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Johns NI, Blazejewski T, Gomes AL, Wang HH. Principles for designing synthetic microbial communities. Curr Opin Microbiol 2016; 31:146-153. [PMID: 27084981 DOI: 10.1016/j.mib.2016.03.010] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 01/21/2023]
Abstract
Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of synthetic microbial communities. Here, we review recent experimental, analytical and computational advances to study and build multi-species microbial communities with defined functions and behavior for various applications. We also highlight outstanding challenges and future directions to advance this field.
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Affiliation(s)
- Nathan I Johns
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, USA
| | - Tomasz Blazejewski
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, USA
| | - Antonio Lc Gomes
- Department of Systems Biology, Columbia University Medical Center, New York, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA.
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Lopatkin AJ, Huang S, Smith RP, Srimani JK, Sysoeva TA, Bewick S, Karig D, You L. Antibiotics as a selective driver for conjugation dynamics. Nat Microbiol 2016; 1:16044. [PMID: 27572835 PMCID: PMC5010019 DOI: 10.1038/nmicrobiol.2016.44] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/02/2016] [Indexed: 01/19/2023]
Abstract
It is generally assumed that antibiotics can promote horizontal gene transfer. However, because of a variety of confounding factors that complicate the interpretation of previous studies, the mechanisms by which antibiotics modulate horizontal gene transfer remain poorly understood. In particular, it is unclear whether antibiotics directly regulate the efficiency of horizontal gene transfer, serve as a selection force to modulate population dynamics after such gene transfer has occurred, or both. Here, we address this question by quantifying conjugation dynamics in the presence and absence of antibiotic-mediated selection. Surprisingly, we find that sublethal concentrations of antibiotics from the most widely used classes do not significantly increase the conjugation efficiency. Instead, our modelling and experimental results demonstrate that conjugation dynamics are dictated by antibiotic-mediated selection, which can both promote and suppress conjugation dynamics. Our findings suggest that the contribution of antibiotics to the promotion of horizontal gene transfer may have been overestimated. These findings have implications for designing effective antibiotic treatment protocols and for assessing the risks of antibiotic use.
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Affiliation(s)
- Allison J. Lopatkin
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Shuqiang Huang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Robert P. Smith
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale FL, USA
| | - Jaydeep K. Srimani
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Tatyana A. Sysoeva
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Sharon Bewick
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - David Karig
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA
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53
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smith J, Strassmann JE, Queller DC. Fine-scale spatial ecology drives kin selection relatedness among cooperating amoebae. Evolution 2016; 70:848-59. [DOI: 10.1111/evo.12895] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 12/29/2022]
Affiliation(s)
- jeff smith
- Department of Biology; Washington University in St. Louis; Saint Louis Missouri 63130
| | - Joan E. Strassmann
- Department of Biology; Washington University in St. Louis; Saint Louis Missouri 63130
| | - David C. Queller
- Department of Biology; Washington University in St. Louis; Saint Louis Missouri 63130
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54
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Lyons NA, Kraigher B, Stefanic P, Mandic-Mulec I, Kolter R. A Combinatorial Kin Discrimination System in Bacillus subtilis. Curr Biol 2016; 26:733-42. [PMID: 26923784 PMCID: PMC4803606 DOI: 10.1016/j.cub.2016.01.032] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/03/2015] [Accepted: 01/13/2016] [Indexed: 12/31/2022]
Abstract
Multicellularity inherently involves a number of cooperative behaviors that are potentially susceptible to exploitation but can be protected by mechanisms such as kin discrimination. Discrimination of kin from non-kin has been observed in swarms of the bacterium Bacillus subtilis, but the underlying molecular mechanism has been unknown. We used genetic, transcriptomic, and bioinformatic analyses to uncover kin recognition factors in this organism. Our results identified many molecules involved in cell-surface modification and antimicrobial production and response. These genes varied significantly in expression level and mutation phenotype among B. subtilis strains, suggesting interstrain variation in the exact kin discrimination mechanism used. Genome analyses revealed a substantial diversity of antimicrobial genes present in unique combinations in different strains, with many likely acquired by horizontal gene transfer. The dynamic combinatorial effect derived from this plethora of kin discrimination genes creates a tight relatedness cutoff for cooperation that has likely led to rapid diversification within the species. Our data suggest that genes likely originally selected for competitive purposes also generate preferential interactions among kin, thus stabilizing multicellular lifestyles.
