1
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Rohner PT, Moczek AP. Vertically inherited microbiota and environment modifying behaviours conceal genetic variation in dung beetle life history. Proc Biol Sci 2024; 291:20240122. [PMID: 38628120 PMCID: PMC11021930 DOI: 10.1098/rspb.2024.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/15/2024] [Indexed: 04/19/2024] Open
Abstract
Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feed back on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating (i) physical environmental modifications and (ii) the vertical inheritance of microbes, we assess how environment modifying behaviour and microbiome transmission shape heritable variation and evolutionary potential. We found that depriving larvae of symbionts and environment modifying behaviours increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that are less amenable to organismal manipulation or restructuring. Our findings also suggest that intact microbiomes, which are commonly thought to increase genetic variation of their hosts, may instead reduce and conceal heritable variation. More broadly, our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.
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Affiliation(s)
- Patrick T. Rohner
- Department of Ecology, Behavior, and Evolution, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
| | - Armin P. Moczek
- Department of Biology, Indiana University Bloomington, Bloomington, IN 47405, USA
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2
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Fromm E, Zinger L, Pellerin F, Di Gesu L, Jacob S, Winandy L, Aguilée R, Parthuisot N, Iribar A, White J, Bestion E, Cote J. Warming effects on lizard gut microbiome depend on habitat connectivity. Proc Biol Sci 2024; 291:20240220. [PMID: 38654642 PMCID: PMC11040258 DOI: 10.1098/rspb.2024.0220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024] Open
Abstract
Climate warming and landscape fragmentation are both factors well known to threaten biodiversity and to generate species responses and adaptation. However, the impact of warming and fragmentation interplay on organismal responses remains largely under-explored, especially when it comes to gut symbionts, which may play a key role in essential host functions and traits by extending its functional and genetic repertoire. Here, we experimentally examined the combined effects of climate warming and habitat connectivity on the gut bacterial communities of the common lizard (Zootoca vivipara) over three years. While the strength of effects varied over the years, we found that a 2°C warmer climate decreases lizard gut microbiome diversity in isolated habitats. However, enabling connectivity among habitats with warmer and cooler climates offset or even reversed warming effects. The warming effects and the association between host dispersal behaviour and microbiome diversity appear to be a potential driver of this interplay. This study suggests that preserving habitat connectivity will play a key role in mitigating climate change impacts, including the diversity of the gut microbiome, and calls for more studies combining multiple anthropogenic stressors when predicting the persistence of species and communities through global changes.
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Affiliation(s)
- Emma Fromm
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, 66055-090, Belém, Pará, Brazil
| | - Félix Pellerin
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
| | - Lucie Di Gesu
- Station d'Écologie Théorique et Expérimentale (SETE), UAR2029, CNRS, Moulis, France
| | - Staffan Jacob
- Station d'Écologie Théorique et Expérimentale (SETE), UAR2029, CNRS, Moulis, France
| | - Laurane Winandy
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
- High Fens Scientific Station, Freshwater and Oceanic Science Unit of Research (FOCUS), University of Liege, Liege, Belgium
| | - Robin Aguilée
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
| | - Nathalie Parthuisot
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
| | - Amaia Iribar
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
| | - Joël White
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
- École Nationale Supérieure de Formation de l'Enseignement Agricole, 2 Route de Narbonne, 31320 Castanet-Tolosan, France
| | - Elvire Bestion
- Station d'Écologie Théorique et Expérimentale (SETE), UAR2029, CNRS, Moulis, France
| | - Julien Cote
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Abstract
The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, California 94720, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
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Kononova S, Litvinova E, Vakhitov T, Skalinskaya M, Sitkin S. Acceptive Immunity: The Role of Fucosylated Glycans in Human Host-Microbiome Interactions. Int J Mol Sci 2021; 22:ijms22083854. [PMID: 33917768 PMCID: PMC8068183 DOI: 10.3390/ijms22083854] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
The growth in the number of chronic non-communicable diseases in the second half of the past century and in the first two decades of the new century is largely due to the disruption of the relationship between the human body and its symbiotic microbiota, and not pathogens. The interaction of the human immune system with symbionts is not accompanied by inflammation, but is a physiological norm. This is achieved via microbiota control by the immune system through a complex balance of pro-inflammatory and suppressive responses, and only a disturbance of this balance can trigger pathophysiological mechanisms. This review discusses the establishment of homeostatic relationships during immune system development and intestinal bacterial colonization through the interaction of milk glycans, mucins, and secretory immunoglobulins. In particular, the role of fucose and fucosylated glycans in the mechanism of interactions between host epithelial and immune cells is discussed.
