1
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Dewar AE, Belcher LJ, Scott TW, West SA. Genes for cooperation are not more likely to be carried by plasmids. Proc Biol Sci 2024; 291:20232549. [PMID: 38412971 PMCID: PMC10898968 DOI: 10.1098/rspb.2023.2549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Cooperation is prevalent across bacteria, but risks being exploited by non-cooperative cheats. Horizontal gene transfer, particularly via plasmids, has been suggested as a mechanism to stabilize cooperation. A key prediction of this hypothesis is that genes which are more likely to be transferred, such as those on plasmids, should be more likely to code for cooperative traits. Testing this prediction requires identifying all genes for cooperation in bacterial genomes. However, previous studies used a method which likely misses some of these genes for cooperation. To solve this, we used a new genomics tool, SOCfinder, which uses three distinct modules to identify all kinds of genes for cooperation. We compared where these genes were located across 4648 genomes from 146 bacterial species. In contrast to the prediction of the hypothesis, we found no evidence that plasmid genes are more likely to code for cooperative traits. Instead, we found the opposite-that genes for cooperation were more likely to be carried on chromosomes. Overall, the vast majority of genes for cooperation are not located on plasmids, suggesting that the more general mechanism of kin selection is sufficient to explain the prevalence of cooperation across bacteria.
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Affiliation(s)
- Anna E Dewar
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | | | - Thomas W Scott
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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2
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Lewin-Epstein O, Jaques Y, Feldman MW, Kaufer D, Hadany L. Evolutionary modeling suggests that addictions may be driven by competition-induced microbiome dysbiosis. Commun Biol 2023; 6:782. [PMID: 37495841 PMCID: PMC10372008 DOI: 10.1038/s42003-023-05099-0] [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: 03/16/2022] [Accepted: 07/05/2023] [Indexed: 07/28/2023] Open
Abstract
Recent studies revealed mechanisms by which the microbiome affects its host's brain, behavior and wellbeing, and that dysbiosis - persistent microbiome-imbalance - is associated with the onset and progress of various chronic diseases, including addictive behaviors. Yet, understanding of the ecological and evolutionary processes that shape the host-microbiome ecosystem and affect the host state, is still limited. Here we propose that competition dynamics within the microbiome, associated with host-microbiome mutual regulation, may promote dysbiosis and aggravate addictive behaviors. We construct a mathematical framework, modeling the dynamics of the host-microbiome ecosystem in response to alterations. We find that when this ecosystem is exposed to substantial perturbations, the microbiome may shift towards a composition that reinforces the new host state. Such a positive feedback loop augments post-perturbation imbalances, hindering attempts to return to the initial equilibrium, promoting relapse episodes and prolonging addictions. We show that the initial microbiome composition is a key factor: a diverse microbiome enhances the ecosystem's resilience, whereas lower microbiome diversity is more prone to lead to dysbiosis, exacerbating addictions. This framework provides evolutionary and ecological perspectives on host-microbiome interactions and their implications for host behavior and health, while offering verifiable predictions with potential relevance to clinical treatments.
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Affiliation(s)
- Ohad Lewin-Epstein
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Yanabah Jaques
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, 94720, USA
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Daniela Kaufer
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA, 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Lilach Hadany
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel.
