Article
Multidisciplinary Sciences
Jeffrey J. Power, Fernanda Pinheiro, Simone Pompei, Viera Kovacova, Melih Yueksel, Isabel Rathmann, Mona Foerster, Michael Laessig, Berenike Maier
Summary: Horizontal gene transfer is an important factor in bacterial evolution, allowing for rapid evolution and increased adaptation in recipient organisms. Adaptive evolution mainly occurs in populations with increased fitness, with HGT selection having a broad genetic basis and showing different types of selection in functional gene networks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
Summary: In this study, a computational toolbox called HGTphyloDetect was developed, which combines high-throughput analysis with phylogenetic inference to accurately identify horizontal gene transfer (HGT) events and illustrate the transmission pathway among evolutionarily distant or closely related species. The HGTphyloDetect toolbox is user-friendly, capable of detecting HGT events with high efficiency and low false discovery rate.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Lina Kloub, Sean Gosselin, Matthew Fullmer, Joerg Graf, Johann Peter Gogarten, Mukul S. Bansal
Summary: Horizontal gene transfer (HGT) is crucial for prokaryotic evolution, yet little is known about the scale of individual HGT events. A computational framework called HoMer is introduced to infer single-gene HGT events and potential multiple-gene transfers, aiding a better understanding of HGT and microbial evolution on a larger scale through systematic inference of HMGTs.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
An N. T. Nguyen, Laura C. Woods, Rebecca Gorrell, Shamitraa Ramanan, Terry Kwok, Michael J. McDonald
Summary: Horizontal gene transfer is vital for microbial evolution, yet we have limited knowledge about the fitness effects and dynamics of these transferred genetic variants. Through evolutionary experiments on laboratory populations of Helicobacter pylori, which naturally take up DNA from their environment, we measured the fitness effects of thousands of transferred genetic variants. Our findings reveal that natural transformation increases the rate of adaptation but comes with a significant genetic load. However, recombination bypasses this cost by enhancing selection efficiency through separating harmful and beneficial genetic variants. Our results demonstrate that adaptation with horizontal gene transfer, which is pervasive in natural microbial populations, is influenced by a combination of selection, recombination, and genetic drift that existing evolutionary models fail to account for.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
M. Julhasur Rahman, Sherry L. Haller, Ana M. M. Stoian, Jie Li, Greg Brennan, Stefan Rothenburg
Summary: This study developed a model to understand the mechanisms of gene transfer in vaccinia virus. The findings indicate that gene capture events are mediated by LINE-1 retrotransposition and highlight the role of host retrotransposons as major drivers for virus evolution.
Article
Biotechnology & Applied Microbiology
Joshua G. Philips, Elena Martin-Avila, Andrea V. Robold
Summary: This review provides updated evidence on the likelihood, factors, and barriers for horizontal gene transfer in genetically modified plants, and presents the legislation and frameworks followed by the Australian Gene Technology Regulator in considering the risks posed by horizontal gene transfer.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biology
Yun Wang, Franz Baumdicker, Paul Schweiger, Sven Kuenzel, Fabian Staubach
Summary: The study reveals the significant impact of microbial genomic variation on host fitness, with the thiamine biosynthesis pathway playing a role in the variation of offspring production in Drosophila. Horizontal gene transfer can enhance microbiome flexibility and potentially contribute to host adaptation.
