cancer, non-small-cell lung cancer (NSCLC) and renal cell carcinoma (RCC). We characterized the marker genes from metagenomic data using our recently developed subtractive assembly approach. We showed that predictors built from these microbial marker genes can provide fast and reasonably accurate prediction of host phenotype given microbiome data. As understanding and making use of microbiome data (our second genome) is becoming vital as we move forward in this age of precision health and precision medicine, we believe that such a repository will be useful for enabling translational applications of microbiome data.
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MESH Headings
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/microbiology
- Carcinoma, Non-Small-Cell Lung/therapy
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/microbiology
- Carcinoma, Renal Cell/therapy
- Computational Biology/methods
- Databases, Genetic
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/microbiology
- Genes, Microbial
- Genetic Markers
- Host Microbial Interactions/genetics
- Humans
- Immunotherapy
- Kidney Neoplasms/genetics
- Kidney Neoplasms/microbiology
- Kidney Neoplasms/therapy
- Liver Cirrhosis/genetics
- Liver Cirrhosis/microbiology
- Lung Neoplasms/genetics
- Lung Neoplasms/microbiology
- Lung Neoplasms/therapy
- Machine Learning
- Metagenomics/methods
- Metagenomics/statistics & numerical data
- Microbiota/genetics
- Phenotype
- Translational Research, Biomedical
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Affiliation(s)
- Wontack Han
- Computer Science Department, Indiana University, Bloomington, IN 47408, USA
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12
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Zavřel T, Faizi M, Loureiro C, Poschmann G, Stühler K, Sinetova M, Zorina A, Steuer R, Červený J. Quantitative insights into the cyanobacterial cell economy. eLife 2019; 8:42508. [PMID: 30714903 PMCID: PMC6391073 DOI: 10.7554/elife.42508] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/01/2019] [Indexed: 01/27/2023] Open
Abstract
Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.
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Affiliation(s)
- Tomáš Zavřel
- Laboratory of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
| | - Marjan Faizi
- Institut für Biologie, Fachinstitut für Theoretische BiologieHumboldt-Universität zu BerlinBerlinGermany
| | - Cristina Loureiro
- Department of Applied PhysicsPolytechnic University of ValenciaValenciaSpain
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZHeinrich-Heine-Universität DüsseldorfDüsseldorfGermany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZHeinrich-Heine-Universität DüsseldorfDüsseldorfGermany
| | - Maria Sinetova
- Timiryazev Institute of Plant PhysiologyRussian Academy of SciencesMoscowRussian Federation
| | - Anna Zorina
- Timiryazev Institute of Plant PhysiologyRussian Academy of SciencesMoscowRussian Federation
| | - Ralf Steuer
- Institut für Biologie, Fachinstitut für Theoretische BiologieHumboldt-Universität zu BerlinBerlinGermany
| | - Jan Červený
- Laboratory of Adaptive BiotechnologiesGlobal Change Research Institute CASBrnoCzech Republic
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