- Sagol school of neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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3
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Wang Q, Wei S, Silva AF, Madsen JS. Cooperative antibiotic resistance facilitates horizontal gene transfer. THE ISME JOURNAL 2023; 17:846-854. [PMID: 36949153 PMCID: PMC10203111 DOI: 10.1038/s41396-023-01393-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/24/2023]
Abstract
The rise of β-lactam resistance among pathogenic bacteria, due to the horizontal transfer of plasmid-encoded β-lactamases, is a current global health crisis. Importantly, β-lactam hydrolyzation by β-lactamases, not only protects the producing cells but also sensitive neighboring cells cooperatively. Yet, how such cooperative traits affect plasmid transmission and maintenance is currently poorly understood. Here we experimentally show that KPC-2 β-lactamase expression and extracellular activity were higher when encoded on plasmids compared with the chromosome, resulting in the elevated rescue of sensitive non-producers. This facilitated efficient plasmid transfer to the rescued non-producers and expanded the potential plasmid recipient pool and the probability of plasmid transfer to new genotypes. Social conversion of non-producers by conjugation was efficient yet not absolute. Non-cooperative plasmids, not encoding KPC-2, were moderately more competitive than cooperative plasmids when β-lactam antibiotics were absent. However, in the presence of a β-lactam antibiotic, strains with non-cooperative plasmids were efficiently outcompeted. Moreover, plasmid-free non-producers were more competitive than non-producers imposed with the metabolic burden of a plasmid. Our results suggest that cooperative antibiotic resistance especially promotes the fitness of replicons that transfer horizontally such as conjugative plasmids.
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Affiliation(s)
- Qinqin Wang
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Shaodong Wei
- National Food Institute, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ana Filipa Silva
- Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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4
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Scott TW, West SA, Dewar AE, Wild G. Is cooperation favored by horizontal gene transfer? Evol Lett 2023; 7:113-120. [PMID: 37251586 PMCID: PMC10210433 DOI: 10.1093/evlett/qrad003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 05/31/2023] Open
Abstract
It has been hypothesized that horizontal gene transfer on plasmids can facilitate the evolution of cooperation, by allowing genes to jump between bacteria, and hence increase genetic relatedness at the cooperative loci. However, we show theoretically that horizontal gene transfer only appreciably increases relatedness when plasmids are rare, where there are many plasmid-free cells available to infect (many opportunities for horizontal gene transfer). In contrast, when plasmids are common, there are few opportunities for horizontal gene transfer, meaning relatedness is not appreciably increased, and so cooperation is not favored. Plasmids, therefore, evolve to be rare and cooperative, or common and noncooperative, meaning plasmid frequency and cooperativeness are never simultaneously high. The overall level of plasmid-mediated cooperation, given by the product of plasmid frequency and cooperativeness, is therefore consistently negligible or low.
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Affiliation(s)
- Thomas W Scott
- Corresponding author: Department of Biology, University of Oxford; Oxford, OX1 3SZ, United Kingdom.
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Geoff Wild
- Department of Mathematics, University of Western Ontario, London, Ontario, Canada
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5
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Hao C, Dewar AE, West SA, Ghoul M. Gene transferability and sociality do not correlate with gene connectivity. Proc Biol Sci 2022; 289:20221819. [PMID: 36448285 PMCID: PMC9709509 DOI: 10.1098/rspb.2022.1819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The connectivity of a gene, defined as the number of interactions a gene's product has with other genes' products, is a key characteristic of a gene. In prokaryotes, the complexity hypothesis predicts that genes which undergo more frequent horizontal transfer will be less connected than genes which are only very rarely transferred. We tested the role of horizontal gene transfer, and other potentially important factors, by examining the connectivity of chromosomal and plasmid genes, across 134 diverse prokaryotic species. We found that (i) genes on plasmids were less connected than genes on chromosomes; (ii) connectivity of plasmid genes was not correlated with plasmid mobility; and (iii) the sociality of genes (cooperative or private) was not correlated with gene connectivity.
