المؤلفون: Mohamed DS; Microbiology & Immunology Department, Faculty of Pharmacy, Sohag University, Sohag Al Gadida City, Egypt., Abd El-Baky RM; Microbiology & Immunology Department, Faculty of Pharmacy, Minia University, Minia, Egypt.; Microbiology and Immunology Department, Faculty of Pharmacy, Deraya University, Minia, Egypt., El-Mokhtar MA; Medical Microbiology & Immunology Department, Faculty of Medicine, Assiut University, El Fateh, Egypt.; Gilbert & Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon., Ghanem SK; Pharmacology & Toxicology Department, Faculty of Pharmacy, Sohag University, Sohag Al Gadida City, Egypt., Yahia R; Microbiology and Immunology Department, Faculty of Pharmacy, Deraya University, Minia, Egypt., Alqahtani AM; Pharmaceutical Chemistry Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia., Abourehab MAS; Pharmaceutics Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia., Ahmed EF; Microbiology & Immunology Department, Faculty of Pharmacy, Sohag University, Sohag Al Gadida City, Egypt.

المصدر: PloS one [PLoS One] 2024 Jun 21; Vol. 19 (6), pp. e0304980. Date of Electronic Publication: 2024 Jun 21 (Print Publication: 2024).

نوع المنشور: Journal Article

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

مواضيع طبية MeSH: Escherichia coli*/drug effects , Escherichia coli*/genetics , Gene Transfer, Horizontal* , Plasmids*/genetics, Metoclopramide/pharmacology ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Bacterial/drug effects ; Conjugation, Genetic ; Drug Resistance, Microbial/genetics ; Drug Resistance, Microbial/drug effects

مستخلص: Background: Antibiotic resistance genes (ARGs) transfer rapidly among bacterial species all over the world contributing to the aggravation of antibiotic resistance crisis. Antibiotics at sub-inhibitory concentration induce horizontal gene transfer (HRT) between bacteria, especially through conjugation. The role of common non-antibiotic pharmaceuticals in the market in disseminating antibiotic resistance is not well studied.
Objectives: In this work, we indicated the effect of some commonly used non-antibiotic pharmaceuticals including antiemetic (metoclopramide HCl) and antispasmodics (hyoscine butyl bromide and tiemonium methyl sulfate) on the plasmid-mediated conjugal transfer of antibiotic resistance genes between pathogenic E. coli in the gastric intestinal tract (GIT).
Methods: Broth microdilution assay was used to test the antibacterial activity of the tested non-antibiotic pharmaceuticals. A conjugation mating system was applied in presence of the studied non-antibiotic pharmaceuticals to test their effect on conjugal transfer frequency. Plasmid extraction and PCR were performed to confirm the conjugation process. Transmission electron microscopy (TEM) was used for imaging the effect of non-antibiotic pharmaceuticals on bacterial cells.
Results: No antibacterial activity was reported for the used non-antibiotic pharmaceuticals. Plasmid-mediated conjugal transfer between isolates was induced by metoclopramide HCl but suppressed by hyoscine butyl bromide. Tiemonium methylsulfate slightly promoted conjugal transfer. Aggregation between cells and periplasmic bridges was clear in the case of metoclopramide HCl while in presence of hyoscine butyl bromide little affinity was observed.
Conclusion: This study indicates the contribution of non-antibiotic pharmaceuticals to the dissemination and evolution of antibiotic resistance at the community level. Metoclopramide HCl showed an important role in the spread of antibiotic resistance.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Mohamed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Morel-Letelier I; Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany., Yuen B; Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany., Kück AC; Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany., Camacho-García YE; Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro, San José, Costa Rica.; Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), Universidad de Costa Rica, San Pedro, San José, Costa Rica.; Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica., Petersen JM; Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria., Lara M; Diving Center Cuajiniquil, Provincia de Guanacaste, Cuajiniquil, Costa Rica., Leray M; Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panamá., Eisen JA; Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America.; Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States of America., Osvatic JT; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria., Gros O; Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, Pointe-à-Pitre, France., Wilkins LGE; Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany.

المصدر: PLoS genetics [PLoS Genet] 2024 May 31; Vol. 20 (5), pp. e1011295. Date of Electronic Publication: 2024 May 31 (Print Publication: 2024).