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Affiliation(s)
- Svetlana Kononova
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
| | - Ekaterina Litvinova
- Scientific-Research Institute of Neurosciences and Medicine, 630117 Novosibirsk, Russia;
- Siberian Federal Scientific Center of Agro-BioTechnologies, Russian Academy of Sciences, Krasnoobsk, 633501 Novosibirsk, Russia
| | - Timur Vakhitov
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
| | - Maria Skalinskaya
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Department of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University Named after I.I. Mechnikov, 191015 St. Petersburg, Russia
| | - Stanislav Sitkin
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Department of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University Named after I.I. Mechnikov, 191015 St. Petersburg, Russia
- Institute of Perinatology and Pediatrics, Almazov National Medical Research Centre, 197341 St. Petersburg, Russia
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6
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Norton JE Jr, Kommineni S, Akrivoulis P, Gutierrez DA, Hazuda DJ, Swaminathan G. Primary Human Dendritic Cells and Whole-Blood Based Assays to Evaluate Immuno-Modulatory Properties of Heat-Killed Commensal Bacteria. Vaccines (Basel) 2021; 9:225. [PMID: 33807734 DOI: 10.3390/vaccines9030225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022] Open
Abstract
There is mounting evidence that the microbiome plays a critical role in training and maturation of the host immune system. Pre-clinical and clinical studies have shown that microbiome perturbation is correlated with sub-optimal host responses to vaccines and cancer immunotherapy. As such, identifying species of commensal bacteria capable of modulating immunological outcomes is of considerable interest. Currently, the lack of reliable primary immune cell-based assays capable of differentiating immuno-modulatory properties of various commensal bacteria is a major limitation. Here, we demonstrate that primary human monocyte-derived dendritic cells (MoDC) are capable of stratifying different strains of live and heat-killed commensal bacteria in an in vitro culture system. Specifically, heat-killed bacterial strains were able to differentially modulate co-stimulation/maturation markers CD80, CD83, and HLA-DR, as well as cytokine/chemokine signatures, such as IL-1b, MIP-1a, and TNFa in primary human MoDC. We further validated our observations using the TruCulture® (Myriad RBM, Inc., Austin, TX, USA) whole-blood ex vivo culture system. Using this ex vivo system allowed us to measure immune-altering effects of commensal bacteria in primary human whole-blood. As such, we report that both these primary in vitro and ex vivo systems are robust and enable identification, stratification, and differentiation of various commensal bacteria as potential modulators of host immunity.
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7
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Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN. Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes 2021; 13:1965698. [PMID: 34455914 PMCID: PMC8432618 DOI: 10.1080/19490976.2021.1965698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.
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Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Erin R. Shanahan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Andrew J. Holmes
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Mark N. Read
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, Australia
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8
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Abstract
Host-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host-microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic.
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Affiliation(s)
- Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudia Arabia;
| | - Derek M Harkins
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
| | - Karen E Nelson
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
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9
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Abstract
To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
| | - Benjamin J Callahan
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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10
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Abstract
To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. This article is part of the theme issue ‘The role of the microbiome in host evolution’.
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Affiliation(s)
- Michael R McLaren
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA
| | - Benjamin J Callahan
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC 27607, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA
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11
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Abstract
The human gut is important for food digestion and absorption, as well as a venue for a large number of microorganisms that coexist with the host. Although numerous in vitro models have been proposed to study intestinal pathology or interactions between intestinal microbes and host, they are far from recapitulating the real intestinal microenvironment in vivo. To assist researchers in further understanding gut physiology, the intestinal microbiome, and disease processes, a novel technology primarily based on microfluidics and cell biology, called "gut-on-chip," was developed to simulate the structure, function, and microenvironment of the human gut. In this review, we first introduce various types of gut-on-chip systems, then highlight their applications in drug pharmacokinetics, host-gut microbiota crosstalk, and nutrition metabolism. Finally, we discuss challenges in this field and prospects for better understanding interactions between intestinal flora and human hosts, and then provide guidance for clinical treatment of related diseases.