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Affiliation(s)
- Chunhui Hao
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Anna E. Dewar
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Stuart A. West
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
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6
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Bakkeren E, Gül E, Huisman JS, Steiger Y, Rocker A, Hardt WD, Diard M. Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium. Nat Commun 2022; 13:1939. [PMID: 35410999 PMCID: PMC9001671 DOI: 10.1038/s41467-022-29597-7] [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: 07/22/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Intestinal inflammation fuels the transmission of Salmonella Typhimurium (S.Tm). However, a substantial fitness cost is associated with virulence expression. Mutations inactivating transcriptional virulence regulators generate attenuated variants profiting from inflammation without enduring virulence cost. Such variants interfere with the transmission of fully virulent clones. Horizontal transfer of functional regulatory genes (HGT) into attenuated variants could nevertheless favor virulence evolution. To address this hypothesis, we cloned hilD, coding for the master regulator of virulence, into a conjugative plasmid that is highly transferrable during intestinal colonization. The resulting mobile hilD allele allows virulence to emerge from avirulent populations, and to be restored in attenuated mutants competing against virulent clones within-host. However, mutations inactivating the mobile hilD allele quickly arise. The stability of virulence mediated by HGT is strongly limited by its cost, which depends on the hilD expression level, and by the timing of transmission. We conclude that robust evolution of costly virulence expression requires additional selective forces such as narrow population bottlenecks during transmission. Salmonella Typhimurium virulence is costly and can be lost by mutation during infection. Bakkeren et al. show that virulence restoration via horizontal gene transfer is only transient while transmission bottlenecks promote long-term virulence stability.
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Plasmids do not consistently stabilize cooperation across bacteria but may promote broad pathogen host-range. Nat Ecol Evol 2021; 5:1624-1636. [PMID: 34750532 PMCID: PMC7612097 DOI: 10.1038/s41559-021-01573-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022]
Abstract
Horizontal gene transfer via plasmids could favour cooperation in bacteria, because transfer of a cooperative gene turns non-cooperative cheats into cooperators. This hypothesis has received support from theoretical, genomic and experimental analyses. In contrast, we show here, with a comparative analysis across 51 diverse species, that genes for extracellular proteins, which are likely to act as cooperative ‘public goods’, were not more likely to be carried on either: (i) plasmids compared to chromosomes; or (ii) plasmids that transfer at higher rates. Our results were supported by theoretical modelling which showed that while horizontal gene transfer can help cooperative genes initially invade a population, it has less influence on the longer-term maintenance of cooperation. Instead, we found that genes for extracellular proteins were more likely to be on plasmids when they coded for pathogenic virulence traits, in pathogenic bacteria with a broad host-range.
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8
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Hernández-Beltrán JCR, San Millán A, Fuentes-Hernández A, Peña-Miller R. Mathematical Models of Plasmid Population Dynamics. Front Microbiol 2021; 12:606396. [PMID: 34803935 PMCID: PMC8600371 DOI: 10.3389/fmicb.2021.606396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.
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Affiliation(s)
| | | | | | - Rafael Peña-Miller
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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9
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Champagnat N, Méléard S, Tran VC. Stochastic analysis of emergence of evolutionary cyclic behavior in population dynamics with transfer. ANN APPL PROBAB 2021. [DOI: 10.1214/20-aap1635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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West SA, Cooper GA, Ghoul MB, Griffin AS. Ten recent insights for our understanding of cooperation. Nat Ecol Evol 2021; 5:419-430. [PMID: 33510431 PMCID: PMC7612052 DOI: 10.1038/s41559-020-01384-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
Since Hamilton published his seminal papers in 1964, our understanding of the importance of cooperation for life on Earth has evolved beyond recognition. Early research was focused on altruism in the social insects, where the problem of cooperation was easy to see. In more recent years, research into cooperation has expanded across the entire tree of life, and has been revolutionized by advances in genetic, microbiological and analytical techniques. We highlight ten insights that have arisen from these advances, which have illuminated generalizations across different taxa, making the world simpler to explain. Furthermore, progress in these areas has opened up numerous new problems to solve, suggesting exciting directions for future research.
