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      Counteraction of antibiotic production and degradation stabilizes microbial communities

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      1 , 1 , * , 2 , * , 1 , 3
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          Summary

          A major challenge in theoretical ecology is understanding how natural microbial communities support species diversity 1- 8 , and in particular how antibiotic producing, sensitive and resistant species coexist 9- 15 . While cyclic “rock-paper-scissors” interactions can stabilize communities in spatial environments 9- 11 , coexistence in unstructured environments remains an enigma 12, 16 . Here, using simulations and analytical models, we show that the opposing actions of antibiotic production and degradation enable coexistence even in well-mixed environments. Coexistence depends on 3-way interactions where an antibiotic degrading species attenuates the inhibitory interactions between two other species. These 3-way interactions enable coexistence that is robust to substantial differences in inherent species growth rates and to invasion by “cheating” species that cease producing or degrading antibiotics. At least two antibiotics are required for stability, with greater numbers of antibiotics enabling more complex communities and diverse dynamical behaviors ranging from stable fixed-points to limit cycles and chaos. Together, these results show how multi-species antibiotic interactions can generate ecological stability in both spatial and mixed microbial communities, suggesting strategies for engineering synthetic ecosystems and highlighting the importance of toxin production and degradation for microbial biodiversity.

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          The Paradox of the Plankton

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            Bacterial competition: surviving and thriving in the microbial jungle.

            Most natural environments harbour a stunningly diverse collection of microbial species. In these communities, bacteria compete with their neighbours for space and resources. Laboratory experiments with pure and mixed cultures have revealed many active mechanisms by which bacteria can impair or kill other microorganisms. In addition, a growing body of theoretical and experimental population studies indicates that the interactions within and between bacterial species can have a profound impact on the outcome of competition in nature. The next challenge is to integrate the findings of these laboratory and theoretical studies and to evaluate the predictions that they generate in more natural settings.
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              Sampling the antibiotic resistome.

              Microbial resistance to antibiotics currently spans all known classes of natural and synthetic compounds. It has not only hindered our treatment of infections but also dramatically reshaped drug discovery, yet its origins have not been systematically studied. Soil-dwelling bacteria produce and encounter a myriad of antibiotics, evolving corresponding sensing and evading strategies. They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                6 August 2015
                28 May 2015
                28 November 2015
                : 521
                : 7553
                : 516-519
                Affiliations
                [1 ] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
                [2 ] Department of Bacteriology and Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
                [3 ] Faculty of Biology and Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
                Author notes
                [* ]Correspondence and requests for materials should be addressed to KV ( kalin@ 123456discovery.wisc.edu ) and RK ( rkishony@ 123456technion.ac.il )
                Article
                NIHMS683292
                10.1038/nature14485
                4551410
                25992546
                318fcf0c-d139-4fca-8264-a0bcb196be06
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