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Zimmermann J, Piecyk A, Sieber M, Petersen C, Johnke J, Moitinho-Silva L, Künzel S, Bluhm L, Traulsen A, Kaleta C, Schulenburg H. Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life. mBio 2024; 15:e0001224. [PMID: 38634692 PMCID: PMC11077962 DOI: 10.1128/mbio.00012-24] [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: 01/02/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function. IMPORTANCE The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.
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Affiliation(s)
- Johannes Zimmermann
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Agnes Piecyk
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Michael Sieber
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Julia Johnke
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lucas Moitinho-Silva
- />Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Lena Bluhm
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Arne Traulsen
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
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Singh A, Luallen RJ. Understanding the factors regulating host-microbiome interactions using Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230059. [PMID: 38497260 PMCID: PMC10945399 DOI: 10.1098/rstb.2023.0059] [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: 08/16/2023] [Accepted: 01/01/2024] [Indexed: 03/19/2024] Open
Abstract
The Human Microbiome Project was a research programme that successfully identified associations between microbial species and healthy or diseased individuals. However, a major challenge identified was the absence of model systems for studying host-microbiome interactions, which would increase our capacity to uncover molecular interactions, understand organ-specificity and discover new microbiome-altering health interventions. Caenorhabditis elegans has been a pioneering model organism for over 70 years but was largely studied in the absence of a microbiome. Recently, ecological sampling of wild nematodes has uncovered a large amount of natural genetic diversity as well as a slew of associated microbiota. The field has now explored the interactions of C. elegans with its associated gut microbiome, a defined and non-random microbial community, highlighting its suitability for dissecting host-microbiome interactions. This core microbiome is being used to study the impact of host genetics, age and stressors on microbiome composition. Furthermore, single microbiome species are being used to dissect molecular interactions between microbes and the animal gut. Being amenable to health altering genetic and non-genetic interventions, C. elegans has emerged as a promising system to generate and test new hypotheses regarding host-microbiome interactions, with the potential to uncover novel paradigms relevant to other systems. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Anupama Singh
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Robert J. Luallen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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3
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Chen KH, Feng J, Bodelier PLE, Yang Z, Huang Q, Delgado-Baquerizo M, Cai P, Tan W, Liu YR. Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields. Nat Commun 2024; 15:3471. [PMID: 38658559 PMCID: PMC11043409 DOI: 10.1038/s41467-024-47827-y] [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: 04/04/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and 13CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, 13CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating 13C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of 13C-metagenome-assembled genomes and 13C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.
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Affiliation(s)
- Kang-Hua Chen
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiao Feng
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB, Wageningen, The Netherlands
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, MI, 48309, USA
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, 41012, Spain
| | - Peng Cai
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
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4
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Gonzalez X, Irazoqui JE. Distinct members of the Caenorhabditis elegans CeMbio reference microbiota exert cryptic virulence that is masked by host defense. Mol Microbiol 2024. [PMID: 38623070 DOI: 10.1111/mmi.15258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/17/2024]
Abstract
Microbiotas are complex microbial communities that colonize specific niches in the host and provide essential organismal functions that are important in health and disease. Understanding the ability of each distinct community member to promote or impair host health, alone or in the context of the community, is imperative for understanding how differences in community structure affect host health and vice versa. Recently, a reference 12-member microbiota for the model organism Caenorhabditis elegans, known as CeMbio, was defined. Here, we show the differential ability of each CeMbio bacterial species to activate innate immunity through the conserved PMK-1/p38 MAPK, ACh-WNT, and HLH-30/TFEB pathways. Although distinct CeMbio members differed in their ability to activate the PMK-1/p38 pathway, the ability to do so did not correlate with bacterial-induced lifespan reduction in wild-type or immunodeficient animals. In contrast, most species activated HLH-30/TFEB and showed virulence toward hlh-30-deficient animals. These results suggest that the microbiota of C. elegans is rife with bacteria that can shorten the host's lifespan if host defense is compromised and that HLH-30/TFEB is a fundamental and key host protective factor.
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Affiliation(s)
- Xavier Gonzalez
- Immunology and Microbiology Graduate Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Javier E Irazoqui
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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5
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Pees B, Peters L, Treitz C, Hamerich IK, Kissoyan KAB, Tholey A, Dierking K. The Caenorhabditis elegans proteome response to two protective Pseudomonas symbionts. mBio 2024; 15:e0346323. [PMID: 38411078 PMCID: PMC11005407 DOI: 10.1128/mbio.03463-23] [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: 01/04/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The Caenorhabditis elegans natural microbiota isolates Pseudomonas lurida MYb11 and Pseudomonas fluorescens MYb115 protect the host against pathogens through distinct mechanisms. While P. lurida produces an antimicrobial compound and directly inhibits pathogen growth, P. fluorescens MYb115 protects the host without affecting pathogen growth. It is unknown how these two protective microbes affect host biological processes. We used a proteomics approach to elucidate the C. elegans response to MYb11 and MYb115. We found that both Pseudomonas isolates increase vitellogenin protein production in young adults, which confirms previous findings on the effect of microbiota on C. elegans reproductive timing. Moreover, the C. elegans responses to MYb11 and MYb115 exhibit common signatures with the response to other vitamin B12-producing bacteria, emphasizing the importance of vitamin B12 in C. elegans-microbe metabolic interactions. We further analyzed signatures in the C. elegans response specific to MYb11 or MYb115. We provide evidence for distinct modifications in lipid metabolism by both symbiotic microbes. We could identify the activation of host-pathogen defense responses as an MYb11-specific proteome signature and provide evidence that the intermediate filament protein IFB-2 is required for MYb115-mediated protection. These results indicate that MYb11 not only produces an antimicrobial compound but also activates host antimicrobial defenses, which together might increase resistance to infection. In contrast, MYb115 affects host processes such as lipid metabolism and cytoskeleton dynamics, which might increase host tolerance to infection. Overall, this study pinpoints proteins of interest that form the basis for additional exploration into the mechanisms underlying C. elegans microbiota-mediated protection from pathogen infection and other microbiota-mediated traits.IMPORTANCESymbiotic bacteria can defend their host against pathogen infection. While some protective symbionts directly interact with pathogenic bacteria, other protective symbionts elicit a response in the host that improves its own pathogen defenses. To better understand how a host responds to protective symbionts, we examined which host proteins are affected by two protective Pseudomonas bacteria in the model nematode Caenorhabditis elegans. We found that the C. elegans response to its protective symbionts is manifold, which was reflected in changes in proteins that are involved in metabolism, the immune system, and cell structure. This study provides a foundation for exploring the contribution of the host response to symbiont-mediated protection from pathogen infection.
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Affiliation(s)
- Barbara Pees
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Lena Peters
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrecht University, Kiel, Germany
| | - Inga K. Hamerich
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Kohar A. B. Kissoyan
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research and Bioanalytics, Institute for Experimental Medicine, Christian-Albrecht University, Kiel, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrecht University, Kiel, Germany
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6
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Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C. Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics. Microbiol Spectr 2024; 12:e0114423. [PMID: 38230938 PMCID: PMC10846184 DOI: 10.1128/spectrum.01144-23] [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: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member Caenorhabditis elegans microbiome community comprising the immune-protective target species Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.IMPORTANCEWhile various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm Caenorhabditis elegans comprising the host-beneficial Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11 in vitro and in vivo. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Inga K. Hamerich
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Reena Debray
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nancy Obeng
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Nutriinformatics, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
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7
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Decaestecker E, Van de Moortel B, Mukherjee S, Gurung A, Stoks R, De Meester L. Hierarchical eco-evo dynamics mediated by the gut microbiome. Trends Ecol Evol 2024; 39:165-174. [PMID: 37863775 DOI: 10.1016/j.tree.2023.09.013] [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: 04/17/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023]
Abstract
The concept of eco-evolutionary (eco-evo) dynamics, stating that ecological and evolutionary processes occur at similar time scales and influence each other, has contributed to our understanding of responses of populations, communities, and ecosystems to environmental change. Phenotypes, central to these eco-evo processes, can be strongly impacted by the gut microbiome. The gut microbiome shapes eco-evo dynamics in the host community through its effects on the host phenotype. Complex eco-evo feedback loops between the gut microbiome and the host communities might thus be common. Bottom-up dynamics occur when eco-evo interactions shaping the gut microbiome affect host phenotypes with consequences at population, community, and ecosystem levels. Top-down dynamics occur when eco-evo dynamics shaping the host community structure the gut microbiome.