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Affiliation(s)
- Stuart A West
- Department of Zoology, University of Oxford, Oxford, UK.
| | - Guy A Cooper
- Department of Zoology, University of Oxford, Oxford, UK
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11
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Zwanzig M. The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling. Comput Struct Biotechnol J 2020; 19:586-599. [PMID: 33510864 PMCID: PMC7807137 DOI: 10.1016/j.csbj.2020.12.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 12/27/2022] Open
Abstract
Many antibiotic resistance genes are associated with plasmids. The ecological success of these mobile genetic elements within microbial communities depends on varying mechanisms to secure their own propagation, not only on environmental selection. Among the most important are the cost of plasmids and their ability to be transferred to new hosts through mechanisms such as conjugation. These are regulated by dynamic control systems of the conjugation machinery and genetic adaptations that plasmid-host pairs can acquire in coevolution. However, in complex communities, these processes and mechanisms are subject to a variety of interactions with other bacterial species and other plasmid types. This article summarizes basic plasmid properties and ecological principles particularly important for understanding the persistence of plasmid-coded antibiotic resistance in aquatic environments. Through selected examples, it further introduces to the features of different types of simulation models such as systems of ordinary differential equations and individual-based models, which are considered to be important tools to understand these complex systems. This ecological perspective aims to improve the way we study and understand the dynamics, diversity and persistence of plasmids and associated antibiotic resistance genes.
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Affiliation(s)
- Martin Zwanzig
- Faculty of Environmental Sciences, Technische Universität Dresden, Pienner Str. 8, D-01737 Tharandt, Germany
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12
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Lewin-Epstein O, Hadany L. Host-microbiome coevolution can promote cooperation in a rock-paper-scissors dynamics. Proc Biol Sci 2020; 287:20192754. [PMID: 32075531 PMCID: PMC7031668 DOI: 10.1098/rspb.2019.2754] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cooperation is a fundamental behaviour observed in all forms of life. The evolution of cooperation has been widely studied, but almost all theories focused on the cooperating individual and its genes. We suggest a different approach, taking into account the microbes carried by the interacting individuals. Accumulating evidence reveals that microbes can affect their host's well-being and behaviour, yet hosts can evolve mechanisms to resist the manipulations of their microbes. We thus propose that coevolution of microbes with their hosts may favour microbes that induce their host to cooperate. Using computational modelling, we show that microbe-induced cooperation can evolve and be maintained in a wide range of conditions, including when facing hosts' resistance to the microbial effect. We find that host-microbe coevolution leads the population to a rock-paper-scissors dynamics that enables maintenance of cooperation in a polymorphic state. Our results suggest a mechanism for the evolution and maintenance of cooperation that may be relevant to a wide variety of organisms, including cases that are difficult to explain by current theories. This study provides a new perspective on the coevolution of hosts and their microbiome, emphasizing the potential role of microbes in shaping their host's behaviour.
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Affiliation(s)
- Ohad Lewin-Epstein
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Lilach Hadany
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997801, Israel
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13
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Abstract
Fields such as behavioural and evolutionary ecology are built on the assumption that natural selection leads to organisms that behave as if they are trying to maximise their fitness. However, there is considerable evidence for selfish genetic elements that change the behaviour of individuals to increase their own transmission. How can we reconcile this contradiction? Here we show that: (1) when selfish genetic elements have a greater impact at the individual level, they are more likely to be suppressed, and suppression spreads more quickly; (2) selection on selfish genetic elements leads them towards a greater impact at the individual level, making them more likely to be suppressed; (3) the majority interest within the genome generally prevails over 'cabals' of a few genes, irrespective of genome size, mutation rate and the sophistication of trait distorters. Overall, our results suggest that even when there is the potential for considerable genetic conflict, this will often have negligible impact at the individual level.
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Affiliation(s)
- Thomas W Scott
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
| | - Stuart A West
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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14
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Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids. Genes (Basel) 2019; 10:genes10110850. [PMID: 31661808 PMCID: PMC6896180 DOI: 10.3390/genes10110850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.