نوع المنشور: Journal Article

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101239074 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7404 (Electronic) Linking ISSN: 15537390 NLM ISO Abbreviation: PLoS Genet Subsets: MEDLINE

مواضيع طبية MeSH: Symbiosis*/genetics , Phylogeny* , Nitrogen Fixation*/genetics , Nitrogen*/metabolism , Bivalvia*/microbiology , Bivalvia*/genetics , Gene Transfer, Horizontal*, Animals ; Bacteria/genetics ; Bacteria/classification ; Bacteria/metabolism ; Adaptation, Physiological/genetics ; Genome, Bacterial ; Caribbean Region ; Panama

مستخلص: Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Morel-Letelier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Aldaihani R; Department of Computer Science, Kuwait University, Kuwait City, State of Kuwait, Kuwait.; Department of Computer Science, Virginia Tech, Blacksburg, VA, United States of America., Heath LS; Department of Computer Science, Virginia Tech, Blacksburg, VA, United States of America.

المصدر: PloS one [PLoS One] 2024 May 02; Vol. 19 (5), pp. e0301172. Date of Electronic Publication: 2024 May 02 (Print Publication: 2024).

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

مواضيع طبية MeSH: Genomic Islands* , Gene Transfer, Horizontal*, Genome, Bacterial ; Genome, Archaeal ; Replication Origin/genetics ; Prokaryotic Cells/metabolism

مستخلص: Horizontal gene transfer (HGT) is a powerful evolutionary force that considerably shapes the structure of prokaryotic genomes and is associated with genomic islands (GIs). A GI is a DNA segment composed of transferred genes that can be found within a prokaryotic genome, obtained through HGT. Much research has focused on detecting GIs in genomes, but here we pursue a new course, which is identifying possible preferred locations of GIs in the prokaryotic genome. Here, we identify the locations of the GIs within prokaryotic genomes to examine patterns in those locations. Prokaryotic GIs were analyzed according to the genome structure that they are located in, whether it be a circular or a linear genome. The analytical investigations employed are: (1) studying the GI locations in relation to the origin of replication (oriC); (2) exploring the distances between GIs; and (3) determining the distribution of GIs across the genomes. For each of the investigations, the analysis was performed on all of the GIs in the data set. Moreover, to void bias caused by the distribution of the genomes represented, the GIs in one genome from each species and the GIs of the most frequent species are also analyzed. Overall, the results showed that there are preferred sites for the GIs in the genome. In the linear genomes, these sites are usually located in the oriC region and terminus region, while in the circular genomes, they are located solely in the terminus region. These results also showed that the distance distribution between the GIs is almost exponential, which proves that GIs have preferred sites within genomes. The oriC and termniuns are preferred sites for the GIs and a possible natural explanation for this could be connected to the content of the oriC region. Moreover, the content of the GIs in terms of its protein families was studied and the results demonstrated that the majority of frequent protein families are close to identical in each section.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Aldaihani, Heath. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Guillén-Chable F; UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México., Valdez Iuit JO; UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México., Avila Castro LA; UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México., Rosas C; UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México., Merino E; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México., Rodríguez-Escamilla Z; Facultad de Sistemas Biológicos e Innovación Tecnológica, Universidad Autónoma 'Benito Juárez' de Oaxaca, Oaxaca de Juárez, Oaxaca, México., Martínez-Núñez MA; UAET-Oaxaca, Instituto de Geografía, Universidad Nacional Autónoma de México, Oaxaca de Juárez, Oaxaca, México.

المصدر: PloS one [PLoS One] 2024 Apr 29; Vol. 19 (4), pp. e0301642. Date of Electronic Publication: 2024 Apr 29 (Print Publication: 2024).

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

مواضيع طبية MeSH: Interspersed Repetitive Sequences*/genetics , Gene Transfer, Horizontal* , Microbiota*/genetics, Mexico ; Bacteria/genetics ; Bacteria/classification ; Proteobacteria/genetics

مستخلص: Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan's microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It's important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Guillén-Chable et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Pompei S; IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy., Bella E; Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16 Milano, Italy., Weitz JS; Department of Biology, University of Maryland, College Park, Maryland, United States of America.; Department of Physics, University of Maryland, College Park, Maryland, United States of America.; Institut de Biologie, École Normale Supérieure, Paris, France., Grilli J; Quantitative Life Sciences, The Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy., Lagomarsino MC; IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.; Dipartimento di Fisica, Università degli Studi di Milano, via Celoria 16 Milano, Italy.; I.N.F.N, via Celoria 16 Milano, Italy.