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Affiliation(s)
- Ellen Decaestecker
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium.
| | - Broos Van de Moortel
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Laboratory of Reproductive Genomics, KU Leuven, B-3000 Leuven, Belgium
| | - Aditi Gurung
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium
| | - Robby Stoks
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, B-3000 Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), D-12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, D-14195 Berlin, Germany
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8
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Chai VZ, Farajzadeh T, Meng Y, Lo SB, Asaed TA, Taylor CJ, Glater EE. Chemical basis of microbiome preference in the nematode C. elegans. Sci Rep 2024; 14:1350. [PMID: 38228683 PMCID: PMC10791660 DOI: 10.1038/s41598-024-51533-6] [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: 08/15/2023] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
Animals are exposed to many microbes in their environment, some of which have been shown to colonize various tissues including the intestine. The composition of the intestinal microbiota affects many aspects of the host's physiology and health. Despite this, very little is known about whether host behavior contributes to the colonization. We approach this question in the nematode C. elegans, which feeds on bacteria and also harbors an intestinal microbiome. We examined the behavior of C. elegans towards CeMbio, a simplified microbiome consisting of twelve strains that represent the bacteria found in the animal's natural environment. We observed that C. elegans raised on E. coli shows a strong preference for three members of CeMbio (Lelliottia amnigena JUb66, Enterobacter hormaechei CEent1, and Pantoea nemavictus BIGb0393) compared to E. coli. Previously, these three bacterial strains have been shown to support faster C. elegans development time than E. coli OP50 and are low colonizers compared to eight other members of CeMbio. We then used gas chromatography coupled to mass spectrometry to identify that these three bacteria release isoamyl alcohol, a previously described C. elegans chemoattractant. We suggest that C. elegans seeks bacteria that release isoamyl alcohol and support faster growth.
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Affiliation(s)
- Victor Z Chai
- Department of Neuroscience, Pomona College, Claremont, CA, USA
| | | | - Yufei Meng
- Department of Neuroscience, Pomona College, Claremont, CA, USA
| | - Sokhna B Lo
- Department of Neuroscience, Pomona College, Claremont, CA, USA
| | - Tymmaa A Asaed
- Department of Neuroscience, Pomona College, Claremont, CA, USA
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9
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Fatemi E, Jung C. Pathogenicity of the root lesion nematode Pratylenchus neglectus depends on pre-culture conditions. Sci Rep 2023; 13:19642. [PMID: 37949971 PMCID: PMC10638436 DOI: 10.1038/s41598-023-46551-9] [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: 09/01/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
The ability of a plant parasitic nematode to infect and reproduce within a host plant depends on its genotype and the environmental conditions before and during infection. We studied the culturing conditions of the root lesion nematode Pratylenchus neglectus to produce inoculum for plant infection tests. Nematodes were either cultivated on carrot calli for different periods or directly isolated from the roots of the host plants. After infection of wheat and barley plants in the greenhouse, nematodes were quantified by RT-qPCR and by visual counting of the nematodes. We observed drastically reduced infection rates after long-term (> 96 weeks) cultivation on carrot callus. In contrast, fresh isolates from cereal roots displayed much higher pathogenicity. We recommend using root lesion nematodes cultivated on carrot calli no longer than 48 weeks to guarantee uniform infection rates.
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Affiliation(s)
- Ehsan Fatemi
- Plant Breeding Institute, Christian-Albrechts University, Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts University, Kiel, Germany.
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10
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Petersen C, Hamerich IK, Adair KL, Griem-Krey H, Torres Oliva M, Hoeppner MP, Bohannan BJM, Schulenburg H. Host and microbiome jointly contribute to environmental adaptation. THE ISME JOURNAL 2023; 17:1953-1965. [PMID: 37673969 PMCID: PMC10579302 DOI: 10.1038/s41396-023-01507-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Most animals and plants have associated microorganisms, collectively referred to as their microbiomes, which can provide essential functions. Given their importance, host-associated microbiomes have the potential to contribute substantially to adaptation of the host-microbiome assemblage (the "metaorganism"). Microbiomes may be especially important for rapid adaptation to novel environments because microbiomes can change more rapidly than host genomes. However, it is not well understood how hosts and microbiomes jointly contribute to metaorganism adaptation. We developed a model system with which to disentangle the contributions of hosts and microbiomes to metaorganism adaptation. We established replicate mesocosms containing the nematode Caenorhabditis elegans co-cultured with microorganisms in a novel complex environment (laboratory compost). After approximately 30 nematode generations (100 days), we harvested worm populations and associated microbiomes, and subjected them to a common garden experiment designed to unravel the impacts of microbiome composition and host genetics on metaorganism adaptation. We observed that adaptation took different trajectories in different mesocosm lines, with some increasing in fitness and others decreasing, and that interactions between host and microbiome played an important role in these contrasting evolutionary paths. We chose two exemplary mesocosms (one with a fitness increase and one with a decrease) for detailed study. For each example, we identified specific changes in both microbiome composition (for both bacteria and fungi) and nematode gene expression associated with each change in fitness. Our study provides experimental evidence that adaptation to a novel environment can be jointly influenced by host and microbiome.
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Affiliation(s)
- Carola Petersen
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | - Inga K Hamerich
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | - Karen L Adair
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Hanne Griem-Krey
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | | | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | | | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany.
- Max-Planck Institute for Evolutionary Biology, Ploen, Germany.
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11
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Shiri TJ, Viau C, Gu X, Xu L, Lu Y, Xia J. The Native Microbiome Member Chryseobacterium sp. CHNTR56 MYb120 Induces Trehalose Production via a Shift in Central Carbon Metabolism during Early Life in C. elegans. Metabolites 2023; 13:953. [PMID: 37623896 PMCID: PMC10456584 DOI: 10.3390/metabo13080953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/01/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Aging is the system-wide loss of homeostasis, eventually leading to death. There is growing evidence that the microbiome not only evolves with its aging host, but also directly affects aging via the modulation of metabolites involved in important cellular functions. The widely used model organism C. elegans exhibits high selectivity towards its native microbiome members which confer a range of differential phenotypes and possess varying functional capacities. The ability of one such native microbiome species, Chryseobacterium sp. CHNTR56 MYb120, to improve the lifespan of C. elegans and to promote the production of Vitamin B6 in the co-colonizing member Comamonas sp. 12022 MYb131 are some of its beneficial effects on the worm host. We hypothesize that studying its metabolic influence on the different life stages of the worm could provide further insights into mutualistic interactions. The present work applied LC-MS untargeted metabolomics and isotope labeling to study the impact of the native microbiome member Chryseobacterium sp. CHNTR56 MYb120 on the metabolism of C. elegans. In addition to the upregulation of biosynthesis and detoxification pathway intermediates, we found that Chryseobacterium sp. CHNTR56 MYb120 upregulates the glyoxylate shunt in mid-adult worms which is linked to the upregulation of trehalose, an important metabolite for desiccation tolerance in older worms.
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Affiliation(s)
- Tanisha Jean Shiri
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Charles Viau
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Xue Gu
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Lei Xu
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada;
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada; (T.J.S.); (C.V.); (X.G.); (L.X.)
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada;
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12
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Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community. Nat Commun 2023; 14:4780. [PMID: 37553336 PMCID: PMC10409746 DOI: 10.1038/s41467-023-40372-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
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Affiliation(s)
- Anna S Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa S Niedermeier
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Alexandra von Strempel
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Anna G Burrichter
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chiara Lincetto
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Johannes Hübner
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany.
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13
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Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C. Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528811. [PMID: 36824941 PMCID: PMC9949166 DOI: 10.1101/2023.02.17.528811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, there is still a lack of approaches that allow to specifically modulate the abundance of individual microbes or microbial functions of interest. Moreover, current approaches for microbiome manipulation such as fecal transfers often entail a non-specific transfer of entire microbial communities with potentially unwanted side effects. To overcome this limitation, we here propose the concept of precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In a first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we present a metabolic modeling network framework that allows us to define precision prebiotics for a two-member C. elegans microbiome model community comprising the immune-protective Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. Thus, we predicted compounds that specifically boost the abundance of the host-beneficial MYb11, four of which were experimentally validated in vitro (L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid). L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that constraint-based metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Inga K Hamerich
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Reena Debray
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nancy Obeng
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Nutriinformatics, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
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14
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Eco-evolutionary implications of helminth microbiomes. J Helminthol 2023; 97:e22. [PMID: 36790127 DOI: 10.1017/s0022149x23000056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host-parasite interactions in light of new technological developments.