Article
Engineering, Environmental
Shuyao Zhu, Bingqing Yang, Yuqian Jia, Feiyu Yu, Zhiqiang Wang, Yuan Liu
Summary: This study aimed to explore the impact of different disinfectants on the horizontal transfer of antibiotic resistance genes (ARGs) and their underlying mechanisms. The results showed that quaternary ammonium salt, organic halogen, alcohol, and guanidine disinfectants significantly facilitated the conjugative transfer, while heavy metals, peroxides, and phenols displayed an inhibitory effect. Furthermore, guanidine disinfectants promoted conjugation through increased cell membrane permeability, over-production of reactive oxygen species (ROS), enhanced SOS response, and altered expression of conjugative transfer-related genes. Moreover, guanidine disinfectants also promoted bacterial energy metabolism and flagellum motility. These findings highlight the potential risks caused by the massive use of guanidine disinfectants, especially during the COVID-19 pandemic.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biology
Brendan Epstein, Peter Tiffin
Summary: This study reveals that symbiosis genes in rhizobial genomes undergo high rates of horizontal transfer, along with signatures of purifying selection. Particularly, genes involved in initiating symbiosis and in mediating benefits to the host show strong patterns of horizontal transfer and purifying selection.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Nuria Marti Gutierrez, Aleksei Mikhalchenko, Hong Ma, Amy Koski, Ying Li, Crystal Van Dyken, Rebecca Tippner-Hedges, David Yoon, Dan Liang, Tomonari Hayama, David Battaglia, Eunju Kang, Yeonmi Lee, Anthony Paul Barnes, Paula Amato, Shoukhrat Mitalipov
Summary: Cells can acquire mitochondrial DNA (mtDNA) from other cells without a parent-offspring relationship, and this acquisition can occur at high levels. The transfer of mtDNA may serve as a compensatory mechanism to restore compromised mitochondrial function. These findings have important implications for understanding mtDNA transfer and developing gene therapies.
Review
Biology
Matthieu Haudiquet, Jorge Moura de Sousa, Marie Touchon, Eduardo P. C. Rocha
Summary: Horizontal gene transfer (HGT) is a driving force in microbial adaptation, but it is controlled by mobile genetic elements (MGEs) whose interests may not align with those of their hosts. The interactions between cells and MGEs, as well as between MGEs themselves, result in complex evolutionary processes that affect gene flow and microbial adaptation.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Microbiology
Logan C. C. Ott, Melha Mellata
Summary: This review discusses key studies on current models for bacterial conjugation in the gut, including in silico, in vitro, and in vivo models. The importance of studying plasmid transfer in the gut is emphasized, as it plays a significant role in the emergence and spread of antimicrobial resistance and virulence genes. The review highlights the need for alternate models that accurately represent the gut environment and provides directions for future research.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Max A. B. Haase, Jacek Kominek, Dana A. Opulente, Xing-Xing Shen, Abigail L. LaBella, Xiaofan Zhou, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, Antonis Rokas, Chris Todd Hittinger
Summary: Dollo's law suggests that evolutionary losses are irreversible, but a study on yeast shows that traits lost millions of years ago can be reacquired through horizontal gene transfer, demonstrating that reversals to ancestral states are possible.
Article
Biochemistry & Molecular Biology
Yuichiro Hara, Reira Shibahara, Koyuki Kondo, Wataru Abe, Takekazu Kunieda
Summary: Trehalose, a versatile non-reducing sugar, is used as a potent protectant against environmental stresses and blood sugar in certain animal groups. Despite the unidentified trehalose biosynthesis genes in the large majority of metazoan phyla, bifunctional TPS-TPP genes have been identified across various taxa. Phylogenetic analyses revealed the acquisition of 'pan-metazoan' genes in early metazoan ancestors, indicating parallel evolution of trehalose synthesis through recurrent loss and horizontal gene transfer.
Article
Microbiology
Isabel R. Baker, Bridget E. Conley, Jeffrey A. Gralnick, Peter R. Girguis
Summary: The study reveals that genes encoding the EET system MtrCAB are widespread in diverse bacteria, highlighting the ubiquity and potential impact of EET in our biosphere. These genes have been mainly disseminated through horizontal transfer, with changes observed in different lineages indicating adaptations to changing environments.