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15
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Aijaz I, Koudelka GB. Cheating, facilitation and cooperation regulate the effectiveness of phage-encoded exotoxins as antipredator molecules. Microbiologyopen 2018; 8:e00636. [PMID: 29675935 PMCID: PMC6391270 DOI: 10.1002/mbo3.636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 01/28/2023] Open
Abstract
Temperate phage encoded Shiga toxin (Stx) kills the bacterivorous predator, Tetrahymena thermophila, providing Stx+Escherichia coli with a survival advantage over Stx− cells. Although bacterial death accompanies Stx release, since bacteria grow clonally the fitness benefits of predator killing accrue to the kin of the sacrificed organism, meaning Stx‐mediated protist killing is a form of self‐destructive cooperation. We show here that the fitness benefits of Stx production are not restricted to the kin of the phage‐encoding bacteria. Instead, nearby “free loading” bacteria, irrespective of their genotype, also reap the benefit of Stx‐mediated predator killing. This finding indicates that the phage‐borne Stx exotoxin behaves as a public good. Stx is encoded by a mobile phage. We find that Stx‐encoding phage can use susceptible bacteria in the population as surrogates to enhance toxin and phage production. Moreover, our findings also demonstrate that engulfment and concentration of Stx‐encoding and susceptible Stx− bacteria in the Tetrahymena phagosome enhances the transfer of Stx‐encoding temperate phage from the host to the susceptible bacteria. This transfer increases the population of cooperating bacteria within the community. Since these bacteria now encode Stx, the predation‐stimulated increase in phage transfer increases the population of toxin encoding bacteria in the environment.
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Affiliation(s)
- Iqbal Aijaz
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerald B Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
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16
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Cavaliere M, Feng S, Soyer OS, Jiménez JI. Cooperation in microbial communities and their biotechnological applications. Environ Microbiol 2017; 19:2949-2963. [PMID: 28447371 PMCID: PMC5575505 DOI: 10.1111/1462-2920.13767] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022]
Abstract
Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross-feeding, which can be understood in the general framework of ecological and evolutionary (eco-evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of 'cheating' cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.
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Affiliation(s)
- Matteo Cavaliere
- School of Informatics, BBSRC/EPSRC/MRC Synthetic Biology Research CentreUniversity of EdinburghEdinburghEH8 9ABUK
| | - Song Feng
- Center for Nonlinear StudiesTheoretical Division (T‐6), Los Alamos National LaboratoryLos AlamosNM 87545USA
| | - Orkun S. Soyer
- School of Life Sciences, BBSRC/EPSRC Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
| | - José I. Jiménez
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordGU2 7XHUK
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17
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Lewin-Epstein O, Aharonov R, Hadany L. Microbes can help explain the evolution of host altruism. Nat Commun 2017; 8:14040. [PMID: 28079112 PMCID: PMC5241693 DOI: 10.1038/ncomms14040] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/23/2016] [Indexed: 01/12/2023] Open
Abstract
The evolution of altruistic behaviour, which is costly to the donor but beneficial for the recipient, is among the most intriguing questions in evolutionary biology. Several theories have been proposed to explain it, including kin selection, group selection and reciprocity. Here we propose that microbes that manipulate their hosts to act altruistically could be favoured by selection, and may play a role in the widespread occurrence of altruism. Using computational models, we find that microbe-induced altruism can explain the evolution of host altruistic behaviour under wider conditions than host-centred theories, including in a fully mixed host population, without repeating interactions or individual recognition. Our results suggest that factors such as antibiotics that kill microbes might negatively affect cooperation in a wide range of organisms.