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15
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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16
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McQueen JP, Gattoni K, Gendron EMS, Schmidt SK, Sommers P, Porazinska DL. Host identity is the dominant factor in the assembly of nematode and tardigrade gut microbiomes in Antarctic Dry Valley streams. Sci Rep 2022; 12:20118. [PMID: 36446870 PMCID: PMC9709161 DOI: 10.1038/s41598-022-24206-5] [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: 07/06/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Recent work examining nematode and tardigrade gut microbiomes has identified species-specific relationships between host and gut community composition. However, only a handful of species from either phylum have been examined. How microbiomes differ among species and what factors contribute to their assembly remains unexplored. Cyanobacterial mats within Antarctic Dry Valley streams host a simple and tractable natural ecosystem of identifiable microinvertebrates to address these questions. We sampled 2 types of coexisting mats (i.e., black and orange) across four spatially isolated streams, hand-picked single individuals of two nematode species (i.e., Eudorylaimus antarcticus and Plectus murrayi) and tardigrades, to examine their gut microbiomes using 16S and 18S rRNA metabarcoding. All gut microbiomes (bacterial and eukaryotic) were significantly less diverse than the mats they were isolated from. In contrast to mats, microinvertebrates' guts were depleted of Cyanobacteria and differentially enriched in taxa of Bacteroidetes, Proteobacteria, and Fungi. Among factors investigated, gut microbiome composition was most influenced by host identity while environmental factors (e.g., mats and streams) were less important. The importance of host identity in predicting gut microbiome composition suggests functional value to the host, similar to other organisms with strong host selected microbiomes.
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Affiliation(s)
- J. Parr McQueen
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Kaitlin Gattoni
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Eli M. S. Gendron
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
| | - Steven K. Schmidt
- grid.266190.a0000000096214564Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Pacifica Sommers
- grid.266190.a0000000096214564Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309 USA
| | - Dorota L. Porazinska
- grid.15276.370000 0004 1936 8091Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611 USA
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17
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Sun Q, Vega NM, Cervantes B, Mancuso CP, Mao N, Taylor MN, Collins JJ, Khalil AS, Gore J, Lu TK. Enhancing nutritional niche and host defenses by modifying the gut microbiome. Mol Syst Biol 2022; 18:e9933. [PMID: 36377768 PMCID: PMC9664710 DOI: 10.15252/msb.20209933] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 08/15/2022] [Accepted: 10/14/2022] [Indexed: 08/18/2023] Open
Abstract
The gut microbiome is essential for processing complex food compounds and synthesizing nutrients that the host cannot digest or produce, respectively. New model systems are needed to study how the metabolic capacity provided by the gut microbiome impacts the nutritional status of the host, and to explore possibilities for altering host metabolic capacity via the microbiome. Here, we colonized the nematode Caenorhabditis elegans gut with cellulolytic bacteria that enabled C. elegans to utilize cellulose, an otherwise indigestible substrate, as a carbon source. Cellulolytic bacteria as a community component in the worm gut can also support additional bacterial species with specialized roles, which we demonstrate by using Lactobacillus plantarum to protect C. elegans against Salmonella enterica infection. This work shows that engineered microbiome communities can be used to endow host organisms with novel functions, such as the ability to utilize alternate nutrient sources or to better fight pathogenic bacteria.
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Affiliation(s)
- Qing Sun
- Synthetic Biology CenterMITCambridgeMAUSA
- Department of Chemical EngineeringTexas A&M UniversityCollege StationTXUSA
| | - Nic M Vega
- Department of PhysicsMITCambridgeMAUSA
- Biology DepartmentEmory UniversityAtlantaGAUSA
| | - Bernardo Cervantes
- Institute for Medical Engineering & Science and Department of Biological EngineeringMITCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Microbiology Graduate ProgramMITCambridgeMAUSA
| | - Christopher P Mancuso
- Biological Design CenterBoston UniversityBostonMAUSA
- Department of Biomedical EngineeringBoston UniversityBostonMAUSA
| | - Ning Mao
- Department of Biomedical EngineeringBoston UniversityBostonMAUSA
| | | | - James J Collins
- Synthetic Biology CenterMITCambridgeMAUSA
- Institute for Medical Engineering & Science and Department of Biological EngineeringMITCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMAUSA
| | - Ahmad S Khalil
- Biological Design CenterBoston UniversityBostonMAUSA
- Department of Biomedical EngineeringBoston UniversityBostonMAUSA
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMAUSA
| | - Jeff Gore
- Department of PhysicsMITCambridgeMAUSA
| | - Timothy K Lu
- Synthetic Biology CenterMITCambridgeMAUSA
- Department of Electrical Engineering and Computer ScienceMITCambridgeMAUSA
- Department of Biological EngineeringMITCambridgeMAUSA
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18
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Murillo-Roos M, Abdullah HSM, Debbar M, Ueberschaar N, Agler MT. Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability. THE ISME JOURNAL 2022; 16:2280-2289. [PMID: 35768644 PMCID: PMC9381498 DOI: 10.1038/s41396-022-01271-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/20/2022] [Accepted: 06/10/2022] [Indexed: 12/27/2022]
Abstract
Leaf microbiomes play crucial roles in plant health, making it important to understand the origins and functional relevance of their diversity. High strain-level leaf bacterial genetic diversity is known to be relevant for interactions with hosts, but little is known about its relevance for interactions with the multitude of diverse co-colonizing microorganisms. In leaves, nutrients like amino acids are major regulators of microbial growth and activity. Using metabolomics of leaf apoplast fluid, we found that different species of the plant genus Flaveria considerably differ in the concentrations of high-cost amino acids. We investigated how these differences affect bacterial community diversity and assembly by enriching leaf bacteria in vitro with only sucrose or sucrose + amino acids as possible carbon sources. Enrichments from F. robusta were dominated by Pantoea sp. and Pseudomonas sp., regardless of carbon source. The latter was unable to grow on sucrose alone but persisted in the sucrose-only enrichment thanks to exchange of diverse metabolites from Pantoea sp. Individual Pseudomonas strains in the enrichments had high genetic similarity but still displayed clear niche partitioning, enabling distinct strains to cross-feed in parallel. Pantoea strains were also closely related, but individuals enriched from F. trinervia fed Pseudomonas more poorly than those from F. robusta. This can be explained in part by the plant environment, since some cross-feeding interactions were selected for, when experimentally evolved in a poor (sucrose-only) environment but selected against in a rich (sucrose + amino acids) one. Together, our work shows that leaf bacterial diversity is functionally relevant in cross-feeding interactions and strongly suggests that the leaf resource environment can shape these interactions and thereby indirectly drive bacterial diversity.
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Affiliation(s)
- Mariana Murillo-Roos
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Hafiz Syed M Abdullah
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Mossaab Debbar
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Nico Ueberschaar
- Mass Spectrometry Platform, Friedrich Schiller University Jena, Jena, Germany
| | - Matthew T Agler
- Plant Microbiosis Lab, Department of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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19
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Tibbs-Cortes LE, Tibbs-Cortes BW, Schmitz-Esser S. Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens. Front Microbiol 2022; 13:866930. [PMID: 35923389 PMCID: PMC9340075 DOI: 10.3389/fmicb.2022.866930] [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: 01/31/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022] Open
Abstract
The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.
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Affiliation(s)
- Laura E. Tibbs-Cortes
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Laura E. Tibbs-Cortes,
| | - Bienvenido W. Tibbs-Cortes
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
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20
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Pérez-Carrascal OM, Choi R, Massot M, Pees B, Narayan V, Shapira M. Host Preference of Beneficial Commensals in a Microbially-Diverse Environment. Front Cell Infect Microbiol 2022; 12:795343. [PMID: 35782135 PMCID: PMC9240469 DOI: 10.3389/fcimb.2022.795343] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Gut bacteria are often described by the neutral term commensals. However, the more we learn about their interactions with hosts, the more apparent it becomes that gut commensals often contribute positively to host physiology and fitness. Whether hosts can prefer beneficial bacteria, and how they do so, is not clear. This is of particular interest in the case of the bacterivore C. elegans, which depends on bacteria as food source, but also as gut colonizers that contribute to its physiology, from development to immunity. It is further unclear to what extent worms living in their microbially-diverse habitats can sense and distinguish between beneficial bacteria, food, and pathogens. Focusing on Enterobacteriaceae and members of closely related families, we isolated gut bacteria from worms raised in compost microcosms, as well as bacteria from the respective environments and evaluated their contributions to host development. Most isolates, from worms or from the surrounding environment, promoted faster development compared to the non-colonizing E. coli food strain. Pantoea strains further showed differential contributions of gut isolates versus an environmental isolate. Characterizing bacterial ability to hinder pathogenic colonization with Pseudomonas aeruginosa, supported the trend of Pantoea gut commensals being beneficial, in contrast to the environmental strain. Interestingly, worms were attracted to the beneficial Pantoea strains, preferring them over non-beneficial bacteria, including the environmental Pantoea strain. While our understanding of the mechanisms underlying these host-microbe interactions are still rudimentary, the results suggest that hosts can sense and prefer beneficial commensals.