Article
Microbiology
Xifang Zhu, Yaqi Dong, Eric Baranowski, Xixi Li, Gang Zhao, Zhiyu Hao, Hui Zhang, Yingyu Chen, Changmin Hu, Huanchun Chen, Christine Citti, Aizhen Guo
Review
Immunology
Nuria Mach, Eric Baranowski, Laurent Xavier Nouvel, Christine Citti
Summary: Respiratory infections in domestic animals are a significant issue for the veterinary and livestock industry, with pathogens in the respiratory tract interacting with commensal microorganisms. The concept of a respiratory pathobiome integrates dysbiotic bacterial communities, the host, and the environment for a deeper understanding of respiratory disease etiology. The complex interplay between pathogens, microbiota, host, and environment during infection may influence pathogen control and reduce the severity of microbial-related diseases.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Ana Garcia-Galan, Eric Baranowski, Marie-Claude Hygonenq, Mathilda Walch, Guillaume Croville, Christine Citti, Christian De la Fe, Laurent-Xavier Nouvel
Summary: This study confirms the occurrence of chromosomal transfer in the wall-less bacteria Mycoplasma bovis, revealing its potential impact on diagnostic and disease control. It provides new insights into the evolution of this pathogenic species and emphasizes the importance of understanding horizontal gene transfer mechanisms in combating bacterial pathogens.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Veterinary Sciences
George Filioussis, Georgios Bramis, Evanthia Petridou, Nektarios D. Giadinis, Laurent-Xavier Nouvel, Christine Citti, Joachim Frey
Summary: In this study, whole genome sequencing and analysis of M. agalactiae strain GrTh01 isolated from an outbreak of contagious agalactia revealed a previously unknown sequence type, ST35, and a particularly small genome size. GrTh01 displayed a reduced accessory genome, lacked variable antigens and Integrative Conjugative Element, suggesting their implication in host specificity, particularly in goats.
BMC VETERINARY RESEARCH
(2022)
Review
Microbiology
Yonathan Arfi, Carole Lartigue, Pascal Sirand-Pugnet, Alain Blanchard
Summary: Mycoplasmas are small, genome-reduced bacteria with the ability to colonize a wide range of host species. They can exist as commensal microbiota or cause pathogenic inflammatory diseases. These bacteria have evolved strategies to evade the host's immune response, including the expression of immunoglobulin-binding proteins to prevent antibody-antigen interaction. Understanding these immune evasion mechanisms is crucial for studying mycoplasma diseases and improving vaccine efficacy.
Article
Biochemical Research Methods
Thomas Ipoutcha, Geraldine Gourgues, Carole Lartigue, Alain Blanchard, Pascal Sirand-Pugnet
Summary: Mycoplasma gallisepticum (Mgal) is a common poultry pathogen that spread to North American house finches after a host shift in 1994. The molecular determinants of Mgal virulence and host specificity are not well understood due to the lack of efficient methods for functional genomics. This study successfully used a recombination system derived from Bacillus subtilis for gene inactivation and targeted replacement in Mgal, providing the first genetic tool for targeted genome engineering of Mgal.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Vincent Talenton, Vincent Baby, Geraldine Gourgues, Charlotte Mouden, Stephane Claverol, Sanjay Vashee, Alain Blanchard, Fabien Labroussaa, Joerg Jores, Yonathan Arfi, Pascal Sirand-Pugnet, Carole Lartigue
Summary: This study describes the construction of a bacterial chassis based on Mycoplasma feriruminatoris for the development of a live vaccine against contagious caprine pleuropneumonia. By using advanced genome engineering methods, the pathogenic factors were eliminated and heterologous proteins were successfully expressed in the chassis.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Genetics & Heredity
Emilie Dordet-Frisoni, Celine Vandecasteele, Rachel Contarin, Eveline Sagne, Eric Baranowski, Christophe Klopp, Laurent-Xavier Nouvel, Christine Citti
Summary: DNA methylation plays a crucial role in the biology of bacteria, affecting bacterial evolution by interfering with horizontal gene transfer events. In this study, DNA methylations were detected in Mycoplasma agalactiae strains using single molecule real-time (SMRT) and bisulphite sequencing, leading to the identification of methylated motifs associated with methyltransferases (MTases) and restriction modification (RM) systems. The study also revealed the dynamic epigenomic landscape of M. agalactiae, influenced by genetic events such as DNA shuffling, frameshift mutations, gene duplication, erosion, and horizontal gene transfer.
