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
Biotechnology & Applied Microbiology
Baiyuan Li, Dan Chen, Fan Lin, Chuanyu Wu, Linyan Cao, Huahai Chen, Yunfei Hu, Yeshi Yin
Summary: Bifidobacteria are important gut microbiota that have probiotic properties. The erythromycin resistance gene erm(X) can be transferred to other bifidobacterial strains through the genomic island BKGI1, which is a novel finding. Genomic islands play an important role in the dissemination of the gene erm(X) among Bifidobacterium species.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
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
Microbiology
Xinxin Shan, Xin-Sheng Li, Stefan Schwarz, Yuxia Chen, Chunyan Xu, Xiang-Dang Du
Summary: This study demonstrates the essential role of a pheromone-responsive conjugative plasmid in the horizontal transfer of a lsa(E)-carrying genomic island in Enterococcus faecalis. The presence of this plasmid enables the dissemination of both plasmid-borne resistance genes and chromosomally-located genomic islands. This finding highlights the importance of pheromone-responsive conjugative plasmids in the genomic evolution of E. faecalis, a leading nosocomial pathogen worldwide.
MICROBIOLOGY SPECTRUM
(2022)
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)
Review
Microbiology
Greg Brennan, Ana M. M. Stoian, Huibin Yu, M. Julhasur Rahman, Shefali Banerjee, Jeannine N. Stroup, Chorong Park, Loubna Tazi, Stefan Rothenburg
Summary: Poxviruses, despite being double-stranded DNA pathogens with proofreading polymerases, have highly adaptable genomes that can rapidly undergo genotypic and phenotypic changes. Recent increase in human-to-human transmission of monkeypox virus serves as an example of this adaptability. Advances in deep sequencing technologies have revealed standing nucleotide variation in poxvirus populations that was previously underestimated. There is also growing understanding of the role of genomic architectural changes in shaping poxvirus evolution, including recombination, gene duplications and loss, and acquisition of new genes through horizontal gene transfer.
Article
Plant Sciences
Michelle T. Hulin, Mojgan Rabiey, Ziyue Zeng, Andrea Vadillo Dieguez, Sophia Bellamy, Phoebe Swift, John W. Mansfield, Robert W. Jackson, Richard J. Harrison
Summary: Through examining the genomic diversity of Pseudomonas syringae in the cherry phyllosphere, it was found that nonpathogenic strains contain reservoirs of T3SE genes and there may be horizontal gene transfer of different T3SE genes in cherry pathogens. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the emergence of new pathotypes. Genome-based epidemiological surveillance can be used to apply timely control measures to prevent disease.
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
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
Isabel R. Baker, Bridget E. Conley, Jeffrey A. Gralnick, Peter R. Girguis
Summary: Some bacteria and archaea have evolved the ability to use extracellular electron transfer (EET) as a means of energy metabolism. The MtrCAB system, which transfers electrons from metabolic substrates to electron acceptors outside the cell, has been found in a diverse range of bacteria. These findings highlight the broad relevance of EET to different taxa and biogeochemical cycles in our biosphere and provide a foundation for further research on its evolution and role in Earth's redox landscape.
Article
Biochemical Research Methods
Nabil Ibtehaz, Ishtiaque Ahmed, Md Sabbir Ahmed, M. Sohel Rahman, Rajeev K. Azad, Md Shamsuzzoha Bayzid
Summary: Genomic Islands (GIs) are clusters of genes mobilized through horizontal gene transfer, playing a key role in bacterial evolution. SSG-LUGIA is an automated and unsupervised approach for identifying GIs and horizontally transferred genes, achieving superior performance in comparison to existing methods with a better precision-recall trade-off. Its nondependency on the functional annotation of genomes makes it suitable for analyzing newly sequenced genomes.
BRIEFINGS IN BIOINFORMATICS
(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
Biochemistry & Molecular Biology
Antonio Palazzo, Elsa Escuder, Pietro D'Addabbo, Domenica Lovero, Rene Massimiliano Marsano
Summary: Horizontal transposon transfers (HTT) have been increasingly reported in metazoan species, especially in nematodes, which may play a role in spreading genetic information. However, mechanisms behind this phenomenon are still not well understood.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biology
Joyeeta Chakraborty, Rudra Prasad Roy, Raghunath Chatterjee, Probal Chaudhuri
Summary: Genomic Islands (GIs) play a crucial role in the evolution and adaptation of prokaryotes. Various GI prediction tools have been developed, but there is a lack of experimentally validated datasets for performance assessment. This study tested the performance of the GI prediction tool Design-Island-II and compared it with other tools. The results showed that Design-Island-II performed the best in terms of sensitivity and F1 score.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Microbiology
Xiaobin Gu, Xiuhai Lu, Shudan Lin, Xinrui Shi, Yue Shen, Qingsong Lu, Yiying Yang, Jing Yang, Jiabei Cai, Chunyan Fu, Yongliang Lou, Meiqin Zheng
Summary: This study identified horizontal gene transfer events between Acanthamoeba and amoeba-resisting microorganisms, shedding light on the pathogenic mechanisms of diseases.
MICROBIOLOGY SPECTRUM
(2022)