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21
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Huang S, Zhang C, Xu T, Shaukat A, He Y, Chen P, Lin L, Yue K, Cao Q, Tong X. Integrated Fecal Microbiome and Metabolomics Reveals a Novel Potential Biomarker for Predicting Tibial Dyschondroplasia in Chickens. Front Physiol 2022; 13:887207. [PMID: 35634144 PMCID: PMC9133743 DOI: 10.3389/fphys.2022.887207] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Tibial dyschondroplasia (TD) is a metabolic tibial-tarsal disorder occurring in fast-growing poultry, and its diagnosis is mainly based on an invasive method. Here, we profiled the fecal gut microbiome and metabolome of broilers with and without TD to identify potential non-invasive and non-stress biomarkers of TD. First, TD broilers with the most pronounced clinical signs during the experiment were screened and faecal samples were collected for integrated microbiome and metabolomics analysis. Moreover, the diagnostic potential of identified biomarkers was further validated throughout the experiment. It was noted that the microbial and metabolic signatures of TD broilers differed from those of normal broilers. TD broilers were characterized by enriched bacterial OTUs of the genus Klebsiella, and depleted genera [Ruminococcus], Dorea, Ruminococcus, Oscillospira, Ochrobactrum, and Sediminibacterium. In addition, a total of 189 fecal differential metabolites were identified, mainly enriched in the purine, vitamin and amino acid metabolism, which were closely associated with differential microbiota and tibia-related indicators. Furthermore, three fecal metabolites were screened, including 4-hydroxybenzaldehyde, which distinguished TD from normal broilers with extremely high specificity and was superior to serum bone markers. These results indicated that gut microbiota equilibrium might influence the pathogenesis of TD by modulating host metabolism, and the identified fecal metabolite 4-hydroxybenzaldehyde might be a potential and non-invasive biomarker for predicting TD in chickens.
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Affiliation(s)
- Shucheng Huang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Shucheng Huang,
| | - Chaodong Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tingting Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Aftab Shaukat
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, China
| | - Yanfeng He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Pan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Luxi Lin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ke Yue
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qinqin Cao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xishuai Tong
- Institutes of Agricultural Science and Technology Development (Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China)/College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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22
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Reproductive Span of Caenorhabditis elegans Is Extended by Microbacterium sp. J Nematol 2022; 54:20220010. [PMID: 35860519 PMCID: PMC9260829 DOI: 10.2478/jofnem-2022-0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 11/20/2022] Open
Abstract
Abstract
The reproductive span (RS) of organisms could be affected by different factors during their lifetime. In the model nematode, Caenorhabditis elegans, RS is affected by both genetic and environmental factors. However, none of the factors identified so far were related to environmental bacteria, which may incidentally appear anywhere in the habitats of C. elegans. We aimed to find environmental bacteria that could affect the RS of C. elegans and related species. We tested 109 bacterial isolates and found that Microbacterium sp. CFBb37 increased the RS and lifespan of C. elegans but reduced its brood size. We studied the effect of M. sp. CFBb37 on the RS of Caenorhabditis briggsae, Caenorhabditis tropicalis, and another Rhabditidae family species, Protorhabditis sp., and found similar trends of RS extension in all three cases, suggesting that this bacterial species may induce the extension of RS broadly among Caenorhabditis species and possibly for many other Rhabditidae. This work will facilitate future research on the mechanism underlying the bacterial extension of RS of nematodes and possibly other animals.
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23
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Xie K, Liu Y, Li X, Zhang H, Zhang S, Mak HY, Liu P. Dietary S. maltophilia induces supersized lipid droplets by enhancing lipogenesis and ER-LD contacts in C. elegans. Gut Microbes 2022; 14:2013762. [PMID: 35112996 PMCID: PMC8816401 DOI: 10.1080/19490976.2021.2013762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Dietary and symbiotic bacteria can exert powerful influence on metazoan lipid metabolism. Recent studies have emerged that microbiota have a role in animal obesity and related health disorders, but the mechanisms by which bacteria influence lipid storage in their host are unknown. To reduce the complexity of the relationship between gut microbiota and the host, Caenorhabditis elegans (C. elegans) has been chosen as a model organism to study interspecies interaction. Here, we demonstrate that feeding C. elegans with an opportunistic pathogenic bacterium Stenotrophomonas maltophilia (S. maltophilia) retards growth and promotes excessive neutral lipid storage. Gene expression analysis reveals that dietary S. maltophilia induces a lipogenic transcriptional response that includes the SREBP ortholog SBP-1, and fatty acid desaturases FAT-6 and FAT-7. Live imaging and ultrastructural analysis suggest that excess neutral lipid is stored in greatly expanded lipid droplets (LDs), as a result of enhanced endoplasmic reticulum (ER)-LD interaction. We also report that loss of function mutations in dpy-9 in C. elegans confers resistance to S. maltophilia. Dietary S. maltophilia induces supersized LDs by enhancing lipogenesis and ER-LD contacts in C. elegans. This work delineates a new model for understanding microbial regulation of metazoan physiology.
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Affiliation(s)
- Kang Xie
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yangli Liu
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Xixia Li
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ho Yi Mak
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,CONTACT Pingsheng Liu National Laboratory of Biomacromolecules, Cas Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
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24
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Lo WS, Sommer RJ. Vitamin B 12 and predatory behavior in nematodes. VITAMINS AND HORMONES 2022; 119:471-489. [PMID: 35337632 DOI: 10.1016/bs.vh.2022.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The round worms or nematodes are the largest phylum of animals with an estimated species number of more than one million. Nematodes have invaded all ecosystems and are known from all continents including Antarctica. Parasitic species infest plants, animals and humans often with high host-specificity. Free-living species are known from marine, fresh water and soil systems, the latter of which contain many culturable species. This includes Caenorhabditis elegans, a species that was developed as one of the most prominent model systems in modern biology since the 1960ies. Pristionchus pacificus is a second nematode model organism that can easily be cultured in the laboratory. This species shows a number of complex traits including omnivorous feeding and the capability of predation on other nematodes. Predation depends on the formation of teeth-like denticles in the mouth of P. pacificus, structures unknown from C. elegans and most other nematodes. Here, we review the current knowledge about the role of vitamin B12 for the predatory behavior in P. pacificus and correlate its role with that on the physiology and development in C. elegans.
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Affiliation(s)
- Wen-Sui Lo
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Ralf J Sommer
- Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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25
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Kissoyan KAB, Peters L, Giez C, Michels J, Pees B, Hamerich IK, Schulenburg H, Dierking K. Exploring Effects of C. elegans Protective Natural Microbiota on Host Physiology. Front Cell Infect Microbiol 2022; 12:775728. [PMID: 35237530 PMCID: PMC8884406 DOI: 10.3389/fcimb.2022.775728] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/14/2022] [Indexed: 11/29/2022] Open
Abstract
The Caenorhabditis elegans natural microbiota was described only recently. Thus, our understanding of its effects on nematode physiology is still in its infancy. We previously showed that the C. elegans natural microbiota isolates Pseudomonas lurida MYb11 and P. fluorescens MYb115 protect the worm against pathogens such as Bacillus thuringiensis (Bt). However, the overall effects of the protective microbiota on worm physiology are incompletely understood. Here, we investigated how MYb11 and MYb115 affect C. elegans lifespan, fertility, and intestinal colonization. We further studied the capacity of MYb11 and MYb115 to protect the worm against purified Bt toxins. We show that while MYb115 and MYb11 affect reproductive timing and increase early reproduction only MYb11 reduces worm lifespan. Moreover, MYb11 aggravates killing upon toxin exposure. We conclude that MYb11 has a pathogenic potential in some contexts. This work thus highlights that certain C. elegans microbiota members can be beneficial and costly to the host in a context-dependent manner, blurring the line between good and bad.
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26
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Haçariz O, Viau C, Gu X, Xia J. Native Microbiome Members of C. elegans Act Synergistically in Biosynthesis of Pyridoxal 5′-Phosphate. Metabolites 2022; 12:metabo12020172. [PMID: 35208245 PMCID: PMC8879373 DOI: 10.3390/metabo12020172] [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: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023] Open
Abstract
The roles of the healthy microbiome on the host and the relationships between members of the microbiome remain to be fully characterized. Due to the complexity of the interactions between the mammalian microbiome and its host, the use of model organisms such as the nematode worm Caenorhabditis elegans is a promising strategy to study host-microbiome interactions in vivo, as well as bacterial crosstalk within the host. Previously it was found that native bacterial isolates of the worm, Chryseobacterium sp. CHNTR56 MYb120 and Comamonas sp. 12022 MYb131, possess genomic diversity in the biosynthesis of the active form of vitamin B6, pyridoxal 5′-phosphate (PLP), and contribute to host fitness and lifespan extension. However, the relative contribution of PLP from each isolate, as well as the existence of interbacterial relationships within the worm gut remain to be characterized. In the present work, we investigated the presence and measured the abundance of PLP in the isolates and in the worms grown with the isolates using ultraperformance liquid chromatography tandem-mass spectrometry (UPLC-MS/MS). Our analyses confirmed the presence of PLP in vitro and in vivo. The elevated abundance of PLP in the isolates (which reached statistically significant levels when the two isolates were combined), and within worms grown with the combination of bacterial isolates, compared to control, indicated synergism between the isolates in the production of PLP. Isotope labeling revealed that Comamonas sp. 12022 MYb131 was the main provider of PLP in worms grown with the combination of bacterial isolates. The dominance of this isolate inside the worm was further confirmed by a colonization assay. An untargeted metabolomics analysis of the bacteria showed that the pathways related to cell growth, protein synthesis and lipid synthesis/energy production were regulated in the combination group in comparison with Comamonas sp. 12022 MYb131 alone. Furthermore, glutamine, involved in the de novo synthesis of purine and pyrimidines, was specifically abundant in this group, indicating the potential role of this metabolite in initiating and sustaining bacterial growth. This bacterial crosstalk is suggested to promote the growth of Comamonas sp. 12022 MYb131 in vivo, and synthesis of bacterial metabolites such as PLP in the worm gut.