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Affiliation(s)
- Nicholas A Lyons
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Barbara Kraigher
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Polonca Stefanic
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ines Mandic-Mulec
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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Abstract
Microbial communities are spatially organized in both the environment and the human body. Although patterns exhibited by these communities are described by microbial biogeography, this discipline has previously only considered large-scale, global patterns. By contrast, the fine-scale positioning of a pathogen within an infection site can greatly alter its virulence potential. In this Review, we highlight the importance of considering spatial positioning in the study of polymicrobial infections and discuss targeting biogeography as a therapeutic strategy.
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56
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Bessa LJ, Mendes Â, Gomes R, Curvelo S, Cravo S, Sousa E, Vasconcelos V, Martins da Costa P. Microbial interaction between a CTXM-15 -producing Escherichia coli and a susceptible Pseudomonas aeruginosa isolated from bronchoalveolar lavage: influence of cefotaxime in the dual-species biofilm formation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:420-426. [PMID: 25625458 DOI: 10.1111/1758-2229.12266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/07/2014] [Indexed: 06/04/2023]
Abstract
Two isolates, Escherichia coli ella00 and Pseudomonas aeruginosa ella01, obtained from bronchoalveolar lavage, were found to be closely associated in clusters in agar medium. Escherichia coli ella00 was multidrug resistant and CTXM-15 extended-spectrum β-lactamase producer, while P. aeruginosa ella01 was susceptible to all antimicrobials tested. These observations impelled for further studies aimed to understand their microbial interaction. The P. aeruginosa ella01 biofilm-forming capacity was reduced and not affected when it was co-cultured with E. coli ella00 and E. coli ATCC 25922 respectively. Interestingly, the co-culture of ella isolates in the presence of high concentrations, such as 160 μg ml(-1) , of cefotaxime allowed the formation of more biofilm than in the absence of the antibiotic. As revealed by fluorescence in situ hybridization, in co-culture, P. aeruginosa ella01 survived and subsequently flourished when exposed to this third-generation cephalosporin at a concentration 10 × higher than its minimum inhibitory concentration (MIC), and this was mostly due to β-lactamases production by E. coli ella00. In fact, it was demonstrated by high-performance liquid chromatography that cefotaxime was absent for the culture medium 4 h after application. In conclusion, we demonstrate that bacterial species can interact differently depending on the surrounding conditions (favourable or stressing), and that those interactions can switch from unprofitable to beneficial.
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Affiliation(s)
- Lucinda J Bessa
- Departmento de Produção Aquática, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal
| | - Ângelo Mendes
- Departmento de Produção Aquática, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Rita Gomes
- +ani+ Clínica Veterinária, Maia, Portugal
| | | | - Sara Cravo
- Centro de Química Medicinal da Universidade do Porto (CEQUIMED-UP), Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Emília Sousa
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal
- Centro de Química Medicinal da Universidade do Porto (CEQUIMED-UP), Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Vitor Vasconcelos
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal
- Departmento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paulo Martins da Costa
- Departmento de Produção Aquática, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Porto, Portugal
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Iranzo J, Lobkovsky AE, Wolf YI, Koonin EV. Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems. BMC Evol Biol 2015; 15:43. [PMID: 25881094 PMCID: PMC4372072 DOI: 10.1186/s12862-015-0324-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/24/2015] [Indexed: 01/09/2023] Open
Abstract
Background Parasite-host arms race is one of the key factors in the evolution of life. Most cellular life forms, in particular prokaryotes, possess diverse forms of defense against pathogens including innate immunity, adaptive immunity and programmed cell death (altruistic suicide). Coevolution of these different but interacting defense strategies yields complex evolutionary regimes. Results We develop and extensively analyze a computational model of coevolution of different defense strategies to show that suicide as a defense mechanism can evolve only in structured populations and when the attainable degree of immunity against pathogens is limited. The general principle of defense evolution seems to be that hosts do not evolve two costly defense mechanisms when one is sufficient. Thus, the evolutionary interplay of innate immunity, adaptive immunity and suicide, leads to an equilibrium state where the combination of all three defense strategies is limited to a distinct, small region of the parameter space. The three strategies can stably coexist only if none of them are highly effective. Coupled adaptive immunity-suicide systems, the existence of which is implied by the colocalization of genes for the two types of defense in prokaryotic genomes, can evolve either when immunity-associated suicide is more efficacious than other suicide systems or when adaptive immunity functionally depends on the associated suicide system. Conclusions Computational modeling reveals a broad range of outcomes of coevolution of anti-pathogen defense strategies depending on the relative efficacy of different mechanisms and population structure. Some of the predictions of the model appear compatible with recent experimental evolution results and call for additional experiments.