المصدر: PLoS computational biology [PLoS Comput Biol] 2023 Oct 04; Vol. 19 (10), pp. e1011532. Date of Electronic Publication: 2023 Oct 04 (Print Publication: 2023).

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

مواضيع طبية MeSH: Gene Transfer, Horizontal*/genetics , Bacteria*/genetics, Humans ; Biological Evolution ; Genome

مستخلص: The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity. Several hypotheses have been proposed to explain this process, including the decreasing gene flow between ecologically distant populations, frequency-dependent selection from linked deleterious allelles, and very high rates of horizontal gene transfer. Here, we propose an additional possible scenario grounded in eco-evolutionary principles. Specifically, we show by a mathematical model and simulations that a metacommunity where species can occupy multiple patches, acting together with a realistic (moderate) HGT rate, helps maintain genome diversity. Assuming a scenario of patches dominated by single species, our model predicts that diversity only decreases moderately upon the arrival of a new beneficial gene, and that losses in diversity can be quickly restored. We explore the generic behaviour of diversity as a function of three key parameters, frequency of insertion of new beneficial genes, migration rates and horizontal transfer rates.Our results provides a testable explanation for how diversity can be maintained by gene-specific sweeps even in the absence of high horizontal gene transfer rates.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Pompei et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Belal NA; Department of Computer Science, Arab Academy for Science, Technology, and Maritime Transport, Alexandria, Egypt., Heath LS; Department of Computer Science, Virginia Tech, Blacksburg, VA, United States of America.

المصدر: PloS one [PLoS One] 2023 Mar 24; Vol. 18 (3), pp. e0281824. Date of Electronic Publication: 2023 Mar 24 (Print Publication: 2023).

نوع المنشور: Journal Article

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

مواضيع طبية MeSH: Gene Transfer, Horizontal* , Evolution, Molecular*, Phylogeny

مستخلص: We present a method for detecting horizontal gene transfer (HGT) using partial orders (posets). The method requires a poset for each species/gene pair, where we have a set of species S, and a set of genes G. Given the posets, the method constructs a phylogenetic tree that is compatible with the set of posets; this is done for each gene. Also, the set of posets can be derived from the tree. The trees constructed for each gene are then compared and tested for contradicting information, where a contradiction suggests HGT.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Belal, Heath. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: McKeithen-Mead SA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America., Grossman AD; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

المصدر: PLoS genetics [PLoS Genet] 2023 Feb 13; Vol. 19 (2), pp. e1010524. Date of Electronic Publication: 2023 Feb 13 (Print Publication: 2023).

نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101239074 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7404 (Electronic) Linking ISSN: 15537390 NLM ISO Abbreviation: PLoS Genet Subsets: MEDLINE

مواضيع طبية MeSH: Conjugation, Genetic* , Gene Transfer, Horizontal*, DNA, Bacterial/genetics ; Chromosomes/metabolism ; Bacteria/genetics ; DNA Transposable Elements

مستخلص: Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.
Competing Interests: The authors declare no competing interests.
(Copyright: © 2023 McKeithen-Mead, Grossman. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Bernabeu M; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain., Manzano-Morales S; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain., Gabaldón T; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.; Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain.

المصدر: PLoS biology [PLoS Biol] 2024 Mar 18; Vol. 22 (3), pp. e3002460. Date of Electronic Publication: 2024 Mar 18 (Print Publication: 2024).

نوع المنشور: Journal Article; Comment

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101183755 Publication Model: eCollection Cited Medium: Internet ISSN: 1545-7885 (Electronic) Linking ISSN: 15449173 NLM ISO Abbreviation: PLoS Biol Subsets: MEDLINE

مواضيع طبية MeSH: Gene Flow* , Biological Evolution*, Phylogeny ; Gene Transfer, Horizontal

مستخلص: A recent study questioned the use of branch length methods to assess the relative timing of horizontal gene transfers because of the effects of so-called "ghost" lineages. This Formal Comment discusses key considerations regarding the potential effect of missing lineages when assessing relative timing of evolutionary events.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Bernabeu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Liu Z; Department of Applied Physics, Stanford University, Stanford, California, United States of America., Good BH; Department of Applied Physics, Stanford University, Stanford, California, United States of America.; Department of Biology, Stanford University, Stanford, California, United States of America.; Chan Zuckerberg Biohub-San Francisco, San Francisco, California, United States of America.