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Affiliation(s)
- Orçun Haçariz
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
| | - Charles Viau
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
| | - Xue Gu
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (O.H.); (C.V.); (X.G.)
- Department of Animal Science, McGill University, Montreal, QC H9X 3V9, Canada
- Correspondence:
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27
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Zheng F, An XL, Zhou GW, Zhu D, Neilson R, Chen B, Yang XR. Mite gut microbiome and resistome exhibited species-specific and dose-dependent effect in response to oxytetracycline exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150802. [PMID: 34626628 DOI: 10.1016/j.scitotenv.2021.150802] [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: 08/13/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The importance of the gut microbiome to host health is well recognized, but the effects of environmental pressures on the gut microbiome of soil fauna are poorly understood. Here, Illumina sequencing and high-throughput qPCR were applied to characterize the gut microbiomes and resistomes of two mites, Nenteria moseri and Chiropturopoda sp. AL5866, exposed to different concentrations of oxytetracycline (0, 0.01, 0.1 and 1 μg mg-1). Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant phyla in the gut microbiomes of both studied mite species, but the relative abundance of them was different between mites. After exposure to oxytetracycline, there was no variation in the gut microbiome and resistome of C. sp. AL5866, whereas the gut microbiome and resistome of N. moseri were altered significantly. The relative abundance of Proteobacteria significantly decreased, and those of Bacteroidetes and Firmicutes significantly increased at the high-concentration antibiotic treatments. Excepting the 0.01 μg mg-1 treatment, gut microbial diversity increased with ascending concentrations. A significant resistome enrichment of relative abundance in N. moseri gut microbiome at low-dose antibiotic treatment was noted. These results indicated that the gut microbiome in N. moseri was potentially more sensitive to antibiotics than C. sp. AL5866, which was supported by the greater relative abundance of key tetracycline-resistant genes in the gut microbiome of C. sp. AL5866 compared to N. moseri. Mite gut microbiomes were correlated with their associated resistomes, demonstrating the consistent changes between microbiome and resistome. Thus, this study showed that oxytetracycline amendment resulted in a dose-dependent and species-specific effect on the gut microbiomes and resistomes of two mite species. It will contribute to understanding the relationship between the soil mite gut microbiome and resistome under antibiotic exposure, and extend our knowledge regarding the emergence and transfer of resistomes in soil food webs.
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Affiliation(s)
- Fei Zheng
- School of Life Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xin-Li An
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guo-Wei Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Dong Zhu
- University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, DD2 5DA, Scotland, UK
| | - Bing Chen
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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28
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Kashinskaya EN, Simonov EP, Vlasenko PG, Markevich GN, Shokurova AV, Andree KB, Solovyev MM. The gut microbiota of Cystidicola farionis parasitizing the swim bladder of the nosed charr morph Salvelinus malma complex in Lake Kronotskoe (Kamchatka, Russia). J Nematol 2021; 53:e2021-106. [PMID: 34957411 PMCID: PMC8672423 DOI: 10.21307/jofnem-2021-106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 12/23/2022] Open
Abstract
Using the approach of sequencing the V3–V4 region of the 16S rRNA gene, we have analyzed the bacterial diversity associated with the gut and “body” (other parts of nematode after dissection: cuticle, epidermis and longitudinal muscles, etc) of Cystidicola farionis parasitizing the swim bladder of different morphotypes of the nosed charr. Comparisons of the gut microbiota of nematodes with their “body” has revealed that the associated microbiota are closely related to each other. Taxonomic analysis indicated that the relative abundances of the dominant nematode-associated bacteria varied with individual fish. The common dominant microbiota of the gut and “body” of nematodes were represented by Aeromonas, Pseudomonas, Shewanella, and Yersinia, while the associated microbiota of the swim bladder of the nosed charr was dominated by Acinetobacter, Cetobacterium, Pajaroellobacter, Paracoccus, Pseudomonas, Shewanella. By comparing the associated microbiota of nematode parasitizing the different morphotypes of the nosed charr the difference in richness estimates (number of OTU’s and Chao1) were revealed between the N1g and N2 morphs.
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Affiliation(s)
- E N Kashinskaya
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - E P Simonov
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,University of Tyumen, Institute of Environmental and Agricultural Biology (X-BIO), 25 Lenina St., Tyumen, 625003, Russia
| | - P G Vlasenko
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | | | - A V Shokurova
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia
| | - K B Andree
- Instituto de Investigación y Tecnología Agroalimentarias; Cultius Aquàtics; San Carlos de la Rapita, Tarragona, ES 08140, Spain
| | - M M Solovyev
- Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences; Research group of physiology and genetics of hydrobionts; Frunze St. 11, Novosibirsk, 630091, Russia.,Tomsk State University; Institute of Biology, Ecology, Soil Science, Agriculture, and Forestry; 36 Lenin Ave, Tomsk, 634050, Russia
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29
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Petersen C, Pees B, Martínez Christophersen C, Leippe M. Preconditioning With Natural Microbiota Strain Ochrobactrum vermis MYb71 Influences Caenorhabditis elegans Behavior. Front Cell Infect Microbiol 2021; 11:775634. [PMID: 34976859 PMCID: PMC8718863 DOI: 10.3389/fcimb.2021.775634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
In comparison with the standard monoxenic maintenance in the laboratory, rearing the nematode Caenorhabditis elegans on its natural microbiota improves its fitness and immunity against pathogens. Although C. elegans is known to exhibit choice behavior and pathogen avoidance behavior, little is known about whether C. elegans actively chooses its (beneficial) microbiota and whether the microbiota influences worm behavior. We examined eleven natural C. elegans isolates in a multiple-choice experiment for their choice behavior toward four natural microbiota bacteria and found that microbiota choice varied among C. elegans isolates. The natural C. elegans isolate MY2079 changed its choice behavior toward microbiota isolate Ochrobactrum vermis MYb71 in both multiple-choice and binary-choice experiments, in particular on proliferating bacteria: O. vermis MYb71 was chosen less than other microbiota bacteria or OP50, but only after preconditioning with MYb71. Examining escape behavior and worm fitness on MYb71, we ruled out pathogenicity of MYb71 and consequently learned pathogen avoidance behavior as the main driver of the behavioral change toward MYb71. The change in behavior of C. elegans MY2079 toward microbiota bacterium MYb71 demonstrates how the microbiota influences the worm's choice. These results might give a baseline for future research on host-microbiota interaction in the C. elegans model.
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Affiliation(s)
- Carola Petersen
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
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30
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Schiffer JA, Stumbur SV, Seyedolmohadesin M, Xu Y, Serkin WT, McGowan NG, Banjo O, Torkashvand M, Lin A, Hosea CN, Assié A, Samuel BS, O’Donnell MP, Venkatachalam V, Apfeld J. Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide. PLoS Pathog 2021; 17:e1010112. [PMID: 34941962 PMCID: PMC8699984 DOI: 10.1371/journal.ppat.1010112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/14/2021] [Indexed: 02/07/2023] Open
Abstract
Hydrogen peroxide (H2O2) is the most common chemical threat that organisms face. Here, we show that H2O2 alters the bacterial food preference of Caenorhabditis elegans, enabling the nematodes to find a safe environment with food. H2O2 induces the nematodes to leave food patches of laboratory and microbiome bacteria when those bacterial communities have insufficient H2O2-degrading capacity. The nematode's behavior is directed by H2O2-sensing neurons that promote escape from H2O2 and by bacteria-sensing neurons that promote attraction to bacteria. However, the input for H2O2-sensing neurons is removed by bacterial H2O2-degrading enzymes and the bacteria-sensing neurons' perception of bacteria is prevented by H2O2. The resulting cross-attenuation provides a general mechanism that ensures the nematode's behavior is faithful to the lethal threat of hydrogen peroxide, increasing the nematode's chances of finding a niche that provides both food and protection from hydrogen peroxide.
