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Ermann Lundberg L, Pallabi Mishra P, Liu P, Forsberg MM, Sverremark-Ekström E, Grompone G, Håkansson S, Linninge C, Roos S. Bifidobacterium longum subsp. longum BG-L47 boosts growth and activity of Limosilactobacillus reuteri DSM 17938 and its extracellular membrane vesicles. Appl Environ Microbiol 2024; 90:e0024724. [PMID: 38888338 PMCID: PMC11267924 DOI: 10.1128/aem.00247-24] [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: 02/12/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
The aim of this study was to identify a Bifidobacterium strain that improves the performance of Limosilactobacillus reuteri DSM 17938. Initial tests showed that Bifidobacterium longum subsp. longum strains boosted the growth of DSM 17938 during in vivo-like conditions. Further characterization revealed that one of the strains, BG-L47, had better bile and acid tolerance compared to BG-L48, as well as mucus adhesion compared to both BG-L48 and the control strain BB536. BG-L47 also had the capacity to metabolize a broad range of carbohydrates and sugar alcohols. Mapping of glycoside hydrolase (GH) genes of BG-L47 and BB536 revealed many GHs associated with plant-fiber utilization. However, BG-L47 had a broader phenotypic fiber utilization capacity. In addition, B. longum subsp. longum cells boosted the bioactivity of extracellular membrane vesicles (MV) produced by L. reuteri DSM 17938 during co-cultivation. Secreted 5'-nucleotidase (5'NT), an enzyme that converts AMP into the signal molecule adenosine, was increased in MV boosted by BG-L47. The MV exerted an improved antagonistic effect on the pain receptor transient receptor potential vanilloid 1 (TRPV1) and increased the expression of the immune development markers IL-6 and IL-1ß in a peripheral blood mononuclear cell (PBMC) model. Finally, the safety of BG-L47 was evaluated both by genome safety assessment and in a human safety study. Microbiota analysis showed that the treatment did not induce significant changes in the composition. In conclusion, B. longum subsp. longum BG-L47 has favorable physiological properties, can boost the in vitro activity of L. reuteri DSM 17938, and is safe for consumption, making it a candidate for further evaluation in probiotic studies. IMPORTANCE By using probiotics that contain a combination of strains with synergistic properties, the likelihood of achieving beneficial interactions with the host can increase. In this study, we first performed a broad screening of Bifidobacterium longum subsp. longum strains in terms of synergistic potential and physiological properties. We identified a superior strain, BG-L47, with favorable characteristics and potential to boost the activity of the known probiotic strain Limosilactobacillus reuteri DSM 17938. Furthermore, we demonstrated that BG-L47 is safe for consumption in a human randomized clinical study and by performing a genome safety assessment. This work illustrates that bacteria-bacteria interactions differ at the strain level and further provides a strategy for finding and selecting companion strains of probiotics.
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Affiliation(s)
- Ludwig Ermann Lundberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- BioGaia, Stockholm, Sweden
| | - Punya Pallabi Mishra
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Manuel Mata Forsberg
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eva Sverremark-Ekström
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Sebastian Håkansson
- BioGaia, Stockholm, Sweden
- Division of Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Caroline Linninge
- BioGaia, Stockholm, Sweden
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Stefan Roos
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- BioGaia, Stockholm, Sweden
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Predl M, Gandolf K, Hofer M, Rattei T. ScyNet: Visualizing interactions in community metabolic models. BIOINFORMATICS ADVANCES 2024; 4:vbae104. [PMID: 39132287 PMCID: PMC11315608 DOI: 10.1093/bioadv/vbae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024]
Abstract
Motivation Genome-scale community metabolic models are used to gain mechanistic insights into interactions between community members. However, existing tools for visualizing metabolic models only cater to the needs of single organism models. Results ScyNet is a Cytoscape app for visualizing community metabolic models, generating networks with reduced complexity by focusing on interactions between community members. ScyNet can incorporate the state of a metabolic model via fluxes or flux ranges, which is shown in a previously published simplified cystic fibrosis airway community model. Availability and implementation ScyNet is freely available under an MIT licence and can be retrieved via the Cytoscape App Store (apps.cytoscape.org/apps/scynet). The source code is available at Github (github.com/univieCUBE/ScyNet).