المصدر: PLoS biology [PLoS Biol] 2024 Feb 08; Vol. 22 (2), pp. e3002472. Date of Electronic Publication: 2024 Feb 08 (Print Publication: 2024).

نوع المنشور: Journal Article

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101183755 Publication Model: eCollection Cited Medium: Internet ISSN: 1545-7885 (Electronic) Linking ISSN: 15449173 NLM ISO Abbreviation: PLoS Biol Subsets: MEDLINE

مواضيع طبية MeSH: Gastrointestinal Microbiome*/genetics , Microbiota*, Humans ; Bacteria/genetics ; Gene Transfer, Horizontal/genetics

مستخلص: Horizontal gene transfer (HGT) is a ubiquitous force in microbial evolution. Previous work has shown that the human gut is a hotspot for gene transfer between species, but the more subtle exchange of variation within species-also known as recombination-remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides an opportunity to measure recent recombination events from sequenced fecal samples, enabling quantitative comparisons across diverse commensal species that inhabit a common environment. By analyzing recent recombination events in the core genomes of 29 human gut bacteria, we observed widespread heterogeneities in the rates and lengths of transferred fragments, which are difficult to explain by existing models of ecological isolation or homology-dependent recombination rates. We also show that natural selection helps facilitate the spread of genetic variants across strain backgrounds, both within individual hosts and across the broader population. These results shed light on the dynamics of in situ recombination, which can strongly constrain the adaptability of gut microbial communities.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Liu, Good. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

المؤلفون: Coyte KZ; Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom., Stevenson C; Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, United Kingdom., Knight CG; Department of Earth and Environmental Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom., Harrison E; Department of Animal and Plant Sciences, The University of Sheffield, Sheffield, United Kingdom., Hall JPJ; Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom., Brockhurst MA; Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.

المصدر: PLoS biology [PLoS Biol] 2022 Nov 09; Vol. 20 (11), pp. e3001847. Date of Electronic Publication: 2022 Nov 09 (Print Publication: 2022).

نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't

بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101183755 Publication Model: eCollection Cited Medium: Internet ISSN: 1545-7885 (Electronic) Linking ISSN: 15449173 NLM ISO Abbreviation: PLoS Biol Subsets: MEDLINE

مواضيع طبية MeSH: Gene Transfer, Horizontal*/genetics , Microbiota*/genetics, Anti-Bacterial Agents/therapeutic use ; Plasmids/genetics

مستخلص: Genes encoding resistance to stressors, such as antibiotics or environmental pollutants, are widespread across microbiomes, often encoded on mobile genetic elements. Yet, despite their prevalence, the impact of resistance genes and their mobility upon the dynamics of microbial communities remains largely unknown. Here we develop eco-evolutionary theory to explore how resistance genes alter the stability of diverse microbiomes in response to stressors. We show that adding resistance genes to a microbiome typically increases its overall stability, particularly for genes on mobile genetic elements with high transfer rates that efficiently spread resistance throughout the community. However, the impact of resistance genes upon the stability of individual taxa varies dramatically depending upon the identity of individual taxa, the mobility of the resistance gene, and the network of ecological interactions within the community. Nonmobile resistance genes can benefit susceptible taxa in cooperative communities yet damage those in competitive communities. Moreover, while the transfer of mobile resistance genes generally increases the stability of previously susceptible recipient taxa to perturbation, it can decrease the stability of the originally resistant donor taxon. We confirmed key theoretical predictions experimentally using competitive soil microcosm communities. Here the stability of a susceptible microbial community to perturbation was increased by adding mobile resistance genes encoded on conjugative plasmids but was decreased when these same genes were encoded on the chromosome. Together, these findings highlight the importance of the interplay between ecological interactions and horizontal gene transfer in driving the eco-evolutionary dynamics of diverse microbiomes.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2022 Coyte et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)