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Affiliation(s)
- Jodie A. Schiffer
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Stephanie V. Stumbur
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Maedeh Seyedolmohadesin
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Yuyan Xu
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - William T. Serkin
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Natalie G. McGowan
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Oluwatosin Banjo
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Mahdi Torkashvand
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Albert Lin
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ciara N. Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael P. O’Donnell
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Vivek Venkatachalam
- Physics Department, Northeastern University, Boston, Massachusetts, United States of America
| | - Javier Apfeld
- Biology Department, Northeastern University, Boston, Massachusetts, United States of America
- Bioengineering Department, Northeastern University, Boston, Massachusetts, United States of America
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31
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Bansept F, Obeng N, Schulenburg H, Traulsen A. Modeling host-associating microbes under selection. THE ISME JOURNAL 2021; 15:3648-3656. [PMID: 34158630 PMCID: PMC8630024 DOI: 10.1038/s41396-021-01039-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/28/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
The concept of fitness is often reduced to a single component, such as the replication rate in a given habitat. For species with multi-step life cycles, this can be an unjustified oversimplification, as every step of the life cycle can contribute to the overall reproductive success in a specific way. In particular, this applies to microbes that spend part of their life cycles associated to a host. In this case, there is a selection pressure not only on the replication rates, but also on the phenotypic traits associated to migrating from the external environment to the host and vice-versa (i.e., the migration rates). Here, we investigate a simple model of a microbial lineage living, replicating, migrating and competing in and between two compartments: a host and an environment. We perform a sensitivity analysis on the overall growth rate to determine the selection gradient experienced by the microbial lineage. We focus on the direction of selection at each point of the phenotypic space, defining an optimal way for the microbial lineage to increase its fitness. We show that microbes can adapt to the two-compartment life cycle through either changes in replication or migration rates, depending on the initial values of the traits, the initial distribution across the two compartments, the intensity of competition, and the time scales involved in the life cycle versus the time scale of adaptation (which determines the adequate probing time to measure fitness). Overall, our model provides a conceptual framework to study the selection on microbes experiencing a host-associated life cycle.
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Affiliation(s)
- Florence Bansept
- grid.419520.b0000 0001 2222 4708Max-Planck-Institute for Evolutionary Biology, Ploen, Germany
| | - Nancy Obeng
- grid.9764.c0000 0001 2153 9986Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- grid.419520.b0000 0001 2222 4708Max-Planck-Institute for Evolutionary Biology, Ploen, Germany ,grid.9764.c0000 0001 2153 9986Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany
| | - Arne Traulsen
- grid.419520.b0000 0001 2222 4708Max-Planck-Institute for Evolutionary Biology, Ploen, Germany
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Vega NM, Ludington WB. From a parts list to assembly instructions and an operating manual: how small host models can re-write microbiome theory. Curr Opin Microbiol 2021; 64:146-151. [PMID: 34739919 DOI: 10.1016/j.mib.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Nic M Vega
- Biology Department, Emory University, Atlanta, GA, United States.
| | - William B Ludington
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD, United States
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Zhu D, Delgado-Baquerizo M, Ding J, Gillings MR, Zhu YG. Trophic level drives the host microbiome of soil invertebrates at a continental scale. MICROBIOME 2021; 9:189. [PMID: 34544484 PMCID: PMC8454154 DOI: 10.1186/s40168-021-01144-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China. RESULTS Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web. CONCLUSIONS Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates. Video abstract.
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Affiliation(s)
- Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai, 264005, China
| | - Michael R Gillings
- Department of Biological Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, 2109, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
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Pees B, Johnke J, Möhl M, Hamerich IK, Leippe M, Petersen C. Microbes to-go: slugs as source for Caenorhabditis elegans microbiota acquisition. Environ Microbiol 2021; 23:6721-6733. [PMID: 34414649 DOI: 10.1111/1462-2920.15730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022]
Abstract
Research on the Caenorhabditis elegans microbiota only recently started, with little known about how C. elegans acquires its microbiota. Slugs live in the same habitat as C. elegans and are known vectors for the worm. Hence, we wondered how the passage through a slug affects the C. elegans gut microbiota and whether worms can acquire bacteria from the slug. Using fluorescently labelled microbiota and 16S rRNA gene amplicon sequencing, we evaluated microbiota persistence and acquisition in C. elegans after slug passage. We compared C. elegans gut microbiomes isolated from wild-caught slugs to the microbiomes of worms after experimental slug passage to compare similarities and differences in microbiome composition. We found that microbiota persists in C. elegans while passing the slug gut and that worms simultaneously acquire additional bacteria species from the slug. Although the amplicon sequencing variant (ASV) richness of worms from the experiment did not exceed the richness of worms that naturally occur in slugs, we found a high number of shared ASVs indicating the importance of commonly associated microbiota. We demonstrate that C. elegans can take advantage of its passage through the slug by acquiring new potential microbiota without losing its native microbiota.
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Affiliation(s)
- Barbara Pees
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Julia Johnke
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Michelle Möhl
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Inga K Hamerich
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Matthias Leippe
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Carola Petersen
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
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Huang Y, Sterken MG, van Zwet K, van Sluijs L, Pijlman GP, Kammenga JE. Heat Stress Reduces the Susceptibility of Caenorhabditis elegans to Orsay Virus Infection. Genes (Basel) 2021; 12:1161. [PMID: 34440335 PMCID: PMC8392475 DOI: 10.3390/genes12081161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
The nematode Caenorhabditis elegans has been a versatile model for understanding the molecular responses to abiotic stress and pathogens. In particular, the response to heat stress and virus infection has been studied in detail. The Orsay virus (OrV) is a natural virus of C. elegans and infection leads to intracellular infection and proteostatic stress, which activates the intracellular pathogen response (IPR). IPR related gene expression is regulated by the genes pals-22 and pals-25, which also control thermotolerance and immunity against other natural pathogens. So far, we have a limited understanding of the molecular responses upon the combined exposure to heat stress and virus infection. We test the hypothesis that the response of C. elegans to OrV infection and heat stress are co-regulated and may affect each other. We conducted a combined heat-stress-virus infection assay and found that after applying heat stress, the susceptibility of C. elegans to OrV was decreased. This difference was found across different wild types of C. elegans. Transcriptome analysis revealed a list of potential candidate genes associated with heat stress and OrV infection. Subsequent mutant screens suggest that pals-22 provides a link between viral response and heat stress, leading to enhanced OrV tolerance of C. elegans after heat stress.
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Affiliation(s)
- Yuqing Huang
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (Y.H.); (M.G.S.); (K.v.Z.); (L.v.S.)
| | - Mark G. Sterken
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (Y.H.); (M.G.S.); (K.v.Z.); (L.v.S.)
| | - Koen van Zwet
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (Y.H.); (M.G.S.); (K.v.Z.); (L.v.S.)
| | - Lisa van Sluijs
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (Y.H.); (M.G.S.); (K.v.Z.); (L.v.S.)
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands;
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (Y.H.); (M.G.S.); (K.v.Z.); (L.v.S.)
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Han R, Wang Y, Deng Y, Zhang Y, Zhang L, Niu Q. Stenotrophomonas strain CPCC 101271, an intestinal lifespan-prolonging bacterium for Caenorhabditis elegans that assists in host resistance to "Bacillus nematocida" colonization. Arch Microbiol 2021; 203:4951-4960. [PMID: 34258643 PMCID: PMC8502144 DOI: 10.1007/s00203-021-02467-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022]
Abstract
The soil-dwelling, opportunistic pathogenic bacterium "Bacillus nematocida" B16 exhibits strong killing activities against a variety of pathogenic nematodes via a “Trojan horse” mechanism that can kill worm species like Caenorhabditis elegans. The bacterial strain CPCC 101271 was previously isolated from the intestines of C. elegans that were recovered from natural habitats and can serve as a probiotic for C. elegans, while also assisting in resistance to infection by the pathogenic strain B16. In this study, the lifespan of C. elegans fed with strain CPCC 101271 cells was extended by approximately 40% compared with that of worms fed with Escherichia coli OP50 cells. In addition, the colonization of C. elegans by the pathogenic bacterium "B. nematocida" B16 was inhibited when pre-fed with strain CPCC 101271. Metagenomic sequence analysis of intestinal microbiota of C. elegans fed with strain CPCC 101271 and infected with B16 revealed that pre-feeding worms with CPCC 101271 improved the diversity of the intestinal bacteria. Moreover, community structure significantly varied in coordination with Stenotrophomonas spp. and Bacillus spp. abundances when competition between strains CPCC 101271 and B16 was evaluated. In conclusion, the nematode microbiota strain CPCC 101271 assisted in its host resistance to colonization by the pathogen "Bacillus nematocida" and can also promote life span-prolongation in C. elegans. These results underscore that understanding the interactions between C. elegans microbiota and pathogens can provide new insights into achieving effective biological control of agricultural pests.