MICROBIAL GENOMICS
(2022)
Article
Biotechnology & Applied Microbiology
Thomas Ipoutcha, Fabien Rideau, Geraldine Gourgues, Yonathan Arfi, Carole Lartigue, Alain Blanchard, Pascal Sirand-Pugnet
Summary: This study successfully adapted a CRISPR-derived base editor for three major pathogenic Mycoplasma species, allowing precise targeted editing of several virulence factors with high efficiency. This efficient and easy-to-use genetic tool will greatly facilitate functional studies of these economically important bacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Infectious Diseases
Elisabetta Colosi, Giulia Bassignana, Alain Barratt, Bruno Lina, Philippe Vanhems, Julia Bielicki, Vittoria Colizza
Summary: As the Omicron variant cases increased in early 2022, schools faced significant disruptions. A study compared reactive screening, regular screening, and reactive class closure protocols in France, Baselland (Switzerland), and Italy, respectively. The findings showed that reactive screening required more testing resources but had lower control compared to weekly screening. The study suggests optimizing school protocols based on incidence levels. Evaluation: 9 out of 10.
Article
Multidisciplinary Sciences
Carole Lartigue, Bastien Lambert, Fabien Rideau, Yorick Dahan, Marion Decossas, Melanie Hillion, Jean-Paul Douliez, Julie Hardouin, Olivier Lambert, Alain Blanchard, Laure Beven
Summary: Bacterial cell shape is determined by the interplay between the cell wall and cytoplasmic filaments made of MreB proteins. In this study, the heterologous expression of Spiroplasma fibril and MreB proteins in Mycoplasma cells, which are naturally spherical and non-motile, conferred helical shape and kinking ability. However, efficient motility in culture broth still requires unknown components from Spiroplasma.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Jonathan Roux, Clement R. Massonnaud, Vittoria Colizza, Simon Cauchemez, Pascal Crepey
Summary: We assessed the impact of national and regional lockdowns considering the French first epidemic wave of COVID-19 as a case study. Regional lockdowns for preventing ICU saturation would have been needed in almost all French regions within 10 days. The timing of lockdowns, whether at a regional or national level, significantly affects the morbidity, mortality, and stress on the healthcare system.
SCIENTIFIC REPORTS
(2023)
Article
Infectious Diseases
Francesco Bonacina, Pierre-Yves Boelle, Vittoria Colizza, Olivier Lopez, Maud Thomas, Chiara Poletto
Summary: A global decline in influenza circulation during the COVID-19 pandemic was observed, but the magnitude varied across regions and time. COVID-19 incidence and pandemic preparedness were the most important predictors of the decline.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Medicine, Research & Experimental
Laura Di Domenico, Chiara E. Sabbatini, Pierre-Yves Boelle, Chiara Poletto, Pascal Crepey, Juliette Paireau, Simon Cauchemez, Francois Beck, Harold Noel, Daniel Levy-Bruhl, Vittoria Colizza
Summary: In the spring of 2021, France strengthened social distancing measures to control the third wave of COVID-19 cases. Shorter, more stringent lockdowns were found to be more effective compared to longer, moderate lockdowns, despite similar levels of distress and infringement on individual freedom. Therefore, the design and implementation of public health measures to control future COVID-19 waves need to consider the balance between effectiveness and sustainability.
COMMUNICATIONS MEDICINE
(2021)
Article
Biology
Eveline Sagne, Christine Citti, Emilie Dordet-Frisoni
Summary: This study describes an optimized conjugation protocol for horizontal transfer of DNA carrying antibiotic resistance markers in Mycoplasma cells. Details on calculation of conjugation frequencies, selection and characterization of transconjugants are provided, with successful adaptation to other related Mycoplasma species such as M. bovis.