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Affiliation(s)
- Ohad Lewin-Epstein
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Ranit Aharonov
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Lilach Hadany
- Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel-Aviv 6997801, Israel
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18
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Pak G, Salcedo DE, Lee H, Oh J, Maeng SK, Song KG, Hong SW, Kim HC, Chandran K, Kim S. Comparison of Antibiotic Resistance Removal Efficiencies Using Ozone Disinfection under Different pH and Suspended Solids and Humic Substance Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:7590-600. [PMID: 27389869 DOI: 10.1021/acs.est.6b01340] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This study mainly evaluated the effectiveness of ozonation toward the enhancement of the removal efficiencies of antibiotic-resistant bacteria (ARB), pB10 plasmid transfer, and pB10 plasmids under different pH and suspended solids (SS) and humic acid concentrations. First, chlorination was tested as a reference disinfection process. Chlorination at a very high dose concentration of Cl2 (75 mg L(-1)) and a long contact time (10 min) were required to achieve approximately 90% ARB and pB10 plasmid transfer removal efficiencies. However, even these stringent conditions only resulted in a 78.8% reduction of pB10 plasmid concentrations. In case of ozonation, the estimated CT (concentration × contact time) value (at C0 = 7 mg L(-1)) for achieving 4-log pB10 plasmid removal efficiency was 127.15 mg·min L(-1), which was 1.04- and 1.25-fold higher than those required for ARB (122.73 mg·min L(-1)) and a model nonantibiotic resistant bacterial strain, E. coli K-12, (101.4 mg·min L(-1)), respectively. In preventing pB10 plasmid transfer, ozonation achieved better performance under conditions of higher concentrations of humic acid and lower pH. Our study results demonstrated that the applicability of CT concept in practice, conventionally used for disinfection, might not be appropriate for antibiotic resistance control in the wastewater treatment process. Further studies should be conducted in wastewater engineering on how to implement multiple barriers including disinfection to prevent ARB and ARG discharge into the environment.
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Affiliation(s)
| | | | - Hansaem Lee
- Water & Environment R&D Team, Research & Development Division, Hyundai Engineering & Construction Co., Ltd. , Seoul 110-920, Republic of Korea
| | | | | | - Kyung Guen Song
- Center for Water Resource Cycle Research, Korea Institute of Science and Technology , Seoul 02792, Republic of Korea
| | - Seok Won Hong
- Center for Water Resource Cycle Research, Korea Institute of Science and Technology , Seoul 02792, Republic of Korea
| | | | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University , 500 West 120th Street, New York, New York 10027, United States
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Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids. PLoS Biol 2016; 14:e1002478. [PMID: 27270455 PMCID: PMC4896427 DOI: 10.1371/journal.pbio.1002478] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/09/2016] [Indexed: 11/19/2022] Open
Abstract
Bacterial genes that confer crucial phenotypes, such as antibiotic resistance, can spread horizontally by residing on mobile genetic elements (MGEs). Although many mobile genes provide strong benefits to their hosts, the fitness consequences of the process of transfer itself are less clear. In previous studies, transfer has been interpreted as a parasitic trait of the MGEs because of its costs to the host but also as a trait benefiting host populations through the sharing of a common gene pool. Here, we show that costly donation is an altruistic act when it spreads beneficial MGEs favoured when it increases the inclusive fitness of donor ability alleles. We show mathematically that donor ability can be selected when relatedness at the locus modulating transfer is sufficiently high between donor and recipients, ensuring high frequency of transfer between cells sharing donor alleles. We further experimentally demonstrate that either population structure or discrimination in transfer can increase relatedness to a level selecting for chromosomal transfer alleles. Both mechanisms are likely to occur in natural environments. The simple process of strong dilution can create sufficient population structure to select for donor ability. Another mechanism observed in natural isolates, discrimination in transfer, can emerge through coselection of transfer and discrimination alleles. Our work shows that horizontal gene transfer in bacteria can be promoted by bacterial hosts themselves and not only by MGEs. In the longer term, the success of cells bearing beneficial MGEs combined with biased transfer leads to an association between high donor ability, discrimination, and mobile beneficial genes. However, in conditions that do not select for altruism, host bacteria promoting transfer are outcompeted by hosts with lower transfer rate, an aspect that could be relevant in the fight against the spread of antibiotic resistance. Altruistic host bacteria can preferentially enhance the horizontal transfer of beneficial plasmids (such as those conferring antibiotic resistance or virulence) to others of their kind. In bacteria, genes can move between cells, sometimes