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Affiliation(s)
- Rui Han
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yu Wang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lin Zhang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
| | - Qiuhong Niu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
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Ortiz A, Vega NM, Ratzke C, Gore J. Interspecies bacterial competition regulates community assembly in the C. elegans intestine. THE ISME JOURNAL 2021; 15:2131-2145. [PMID: 33589765 PMCID: PMC8245486 DOI: 10.1038/s41396-021-00910-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host-microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species' taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host-microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.
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Affiliation(s)
- Anthony Ortiz
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Nicole M. Vega
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.189967.80000 0001 0941 6502Present Address: Department of Biology, Emory University, Atlanta, GA USA
| | - Christoph Ratzke
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.10392.390000 0001 2190 1447Present Address: Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘CMFI’, University of Tübingen, Tübingen, Germany
| | - Jeff Gore
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
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Zhang F, Weckhorst JL, Assié A, Hosea C, Ayoub CA, Khodakova AS, Cabrera ML, Vidal Vilchis D, Félix MA, Samuel BS. Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut. Curr Biol 2021; 31:2603-2618.e9. [PMID: 34048707 PMCID: PMC8222194 DOI: 10.1016/j.cub.2021.04.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the strain-level phylogenetic diversity naturally encountered by C. elegans in the wild. Using this community, we show that C. elegans utilizes immune, xenobiotic, and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of DAF-2/IGFR and modulated by the competitive action of insulin signaling transcription factors DAF-16/FOXO and PQM-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum as adults is correlated with faster animal growth rates and larger body size at the end of development. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of gut microbiome composition in C. elegans.
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Affiliation(s)
- Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jessica L Weckhorst
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Ciara Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christopher A Ayoub
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Anastasia S Khodakova
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Mario Loeza Cabrera
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniela Vidal Vilchis
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Marie-Anne Félix
- Ecole Normale Supérieure, IBENS, CNRS UMR8197, INSERM U1024, Paris, France
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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Renwick S, Ganobis CM, Elder RA, Gianetto-Hill C, Higgins G, Robinson AV, Vancuren SJ, Wilde J, Allen-Vercoe E. Culturing Human Gut Microbiomes in the Laboratory. Annu Rev Microbiol 2021; 75:49-69. [PMID: 34038159 DOI: 10.1146/annurev-micro-031021-084116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Simone Renwick
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Caroline M Ganobis
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Riley A Elder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Connor Gianetto-Hill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Gregory Higgins
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Avery V Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Jacob Wilde
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada; , , , , , , , ,
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Haçariz O, Viau C, Karimian F, Xia J. The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension. BMC Genomics 2021; 22:364. [PMID: 34011272 PMCID: PMC8136213 DOI: 10.1186/s12864-021-07695-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
Background A healthy microbiome influences host physiology through a mutualistic relationship, which can be important for the host to cope with cellular stress by promoting fitness and survival. The mammalian microbiome is highly complex and attributing host phenotypes to a specific member of the microbiome can be difficult. The model organism Caenorhabditis elegans and its native microbiome, discovered recently, can serve as a more tractable, experimental model system to study host-microbiome interactions. In this study, we investigated whether certain members of C. elegans native microbiome would offer a benefit to their host and putative molecular mechanisms using a combination of phenotype screening, omics profiling and functional validation. Results A total of 16 members of C. elegans microbiome were screened under chemically-induced toxicity. Worms grown with Chryseobacterium sp. CHNTR56 MYb120 or Comamonas sp. 12022 MYb131, were most resistant to oxidative chemical stress (SiO2 nanoparticles and juglone), as measured by progeny output. Further investigation showed that Chryseobacterium sp. CHNTR56 positively influenced the worm’s lifespan, whereas the combination of both isolates had a synergistic effect. RNAseq analysis of young adult worms, grown with either isolate, revealed the enrichment of cellular detoxification mechanisms (glutathione metabolism, drug metabolism and metabolism of xenobiotics) and signaling pathways (TGF-beta and Wnt signaling pathways). Upregulation of cysteine synthases (cysl genes) in the worms, associated with glutathione metabolism, was also observed. Nanopore sequencing uncovered that the genomes of the two isolates have evolved to favor the specific route of the de novo synthesis pathway of vitamin B6 (cofactor of cysl enzymes) through serC or pdxA2 homologs. Finally, co-culture with vitamin B6 extended worm lifespan. Conclusions In summary, our study indicates that certain colonizing members of C. elegans have genomic diversity in vitamin B6 synthesis and promote host fitness and lifespan extension. The regulation of host cellular detoxification genes (i.e. gst) along with cysl genes at the transcriptome level and the bacterium-specific vitamin B6 synthesis mechanism at the genome level are in an agreement with enhanced host glutathione-based cellular detoxification due to this interspecies relationship. C. elegans is therefore a promising alternative model to study host-microbiome interactions in host fitness and lifespan. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07695-y.
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Affiliation(s)
- Orçun Haçariz
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Charles Viau
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Farial Karimian
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada. .,Department of Animal Science, McGill University, Montreal, Quebec, Canada.
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41
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Backes C, Martinez-Martinez D, Cabreiro F. C. elegans: A biosensor for host-microbe interactions. Lab Anim (NY) 2021; 50:127-135. [PMID: 33649581 DOI: 10.1038/s41684-021-00724-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/27/2021] [Indexed: 01/31/2023]
Abstract
Microbes are an integral part of life on this planet. Microbes and their hosts influence each other in an endless dance that shapes how the meta-organism interacts with its environment. Although great advances have been made in microbiome research over the past 20 years, the mechanisms by which both hosts and their microbes interact with each other and the environment are still not well understood. The nematode Caenorhabditis elegans has been widely used as a model organism to study a remarkable number of human-like processes. Recent evidence shows that the worm is a powerful tool to investigate in fine detail the complexity that exists in microbe-host interactions. By combining the large array of genetic tools available for both organisms together with deep phenotyping approaches, it has been possible to uncover key effectors in the complex relationship between microbes and their hosts. In this perspective, we survey the literature for insightful discoveries in the microbiome field using the worm as a model. We discuss the latest conceptual and technological advances in the field and highlight the strengths that make C. elegans a valuable biosensor tool for the study of microbe-host interactions.
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Affiliation(s)
- Cassandra Backes
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | | | - Filipe Cabreiro
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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Host Immunity Alters Community Ecology and Stability of the Microbiome in a Caenorhabditis elegans Model. mSystems 2021; 6:6/2/e00608-20. [PMID: 33879498 PMCID: PMC8561663 DOI: 10.1128/msystems.00608-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A growing body of data suggests that the microbiome of a species can vary considerably from individual to individual, but the reasons for this variation—and the consequences for the ecology of these communities—remain only partially explained. In mammals, the emerging picture is that the metabolic state and immune system status of the host affect the composition of the microbiome, but quantitative ecological microbiome studies are challenging to perform in higher organisms. Here, we show that these phenomena can be quantitatively analyzed in the tractable nematode host Caenorhabditis elegans. Mutants in innate immunity, in particular the DAF-2/insulin growth factor (IGF) pathway, are shown to contain a microbiome that differs from that of wild-type nematodes. We analyzed the underlying basis of these differences from the perspective of community ecology by comparing experimental observations to the predictions of a neutral sampling model and concluded that fundamental differences in microbiome ecology underlie the observed differences in microbiome composition. We tested this hypothesis by introducing a minor perturbation into the colonization conditions, allowing us to assess stability of communities in different host strains. Our results show that altering host immunity changes the importance of interspecies interactions within the microbiome, resulting in differences in community composition and stability that emerge from these differences in host-microbe ecology. IMPORTANCE Here, we used a Caenorhabditis elegans microbiome model to demonstrate how genetic differences in innate immunity alter microbiome composition, diversity, and stability by changing the ecological processes that shape these communities. These results provide insight into the role of host genetics in controlling the ecology of the host-associated microbiota, resulting in differences in community composition, successional trajectories, and response to perturbation.