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Affiliation(s)
- Yunqing Xiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yue Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiongfei Fu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuqiang Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
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12
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Dickson RP, Erb-Downward JR, Falkowski NR, Hunter EM, Ashley SL, Huffnagle GB. The Lung Microbiota of Healthy Mice Are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity. Am J Respir Crit Care Med 2019. [PMID: 29533677 DOI: 10.1164/rccm.201711-2180oc] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RATIONALE The "gut-lung axis" is commonly invoked to explain the microbiome's influence on lung inflammation. Yet the lungs harbor their own microbiome, which is altered in respiratory disease. The relative influence of gut and lung bacteria on lung inflammation is unknown. OBJECTIVES To determine whether baseline lung immune tone reflects local (lung-lung) or remote (gut-lung) microbe-host interactions. METHODS We compared lung, tongue, and cecal bacteria in 40 healthy, genetically identical, 10-week-old mice, using 16S ribosomal RNA gene quantification and sequencing. We measured inflammatory cytokines, using a multiplex assay of homogenized lung tissue. We compared lung bacteria in healthy mice treated with varied durations of systemic antibiotics. MEASUREMENTS AND MAIN RESULTS Lung bacterial communities are highly variable among mice, cluster strongly by cage, shipment, and vendor, and are altered by antibiotics in a microbiologically predictable manner. Baseline lung concentrations of two key inflammatory cytokines (IL-1α and IL-4) are correlated with the diversity and community composition of lung bacterial communities. Lung concentrations of these inflammatory cytokines correlate more strongly with variation in lung bacterial communities than with that of the gut or mouth. CONCLUSIONS In the lungs of healthy mice, baseline innate immune tone more strongly reflects local (lung-lung) microbe-host interactions than remote (gut-lung) microbe-host interactions. Our results independently confirm the existence and immunologic significance of the murine lung microbiome, even in health. Variation in lung microbiota is likely an important, underappreciated source of experimental and clinical variability. The lung microbiome is an unexplored therapeutic target for the prevention and treatment of inflammatory lung disease.
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Affiliation(s)
- Robert P Dickson
- 1 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and.,2 Michigan Center for Integrative Research in Critical Care, Ann Arbor, Michigan; and
| | - John R Erb-Downward
- 1 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and
| | - Nicole R Falkowski
- 1 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and
| | - Ellen M Hunter
- 1 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and
| | - Shanna L Ashley
- 1 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and
| | - Gary B Huffnagle
- 1 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and.,3 Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan.,4 Department of Molecular, Cellular, and Developmental Biology and.,5 Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, Michigan
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13
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Rosario D, Benfeitas R, Bidkhori G, Zhang C, Uhlen M, Shoaie S, Mardinoglu A. Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling. Front Physiol 2018; 9:775. [PMID: 29988585 PMCID: PMC6026676 DOI: 10.3389/fphys.2018.00775] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Dysbiosis in the gut microbiome composition may be promoted by therapeutic drugs such as metformin, the world’s most prescribed antidiabetic drug. Under metformin treatment, disturbances of the intestinal microbes lead to increased abundance of Escherichia spp., Akkermansia muciniphila, Subdoligranulum variabile and decreased abundance of Intestinibacter bartlettii. This alteration may potentially lead to adverse effects on the host metabolism, with the depletion of butyrate producer genus. However, an increased production of butyrate and propionate was verified in metformin-treated Type 2 diabetes (T2D) patients. The mechanisms underlying these nutritional alterations and their relation with gut microbiota dysbiosis remain unclear. Here, we used Genome-scale Metabolic Models of the representative gut bacteria Escherichia spp., I. bartlettii, A. muciniphila, and S. variabile to elucidate their bacterial metabolism and its effect on intestinal nutrient pool, including macronutrients (e.g., amino acids and short chain fatty acids), minerals and chemical elements (e.g., iron and oxygen). We applied flux balance analysis (FBA) coupled with synthetic lethality analysis interactions to identify combinations of reactions and extracellular nutrients whose absence prevents growth. Our analyses suggest that Escherichia sp. is the bacteria least vulnerable to nutrient availability. We have also examined bacterial contribution to extracellular nutrients including short chain fatty acids, amino acids, and gasses. For instance, Escherichia sp. and S. variabile may contribute to the production of important short chain fatty acids (e.g., acetate and butyrate, respectively) involved in the host physiology under aerobic and anaerobic conditions. We have also identified pathway susceptibility to nutrient availability and reaction changes among the four bacteria using both FBA and flux variability analysis. For instance, lipopolysaccharide synthesis, nucleotide sugar metabolism, and amino acid metabolism are pathways susceptible to changes in Escherichia sp. and A. muciniphila. Our observations highlight important commensal and competing behavior, and their association with cellular metabolism for prevalent gut microbes. The results of our analysis have potential important implications for development of new therapeutic approaches in T2D patients through the development of prebiotics, probiotics, or postbiotics.