with the donor host cell actively involved in the gene transfer mechanisms. This movement of genes is called horizontal gene transfer, and it increases the prevalence of mobile genes in bacterial populations. However, it is not clear if donor host cells benefit from gene spread, or are simply exploited by selfish genes. Here, we show with both modelling and experiments that for the donor host, investing in the transfer of beneficial genes—such as those conferring antibiotic resistance—can be understood as an altruistic behaviour. This behaviour is costly to the donor but beneficial to recipients and can be selected for if a sufficient proportion of recipient cells share the donors’ transfer allele. Preferential transfer from donors towards recipients that share this allele occurs when dispersal is limited or if discrimination mechanisms are present. Our work suggests that both processes are likely to be widespread in nature, promoting horizontal gene spread by host donor cells. As many antimicrobial resistance and virulence genes are mobile, our work further implies that the spread of harmful traits among human pathogens may be modulated by host bacteria in a direction that depends on the bacterial ability to transfer the traits specifically to their kind.
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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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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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Ray S, Dasgupta AK. Probiotics as cheater cells: parameter space clustering for individualized prescription. J Theor Biol 2014; 361:165-74. [PMID: 25066785 DOI: 10.1016/j.jtbi.2014.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/28/2022]
Abstract
Clinicians often perform infection management administering probiotics along with antibiotics. Such probiotics added to an infecting population showing antibiotic resistance can be compared to a dynamical system composed of cheaters and workers. The presence of cheater strains is known to modulate the fitness of the infecting population. We propose a model where probiotics as cheater strain re-establishes the susceptibility of a resistant population towards an antibiotic. Control parameters must assume optimal values in order to attain minimum worker number within a finite time-scale feasible in a clinical set-up. The problem is made non-trivial by the complicated interplay between parameters. The model is an extension of a logistic framework, where a pay-off function has been included to account for the effect of instantaneous worker number on death rates of each species. The outcomes for a randomized set of parameter values and initial conditions are utilized in partitioning the set and desired clusters were identified. For a test case, one can take random combinations of controllable parameters and combine them with fixed parameters and find out the closeness of the points to the desired cluster centroids. This process leads to the identification of optimum antibiotic versus probiotic dosage range leading to elimination or limited existence of the genetically resistant population.
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Affiliation(s)
- Sanhita Ray
- Department of Biochemistry and Center for Excellence in Systems Biology and Biomedical Engineering, University of Calcutta, Kolkata, India.
| | - Anjan Kr Dasgupta
- Department of Biochemistry and Center for Excellence in Systems Biology and Biomedical Engineering, University of Calcutta, Kolkata, India.
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23
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Abstract
Many bacterial species are social, producing costly secreted "public good" molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria.
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24
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Abstract
We introduce the field of Hamiltonian medicine, which centres on the roles of genetic relatedness in human health and disease. Hamiltonian medicine represents the application of basic social-evolution theory, for interactions involving kinship, to core issues in medicine such as pathogens, cancer, optimal growth and mental illness. It encompasses three domains, which involve conflict and cooperation between: (i) microbes or cancer cells, within humans, (ii) genes expressed in humans, (iii) human individuals. A set of six core principles, based on these domains and their interfaces, serves to conceptually organize the field, and contextualize illustrative examples. The primary usefulness of Hamiltonian medicine is that, like Darwinian medicine more generally, it provides novel insights into what data will be productive to collect, to address important clinical and public health problems. Our synthesis of this nascent field is intended predominantly for evolutionary and behavioural biologists who aspire to address questions directly relevant to human health and disease.
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Affiliation(s)
- Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, CanadaV5A 1S6
| | - Kevin Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Francisco Úbeda
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
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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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