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Take a Walk to the Wild Side of Caenorhabditis elegans-Pathogen Interactions. Microbiol Mol Biol Rev 2021; 85:85/2/e00146-20. [PMID: 33731489 DOI: 10.1128/mmbr.00146-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Microbiomes form intimate functional associations with their hosts. Much has been learned from correlating changes in microbiome composition to host organismal functions. However, in-depth functional studies require the manipulation of microbiome composition coupled with the precise interrogation of organismal physiology-features available in few host study systems. Caenorhabditis elegans has proven to be an excellent genetic model organism to study innate immunity and, more recently, microbiome interactions. The study of C. elegans-pathogen interactions has provided in depth understanding of innate immune pathways, many of which are conserved in other animals. However, many bacteria were chosen for these studies because of their convenience in the lab setting or their implication in human health rather than their native interactions with C. elegans In their natural environment, C. elegans feed on a variety of bacteria found in rotting organic matter, such as rotting fruits, flowers, and stems. Recent work has begun to characterize the native microbiome and has identified a common set of bacteria found in the microbiome of C. elegans While some of these bacteria are beneficial to C. elegans health, others are detrimental, leading to a complex, multifaceted understanding of bacterium-nematode interactions. Current research on nematode-bacterium interactions is focused on these native microbiome components, both their interactions with each other and with C. elegans We will summarize our knowledge of bacterial pathogen-host interactions in C. elegans, as well as recent work on the native microbiome, and explore the incorporation of these bacterium-nematode interactions into studies of innate immunity and pathogenesis.
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Zimmermann J, Kaleta C, Waschina S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol 2021; 22:81. [PMID: 33691770 PMCID: PMC7949252 DOI: 10.1186/s13059-021-02295-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.
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Affiliation(s)
- Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
| | - Christoph Kaleta
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
| | - Silvio Waschina
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
- Christian-Albrechts-University Kiel, Institute of Human Nutrition and Food Science, Nutriinformatics, Heinrich-Hecht-Platz 10, Kiel, 24118 Germany
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Abstract
In its natural habitat, C. elegans encounters a wide variety of microbes, including food, commensals and pathogens. To be able to survive long enough to reproduce, C. elegans has developed a complex array of responses to pathogens. These activities are coordinated on scales that range from individual organelles to the entire organism. Often, the response is triggered within cells, by detection of infection-induced damage, mainly in the intestine or epidermis. C. elegans has, however, a capacity for cell non-autonomous regulation of these responses. This frequently involves the nervous system, integrating pathogen recognition, altering host biology and governing avoidance behavior. Although there are significant differences with the immune system of mammals, some mechanisms used to limit pathogenesis show remarkable phylogenetic conservation. The past 20 years have witnessed an explosion of host-pathogen interaction studies using C. elegans as a model. This review will discuss the broad themes that have emerged and highlight areas that remain to be fully explored.
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Affiliation(s)
- Céline N Martineau
- Aix Marseille Université, Inserm, CNRS, CIML, Turing Centre for Living Systems, Marseille, France
| | | | - Nathalie Pujol
- Aix Marseille Université, Inserm, CNRS, CIML, Turing Centre for Living Systems, Marseille, France.
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Obeng N, Bansept F, Sieber M, Traulsen A, Schulenburg H. Evolution of Microbiota-Host Associations: The Microbe's Perspective. Trends Microbiol 2021; 29:779-787. [PMID: 33674142 DOI: 10.1016/j.tim.2021.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
Microbiota-host associations are ubiquitous in nature. They are often studied using a host-centered view, while microbes are assumed to have coevolved with hosts or colonize hosts as nonadapted entities. Both assumptions are often incorrect. Instead, many host-associated microbes are adapted to a biphasic life cycle in which they alternate between noncoadapted hosts and a free-living phase. Full appreciation of microbiota-host symbiosis thus needs to consider how microbes optimize fitness across this life cycle. Here, we evaluate the key stages of the biphasic life cycle and propose a new conceptual framework for microbiota-host interactions which includes an integrative measure of microbial fitness, related to the parasite fitness parameter R0, and which will help in-depth assessment of the evolution of these widespread associations.
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Affiliation(s)
- Nancy Obeng
- Department of Evolutionary Ecology and Genetics, University of Kiel, Am Botanischen Garten 1- 9, 24118 Kiel, Germany
| | - Florence Bansept
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Michael Sieber
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Arne Traulsen
- Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Am Botanischen Garten 1- 9, 24118 Kiel, Germany; Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Ploen, Germany.
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47
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Zimmermann M, Patil KR, Typas A, Maier L. Towards a mechanistic understanding of reciprocal drug-microbiome interactions. Mol Syst Biol 2021; 17:e10116. [PMID: 33734582 PMCID: PMC7970330 DOI: 10.15252/msb.202010116] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/10/2021] [Accepted: 01/25/2021] [Indexed: 02/06/2023] Open
Abstract
Broad-spectrum antibiotics target multiple gram-positive and gram-negative bacteria, and can collaterally damage the gut microbiota. Yet, our knowledge of the extent of damage, the antibiotic activity spectra, and the resistance mechanisms of gut microbes is sparse. This limits our ability to mitigate microbiome-facilitated spread of antibiotic resistance. In addition to antibiotics, non-antibiotic drugs affect the human microbiome, as shown by metagenomics as well as in vitro studies. Microbiome-drug interactions are bidirectional, as microbes can also modulate drugs. Chemical modifications of antibiotics mostly function as antimicrobial resistance mechanisms, while metabolism of non-antibiotics can also change the drugs' pharmacodynamic, pharmacokinetic, and toxic properties. Recent studies have started to unravel the extensive capacity of gut microbes to metabolize drugs, the mechanisms, and the relevance of such events for drug treatment. These findings raise the question whether and to which degree these reciprocal drug-microbiome interactions will differ across individuals, and how to take them into account in drug discovery and precision medicine. This review describes recent developments in the field and discusses future study areas that will benefit from systems biology approaches to better understand the mechanistic role of the human gut microbiota in drug actions.
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Affiliation(s)
- Michael Zimmermann
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- The Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Athanasios Typas
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenTübingenGermany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’University of TübingenTübingenGermany
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Dirksen P, Assié A, Zimmermann J, Zhang F, Tietje AM, Marsh SA, Félix MA, Shapira M, Kaleta C, Schulenburg H, Samuel BS. CeMbio - The Caenorhabditis elegans Microbiome Resource. G3 (BETHESDA, MD.) 2020; 10:3025-3039. [PMID: 32669368 PMCID: PMC7466993 DOI: 10.1534/g3.120.401309] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/07/2020] [Indexed: 12/23/2022]
Abstract
The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.
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Affiliation(s)
- Philipp Dirksen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
| | - Johannes Zimmermann
- Medical Systems Biology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
| | - Adina-Malin Tietje
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | | | - Marie-Anne Félix
- Institute of Biology of the Ecole Normale Supérieure, Paris, France
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley CA
| | - Christoph Kaleta
- Medical Systems Biology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
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Dierking K, Pita L. Receptors Mediating Host-Microbiota Communication in the Metaorganism: The Invertebrate Perspective. Front Immunol 2020; 11:1251. [PMID: 32612612 PMCID: PMC7308585 DOI: 10.3389/fimmu.2020.01251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022] Open
Abstract
Multicellular organisms live in close association with a plethora of microorganism, which have a profound effect on multiple host functions. As such, the microbiota and its host form an intimate functional entity, termed the metaorganism or holobiont. But how does the metaorganism communicate? Which receptors recognize microbial signals, mediate the effect of the microbiota on host physiology or regulate microbiota composition and homeostasis? In this review we provide an overview on the function of different receptor classes in animal host-microbiota communication. We put a special focus on invertebrate hosts, including both traditional invertebrate models such as Drosophila melanogaster and Caenorhabditis elegans and “non-model” invertebrates in microbiota research. Finally, we highlight the potential of invertebrate systems in studying mechanism of host-microbiota interactions.
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Affiliation(s)
- Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Lucía Pita
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
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Syntrophic splitting of central carbon metabolism in host cells bearing functionally different symbiotic bacteria. ISME JOURNAL 2020; 14:1982-1993. [PMID: 32350409 DOI: 10.1038/s41396-020-0661-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023]
Abstract
Insects feeding on the nutrient-poor diet of xylem plant sap generally bear two microbial symbionts that are localized to different organs (bacteriomes) and provide complementary sets of essential amino acids (EAAs). Here, we investigate the metabolic basis for the apparent paradox that xylem-feeding insects are under intense selection for metabolic efficiency but incur the cost of maintaining two symbionts for functions mediated by one symbiont in other associations. Using stable isotope analysis of central carbon metabolism and metabolic modeling, we provide evidence that the bacteriomes of the spittlebug Clastoptera proteus display high rates of aerobic glycolysis, with syntrophic splitting of glucose oxidation. Specifically, our data suggest that one bacteriome (containing the bacterium Sulcia, which synthesizes seven EAAs) predominantly processes glucose glycolytically, producing pyruvate and lactate, and the exported pyruvate and lactate is assimilated by the second bacteriome (containing the bacterium Zinderia, which synthesizes three energetically costly EAAs) and channeled through the TCA cycle for energy generation by oxidative phosphorylation. We, furthermore, calculate that this metabolic arrangement supports the high ATP demand in Zinderia bacteriomes for Zinderia-mediated synthesis of energy-intensive EAAs. We predict that metabolite cross-feeding among host cells may be widespread in animal-microbe symbioses utilizing low-nutrient diets.
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