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Affiliation(s)
- Michael Predl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna 1030, Austria
| | - Kilian Gandolf
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Michael Hofer
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna 1030, Austria
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3
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Lambert A, Budinich M, Mahé M, Chaffron S, Eveillard D. Community metabolic modeling of host-microbiota interactions through multi-objective optimization. iScience 2024; 27:110092. [PMID: 38952683 PMCID: PMC11215293 DOI: 10.1016/j.isci.2024.110092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/12/2024] [Accepted: 05/21/2024] [Indexed: 07/03/2024] Open
Abstract
The human gut microbiota comprises various microorganisms engaged in intricate interactions among themselves and with the host, affecting its health. While advancements in omics technologies have led to the inference of clear associations between microbiome composition and health conditions, we usually lack a causal and mechanistic understanding of these associations. For modeling mechanisms driving the interactions, we simulated the organism's metabolism using in silico genome-scale metabolic models (GEMs). We used multi-objective optimization to predict and explain metabolic interactions among gut microbes and an intestinal epithelial cell. We developed a score integrating model simulation results to predict the type (competition, neutralism, mutualism) and quantify the interaction between several organisms. This framework uncovered a potential cross-feeding for choline, explaining the predicted mutualism between Lactobacillus rhamnosus GG and the epithelial cell. Finally, we analyzed a five-organism ecosystem, revealing that a minimal microbiota can favor the epithelial cell's maintenance.
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Affiliation(s)
- Anna Lambert
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
| | - Marko Budinich
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
| | - Maxime Mahé
- Nantes Université, Inserm, TENS UMR1235, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes, France
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Samuel Chaffron
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
| | - Damien Eveillard
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, 44000 Nantes, France
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4
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Garmendia J, Cebollero‐Rivas P. Environmental exposures, the oral-lung axis and respiratory health: The airway microbiome goes on stage for the personalized management of human lung function. Microb Biotechnol 2024; 17:e14506. [PMID: 38881505 PMCID: PMC11180993 DOI: 10.1111/1751-7915.14506] [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: 04/02/2024] [Revised: 05/19/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
The human respiratory system is constantly exposed to environmental stimuli, sometimes including toxicants, which can trigger dysregulated lung immune responses that lead to respiratory symptoms, impaired lung function and airway diseases. Evidence supports that the microbiome in the lungs has an indispensable role in respiratory health and disease, acting as a local gatekeeper that mediates the interaction between the environmental cues and respiratory health. Moreover, the microbiome in the lungs is intimately intertwined with the oral microbiome through the oral-lung axis. Here, we discuss the intricate three-way relationship between (i) cigarette smoking, which has strong effects on the microbial community structure of the lung; (ii) microbiome dysbiosis and disease in the oral cavity; and (iii) microbiome dysbiosis in the lung and its causal role in patients suffering chronic obstructive pulmonary disease (COPD), a leading cause of morbidity and mortality worldwide. We highlight exciting outcomes arising from recently established interactions in the airway between environmental exposures, microbiome, metabolites-functional attributes and the host, as well as how these associations have the potential to predict the respiratory health status of the host through an airway microbiome health index. For completion, we argue that incorporating (synthetic) microbial community ecology in our contemporary understanding of lung disease presents challenges and also rises novel opportunities to exploit the oral-lung axis and its microbiome towards innovative airway disease diagnostics, prognostics, patient stratification and microbiota-targeted clinical interventions in the context of current therapies.