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Affiliation(s)
- Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Alexander E Lobkovsky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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58
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Misevic D, Frénoy A, Lindner AB, Taddei F. Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations. Evolution 2015; 69:788-802. [PMID: 25639379 PMCID: PMC4409860 DOI: 10.1111/evo.12616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/02/2015] [Indexed: 11/29/2022]
Abstract
Natural cooperative systems take many forms, ranging from one-dimensional cyanobacteria arrays to fractal-like biofilms. We use in silico experimental systems to study a previously overlooked factor in the evolution of cooperation, physical shape of the population. We compare the emergence and maintenance of cooperation in populations of digital organisms that inhabit bulky (100 × 100 cells) or slender (4 × 2500) toroidal grids. Although more isolated subpopulations of secretors in a slender population could be expected to favor cooperation, we find the opposite: secretion evolves to higher levels in bulky populations. We identify the mechanistic explanation for the shape effect by analyzing the lifecycle and dynamics of cooperator patches, from their emergence and growth, to invasion by noncooperators and extinction. Because they are constrained by the population shape, the cooperator patches expand less in slender than in bulky populations, leading to fewer cooperators, less public good secretion, and generally lower cooperation. The patch dynamics and mechanisms of shape effect are robust across several digital cooperation systems and independent of the underlying basis for cooperation (public good secretion or a cooperation game). Our results urge for a greater consideration of population shape in the study of the evolution of cooperation across experimental and modeling systems.
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Affiliation(s)
- Dusan Misevic
- Center for Research and Interdisciplinarity, INSERM U1001, Medicine Faculty, site Cochin Port-Royal, University Paris Descartes, Sorbonne Paris Cité, 24, rue du Faubourg Saint Jacques, 75014, Paris, France.
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Dimitriu T, Misevic D, Lindner AB, Taddei F. Mobile genetic elements are involved in bacterial sociality. Mob Genet Elements 2015; 5:7-11. [PMID: 26435881 PMCID: PMC4588217 DOI: 10.1080/2159256x.2015.1006110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/19/2014] [Accepted: 01/07/2015] [Indexed: 12/02/2022] Open
Abstract
Mobile genetic elements in bacteria are enriched in genes participating in social behaviors, suggesting an evolutionary link between gene mobility and social evolution. Cooperative behaviors, like the production of secreted public good molecules, are susceptible to the invasion of non-cooperative individuals, and their evolutionary maintenance requires mechanisms ensuring that benefits are directed preferentially to cooperators. In order to investigate the reasons for the mobility of public good genes, we designed a synthetic bacterial system where we control and quantify the transfer of public good production genes. In our recent study, we have experimentally shown that horizontal transfer helps maintain public good production in the face of both non-producer organisms and non-producer plasmids. Transfer spreads genes to neighboring cells, thus increasing relatedness and directing a higher proportion of public good benefits to producers. The effect is the strongest when public good genes undergo epidemics dynamics, making horizontal transfer especially relevant for pathogenic bacteria that repeatedly infect new hosts and base their virulence on costly public goods. The promotion of cooperation may be a general consequence of horizontal gene transfer in prokaryotes. Our work has an intriguing parallel, cultural transmission, where horizontal transfer, such as teaching, may preferentially promote cooperative behaviors.
