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      Biofilms preserve the transmissibility of a multi-drug resistance plasmid

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          Abstract

          Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absence of antibiotics longer than well-mixed planktonic populations and that (ii) the evolutionary trajectories that account for the improvement of plasmid persistence over time differ between biofilms and planktonic populations. In this study, we evolved Acinetobacter baumannii with an MDR plasmid in biofilm and planktonic populations with and without antibiotic selection. In the absence of selection, biofilm populations were better able to maintain the MDR plasmid than planktonic populations. In planktonic populations, plasmid persistence improved rapidly but was accompanied by a loss of genes required for the horizontal transfer of plasmids. In contrast, in biofilms, most plasmids retained their transfer genes, but on average, plasmid, persistence improved less over time. Our results showed that biofilms can act as refugia of MDR plasmids and favor the horizontal mode of plasmid transfer, which has important implications for the spread of MDR.

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          Bacterial biofilms: a common cause of persistent infections.

          Bacteria that attach to surfaces aggregate in a hydrated polymeric matrix of their own synthesis to form biofilms. Formation of these sessile communities and their inherent resistance to antimicrobial agents are at the root of many persistent and chronic bacterial infections. Studies of biofilms have revealed differentiated, structured groups of cells with community properties. Recent advances in our understanding of the genetic and molecular basis of bacterial community behavior point to therapeutic targets that may provide a means for the control of biofilm infections.
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            Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq.

            Next-generation DNA sequencing (NGS) can be used to reconstruct eco-evolutionary population dynamics and to identify the genetic basis of adaptation in laboratory evolution experiments. Here, we describe how to run the open-source breseq computational pipeline to identify and annotate genetic differences found in whole-genome and whole-population NGS data from haploid microbes where a high-quality reference genome is available. These methods can also be used to analyze mutants isolated in genetic screens and to detect unintended mutations that may occur during strain construction and genome editing.
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              Bacteria and archaea on Earth and their abundance in biofilms

              Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the 'big five' habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20-80% of cells in the subsurface exist as biofilms. Hence, overall, 40-80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.
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                Author and article information

                Contributors
                evatop@uidaho.edu
                Journal
                NPJ Biofilms Microbiomes
                NPJ Biofilms Microbiomes
                NPJ Biofilms and Microbiomes
                Nature Publishing Group UK (London )
                2055-5008
                9 December 2022
                9 December 2022
                2022
                : 8
                : 95
                Affiliations
                [1 ]GRID grid.266456.5, ISNI 0000 0001 2284 9900, Department of Biological Sciences, , University of Idaho, ; Moscow, ID USA
                [2 ]GRID grid.266456.5, ISNI 0000 0001 2284 9900, Institute for Interdisciplinary Data Sciences, , University of Idaho, ; Moscow, ID USA
                [3 ]Bioinformatics and Computational Biology Graduate Program (BCB), Moscow, ID USA
                [4 ]GRID grid.266456.5, ISNI 0000 0001 2284 9900, Department of Mathematics and Statistical Science, , University of Idaho, ; Moscow, ID USA
                Author information
                http://orcid.org/0000-0001-8271-4629
                http://orcid.org/0000-0002-6380-8782
                Article
                357
                10.1038/s41522-022-00357-1
                9732292
                36481746
                74be881f-bafb-4202-ab5d-f64a8dd1097b
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 May 2022
                : 14 November 2022
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000060, U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID);
                Award ID: R01 AI084918
                Award ID: R01 AI084918
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000057, U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS);
                Award ID: P30 GM103324
                Award ID: P30 GM103324
                Award Recipient :
                Funded by: Bioinformatics and Computational Biology Program at the University of Idaho in partnership with the Institute for Bioinformatics and Evolutionary Studies (now Institute for Interdisciplinary Data Sciences, IIDS)
                Funded by: FundRef https://doi.org/10.13039/100000005, U.S. Department of Defense (United States Department of Defense);
                Award ID: DM110149
                Award ID: DOD-DM110149
                Award ID: DM110149
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)
                Funded by: U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)
                Categories
                Article
                Custom metadata
                © The Author(s) 2022

                biofilms,molecular evolution,microbial genetics
                biofilms, molecular evolution, microbial genetics

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