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Affiliation(s)
- Dorines Rosario
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Rui Benfeitas
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Gholamreza Bidkhori
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Dental Institute, King's College London, London, United Kingdom.,Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R. Functional Genomics of Host-Microbiome Interactions in Humans. Trends Genet. 2018;34:30-40. [PMID: 29107345 DOI: 10.1016/j.tig.2017.10.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 02/06/2023]
Abstract
The human microbiome has been linked to various host phenotypes and has been implicated in many complex human diseases. Recent genome-wide association studies (GWASs) have used microbiome variation as a complex trait and have uncovered human genetic variants that are associated with the microbiome. Here we summarize results from these studies and illustrate potential regulatory mechanisms by which host genetic variation can interact with microbiome composition. We argue that, similar to human GWASs, it is important to use functional genomics techniques to gain a mechanistic understanding of causal host-microbiome interactions and their role in human disease. We highlight experimental, functional, and computational genomics methodologies for the study of the genomic basis of host-microbiome interactions and describe how these approaches can be utilized to explain how human genetic variation can modulate the effects of the microbiome on the host.
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15
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Antwis RE, Griffiths SM, Harrison XA, Aranega-Bou P, Arce A, Bettridge AS, Brailsford FL, de Menezes A, Devaynes A, Forbes KM, Fry EL, Goodhead I, Haskell E, Heys C, James C, Johnston SR, Lewis GR, Lewis Z, Macey MC, McCarthy A, McDonald JE, Mejia-Florez NL, O'Brien D, Orland C, Pautasso M, Reid WDK, Robinson HA, Wilson K, Sutherland WJ. Fifty important research questions in microbial ecology. FEMS Microbiol Ecol 2017; 93:3098413. [PMID: 28379446 DOI: 10.1093/femsec/fix044] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/31/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.
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Affiliation(s)
- Rachael E Antwis
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, Greater Manchester M1 5GD, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, London NW1 4RY, UK
| | - Paz Aranega-Bou
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Andres Arce
- Silwood Park, Faculty of Natural Sciences, Imperial College London, London, London SW7 2AZ, UK
| | - Aimee S Bettridge
- School of Biosciences, Cardiff University, Cardiff, South Glamorgan CF10 3XQ, UK
| | - Francesca L Brailsford
- School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Alexandre de Menezes
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Andrew Devaynes
- Biosciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
| | - Kristian M Forbes
- Department of Virology, University of Helsinki, Helsinki 00014, Finland
| | - Ellen L Fry
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK
| | - Ian Goodhead
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Erin Haskell
- Department of Biology, University of York, York, North Yorkshire YO10 5DD, UK
| | - Chloe Heys
- Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK
| | - Chloe James
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford M5 4WT, UK
| | - Sarah R Johnston
- School of Biosciences, Cardiff University, Cardiff, South Glamorgan CF10 3XQ, UK
| | - Gillian R Lewis
- Biosciences, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK
| | - Zenobia Lewis
- Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK
| | - Michael C Macey
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Alan McCarthy
- Institute of Integrative Biology/School of Life Sciences, University of Liverpool, Liverpool, Merseyside L69 3BX, UK
| | - James E McDonald
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | | | | | - Chloé Orland
- Department of Plant Sciences, University of Cambridge, Cambridge, Cambridgeshire CB2 1TN, UK
| | - Marco Pautasso
- Animal and Plant Health Unit, European Food Safety Authority, Parma 43126, Italy
| | - William D K Reid
- School of Biology, Newcastle University, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
| | - Heather A Robinson
- School of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PT, UK
| | - Kenneth Wilson
- Lancaster Environment Centre, Lancaster University, Lancaster, Lancashire LA1 4YW, UK
| | - William J Sutherland
- Conservation Science Group, Department of Zoology, University of Cambridge, Cambridge, Cambridgeshire CB2 1TN, UK
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