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Affiliation(s)
- Junkal Garmendia
- Instituto de AgrobiotecnologíaConsejo Superior de Investigaciones Científicas (IdAB‐CSIC)‐Gobierno de NavarraMutilvaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES)MadridSpain
| | - Pilar Cebollero‐Rivas
- Servicio de NeumologíaHospital Universitario de NavarraNavarraSpain
- Universidad Pública de Navarra (UPNa)NavarraSpain
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Zhang J, Liang Q, Mu D, Lian F, Gong Y, Ye M, Chen G, Ye Y, Du Z. Cultivating the uncultured: Harnessing the "sandwich agar plate" approach to isolate heme-dependent bacteria from marine sediment. MLIFE 2024; 3:143-155. [PMID: 38827516 PMCID: PMC11139205 DOI: 10.1002/mlf2.12093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/18/2023] [Accepted: 10/10/2023] [Indexed: 06/04/2024]
Abstract
In the classical microbial isolation technique, the isolation process inevitably destroys all microbial interactions and thus makes it difficult to culture the many microorganisms that rely on these interactions for survival. In this study, we designed a simple coculture technique named the "sandwich agar plate method," which maintains microbial interactions throughout the isolation and pure culture processes. The total yield of uncultured species in sandwich agar plates based on eight helper strains was almost 10-fold that of the control group. Many uncultured species displayed commensal lifestyles. Further study found that heme was the growth-promoting factor of some marine commensal bacteria. Subsequent genomic analysis revealed that heme auxotrophies were common in various biotopes and prevalent in many uncultured microbial taxa. Moreover, our study supported that the survival strategies of heme auxotrophy in different habitats varied considerably. These findings highlight that cocultivation based on the "sandwich agar plate method" could be developed and used to isolate more uncultured bacteria.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | | | - Da‐Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
| | | | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Mengqi Ye
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Guan‐Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
| | - Yuqi Ye
- Marine CollegeShandong UniversityWeihaiChina
| | - Zong‐Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial TechnologyShandong UniversityQingdaoChina
- Marine CollegeShandong UniversityWeihaiChina
- Shandong University‐Weihai Research Institute of Industrial TechnologyWeihaiChina
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6
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Sánchez Á, Arrabal A, San Román M, Díaz-Colunga J. The optimization of microbial functions through rational environmental manipulations. Mol Microbiol 2024. [PMID: 38372207 DOI: 10.1111/mmi.15236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/20/2024]
Abstract
Microorganisms play a central role in biotechnology and it is key that we develop strategies to engineer and optimize their functionality. To this end, most efforts have focused on introducing genetic manipulations in microorganisms which are then grown either in monoculture or in mixed-species consortia. An alternative strategy to optimize microbial processes is to rationally engineer the environment in which microbes grow. The microbial environment is multidimensional, including factors such as temperature, pH, salinity, nutrient composition, etc. These environmental factors all influence the growth and phenotypes of microorganisms and they generally "interact" with one another, combining their effects in complex, non-additive ways. In this piece, we overview the origins and consequences of these "interactions" between environmental factors and discuss how they have been built into statistical, bottom-up predictive models of microbial function to identify optimal environmental conditions for monocultures and microbial consortia. We also overview alternative "top-down" approaches, such as genetic algorithms, to finding optimal combinations of environmental factors. By providing a brief summary of the state of this field, we hope to stimulate further work on the rational manipulation and optimization of the microbial environment.
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Affiliation(s)
- Álvaro Sánchez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB - CSIC, Campus de Cantoblanco, Madrid, Spain
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Andrea Arrabal
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB - CSIC, Campus de Cantoblanco, Madrid, Spain
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Magdalena San Román
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB - CSIC, Campus de Cantoblanco, Madrid, Spain
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Juan Díaz-Colunga
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB - CSIC, Campus de Cantoblanco, Madrid, Spain
- Instituto de Biología Funcional y Genómica, IBFG-CSIC, Universidad de Salamanca, Salamanca, Spain
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7
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Pei TT, Luo H, Wang Y, Li H, Wang XY, Zhang YQ, An Y, Wu LL, Ma J, Liang X, Yan A, Yang L, Chen C, Dong T. Filamentous prophage Pf4 promotes genetic exchange in Pseudomonas aeruginosa. THE ISME JOURNAL 2024; 18:wrad025. [PMID: 38365255 PMCID: PMC10837833 DOI: 10.1093/ismejo/wrad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Filamentous prophages are widespread among bacteria and play crucial functions in virulence, antibiotic resistance, and biofilm structures. The filamentous Pf4 particles, extruded by an important pathogen Pseudomonas aeruginosa, can protect producing cells from adverse conditions. Contrary to the conventional belief that the Pf4-encoding cells resist reinfection, we herein report that the Pf4 prophage is reciprocally and commonly exchanged within P. aeruginosa colonies, which can repair defective Pf4 within the community. By labeling the Pf4 locus with antibiotic resistance and fluorescence markers, we demonstrate that the Pf4 locus is frequently exchanged within colony biofilms, in artificial sputum media, and in infected mouse lungs. We further show that Pf4 trafficking is a rapid process and capable of rescuing Pf4-defective mutants. The Pf4 phage is highly adaptable and can package additional DNA doubling its genome size. We also report that two clinical P. aeruginosa isolates are susceptible to the Pf4-mediated exchange, and the Pf5 prophage can be exchanged between cells as well. These findings suggest that the genetic exchanging interactions by filamentous prophages may facilitate defect rescue and the sharing of prophage-dependent benefits and costs within the P. aeruginosa community.
