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
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
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
Ecology
Yukihiko Toquenaga, Takuya Gagne
Summary: In this study, the researchers reconstructed the reference sequence of a small circular genome phiX174 from 50 random read data sets using 14 assembly programs. Nine out of 14 programs were capable of reconstructing the circular genome reference, with Unicycler being the most successful. However, even successful reconstructions had minor defects, which varied among assembly programs. The centroids of contigs for most assembly programs differed slightly from the reference, indicating a need for additional statistical methods in genetic assembly.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
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)
Article
Agricultural Engineering
Erfan Ghasemi Tousi, Jennifer G. Duan, Patricia M. Gundy, Kelly R. Bright, Charles P. Gerba
Summary: The study found that the resuspension rate of PhiX174 in irrigation canal bed sediment increases with bed shear stress, and proposed two models to correlate PhiX174 concentration with bed shear stress for different sediment types, providing insights into the relationship between viruses in water and sediment.
JOURNAL OF IRRIGATION AND DRAINAGE ENGINEERING
(2021)
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.
Review
Virology
Sarah M. Doore, Bentley A. Fane
Article
Virology
Sarah M. Doore, Nicholas J. Schweers, Bentley A. Fane
Article
Virology
Sarah M. Doore, Jason R. Schrad, William F. Dean, John A. Dover, Kristin N. Parent
JOURNAL OF VIROLOGY
(2018)
Article
Biochemistry & Molecular Biology
Sarah M. Doore, Cameron D. Baird, Aaron P. Roznowski, Bentley A. Fane
MOLECULAR BIOLOGY AND EVOLUTION
(2014)
Article
Neurosciences
S. Ferguson, B. Mouzon, G. Kayihan, M. Wood, F. Poon, S. Doore, V. Mathura, J. Humphrey, B. O'Steen, R. Hayes, A. Roses, M. Mullan, F. Crawford
Article
Virology
Aaron P. Roznowski, Sarah M. Doore, Sundance Z. Kemp, Bentley A. Fane
JOURNAL OF VIROLOGY
(2020)
Article
Virology
Sarah M. Doore, Jason R. Schrad, Hailee R. Perrett, Kevin P. Schrad, William F. Dean, Kristin N. Parent
Article
Biochemistry & Molecular Biology
Kendal R. Tinney, John A. Dover, Sarah M. Doore, Kristin N. Parent
Summary: Viruses rely on hosts for replication, so identifying suitable host cells is a critical step in the infection process. Bacterial viruses, or phages, use receptor binding proteins to distinguish between susceptible and non-susceptible hosts. Bacteria with modified or deleted receptor genes often undergo positive selection in the presence of phages, and this can have various effects on the bacteria's phenotype.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Virology
Sundharraman Subramanian, John A. Dover, Kristin N. Parent, Sarah M. Doore
Summary: The first critical step in a virus's infection cycle is attachment to its host. This study focused on the interaction between bacteriophage Sf6 and its host Shigella flexneri. The phage utilizes a two-step process to recognize and bind to its host, first recognizing the lipopolysaccharide (LPS) of the host and then binding to outer membrane proteins. Through experimental evolution, mutations were observed in the receptor-binding tailspike protein that dramatically affected the binding of the receptors, providing flexibility for the phage in identifying host cells and altering its host range.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemical Research Methods
H. Fai Poon, Laila Abdullah, Jon Reed, Sarah M. Doore, Cyndi Laird, Venkat Mathura, Michael Mullan, Fiona Crawford
BIOLOGICAL PROCEDURES ONLINE
(2007)
Article
Plant Sciences
A. M. Clore, S. M. Doore, S. M. N. Tinnirello
PLANT CELL AND ENVIRONMENT
(2008)