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Affiliation(s)
- Tatiana Dimitriu
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
| | - Dusan Misevic
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
| | - Ariel B Lindner
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
| | - François Taddei
- Institut National de la Santé et de la Recherche Médicale; Université Paris Descartes; Paris, France
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60
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Ohland CL, Jobin C. Microbial activities and intestinal homeostasis: A delicate balance between health and disease. Cell Mol Gastroenterol Hepatol 2014; 1:28-40. [PMID: 25729763 PMCID: PMC4339954 DOI: 10.1016/j.jcmgh.2014.11.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The concept that the intestinal microbiota modulates numerous physiological processes including immune development and function, nutrition and metabolism as well as pathogen exclusion is relatively well established in the scientific community. The molecular mechanisms driving these various effects and the events leading to the establishment of a "healthy" microbiome are slowly emerging. The objective of this review is to bring into focus important aspects of microbial/host interactions in the intestine and to discuss key molecular mechanisms controlling health and disease states. We will discuss recent evidence on how microbes interact with the host and one another and their impact on intestinal homeostasis.
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Affiliation(s)
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, Florida
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida
- Correspondence Address correspondence to: Christian Jobin, PhD, Department of Medicine, University of Florida, 2033 Mowry Road, Office 461, Gainesville, Florida 32610. fax: (352) 392-3944.
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61
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Penny D. Cooperation and selfishness both occur during molecular evolution. Biol Direct 2014; 10:26. [PMID: 25486885 PMCID: PMC4266915 DOI: 10.1186/s13062-014-0026-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/14/2014] [Indexed: 11/10/2022] Open
Abstract
Perhaps the 'selfish' aspect of evolution has been over-emphasised, and organisms considered as basically selfish. However, at the macromolecular level of genes and proteins the cooperative aspect of evolution is more obvious and balances this self-centred aspect. Thousands of proteins must function together in an integrated manner to use and to produce the many molecules necessary for a functioning cell. The macromolecules have no idea whether they are functioning cooperatively or competitively with other genes and gene products (such as proteins). The cell is a giant cooperative system of thousands of genes/proteins that function together, even if it has to simultaneously resist 'parasites'. There are extensive examples of cooperative behavior among genes and proteins in both functioning cells and in the origin of life, so this cooperative nature, along with selfishness, must be considered part of normal evolution. The principles also apply to very large numbers of examples of 'positive interactions' between organisms, including both eukaryotes and akaryotes (prokaryotes). This does not negate in any way the 'selfishness' of genes - but macromolecules have no idea when they are helping, or hindering, other groups of macromolecules. We need to assert more strongly that genes, and gene products, function together as a cooperative unit.
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Affiliation(s)
- David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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62
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Leggett HC, Brown SP, Reece SE. War and peace: social interactions in infections. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130365. [PMID: 24686936 PMCID: PMC3982666 DOI: 10.1098/rstb.2013.0365] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
One of the most striking facts about parasites and microbial pathogens that has emerged in the fields of social evolution and disease ecology in the past few decades is that these simple organisms have complex social lives, indulging in a variety of cooperative, communicative and coordinated behaviours. These organisms have provided elegant experimental tests of the importance of relatedness, kin discrimination, cooperation and competition, in driving the evolution of social strategies. Here, we briefly review the social behaviours of parasites and microbial pathogens, including their contributions to virulence, and outline how inclusive fitness theory has helped to explain their evolution. We then take a mechanistically inspired ‘bottom-up’ approach, discussing how key aspects of the ways in which parasites and pathogens exploit hosts, namely public goods, mobile elements, phenotypic plasticity, spatial structure and multi-species interactions, contribute to the emergent properties of virulence and transmission. We argue that unravelling the complexities of within-host ecology is interesting in its own right, and also needs to be better incorporated into theoretical evolution studies if social behaviours are to be understood and used to control the spread and severity of infectious diseases.
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Affiliation(s)
- Helen C Leggett
- Department of Zoology, Oxford University, , South Parks Road, Oxford OX1 3PS, UK
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