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Affiliation(s)
- Tong-Tong Pei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Han Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Wang
- Unit of Pathogenic Fungal Infection and Host Immunity, Key Laboratory of Molecular Virology and Immunology, Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xing-Yu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi-Qiu Zhang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying An
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Li-Li Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junhua Ma
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoye Liang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Changbin Chen
- Unit of Pathogenic Fungal Infection and Host Immunity, Key Laboratory of Molecular Virology and Immunology, Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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8
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Turner CB, Blount ZD, Mitchell DH, Lenski RE. Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001390. [PMID: 37650867 PMCID: PMC10482366 DOI: 10.1099/mic.0.001390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
The evolution of a novel trait can profoundly change an organism's effects on its environment, which can in turn affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following the evolution of a novel function in the Long-Term Evolution Experiment (LTEE) with Escherichia coli. A characteristic feature of E. coli is its inability to grow aerobically on citrate (Cit-). Nonetheless, a Cit+ variant with this capacity evolved in one LTEE population after 31 000 generations. The Cit+ clade then coexisted stably with another clade that retained the ancestral Cit- phenotype. This coexistence was shaped by the evolution of a cross-feeding relationship based on C4-dicarboxylic acids, particularly succinate, fumarate, and malate, that the Cit+ variants release into the medium. Both the Cit- and Cit+ cells evolved to grow on these excreted resources. The evolution of aerobic growth on citrate thus led to a transition from an ecosystem based on a single limiting resource, glucose, to one with at least five resources that were either shared or partitioned between the two coexisting clades. Our findings show that evolutionary novelties can change environmental conditions in ways that facilitate diversity by altering ecosystem structure and the evolutionary trajectories of coexisting lineages.
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Affiliation(s)
- Caroline B. Turner
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
- Present address: Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Zachary D. Blount
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Daniel H. Mitchell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Present address: Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Richard E. Lenski
- Department of Microbiology and Molecular Genetics; and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
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9
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Hu J, Vandenkoornhuyse P, Khalfallah F, Causse‐Védrines R, Mony C. Ecological corridors homogenize plant root endospheric mycobiota. THE NEW PHYTOLOGIST 2023; 237:1347-1362. [PMID: 36349407 PMCID: PMC10107361 DOI: 10.1111/nph.18606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind, while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of 1 m over 2 years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We showed that plant root endospheric mycobiota were sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.
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Affiliation(s)
- Jie Hu
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
- Ecology and Biodiversity group, Institute of Environmental BiologyUniversity of UtrechtH.R. Kruyt building, Padualaan 83584 CHUtrechtthe Netherlands
- Present address:
Department of Microbial EcologyNetherlands Institute of EcologyDroevendaalsesteeg 106708 PBWageningenthe Netherlands
| | | | - Fadwa Khalfallah
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
- UMR IAM, INRAEUniversité de LorraineRue d'amance54280ChampenouxFrance
| | - Romain Causse‐Védrines
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
| | - Cendrine Mony
- UMR 6553 EcobioCNRS‐University of RennesAvenue du Général Leclerc35042Rennes CedexFrance
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10
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Biget M, Wang T, Mony C, Xu Q, Lecoq L, Chable V, Theis KR, Ling N, Vandenkoornhuyse P. Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants. iScience 2023; 26:106031. [PMID: 36824281 PMCID: PMC9941212 DOI: 10.1016/j.isci.2023.106031] [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: 06/12/2022] [Revised: 09/07/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.
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Affiliation(s)
- Marine Biget
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Tingting Wang
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lucie Lecoq
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Véronique Chable
- UMR BAGAP INRAE, Centre Bretagne-Normandie, Domaine de la Motte, BP35327, 35653 Le Rheu Cedex, France
| | - Kevin R. Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China,Corresponding author
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France,Corresponding author
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Arnault G, Mony C, Vandenkoornhuyse P. Plant microbiota dysbiosis and the Anna Karenina Principle. TRENDS IN PLANT SCIENCE 2023; 28:18-30. [PMID: 36127241 DOI: 10.1016/j.tplants.2022.08.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/19/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.
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Affiliation(s)
- Gontran Arnault
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
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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: 9] [Impact Index Per Article: 4.5] [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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