Article
Virology
Rodrigo A. L. Rodrigues, Victoria F. Queiroz, Jayadri Ghosh, David D. Dunigan, James L. Van Etten
Summary: This study performed a functional genomic analysis of chloroviruses that infect different hosts, revealing the characteristics of the pan-genome and the core genome of these viruses. These findings are important for understanding the evolution and ecology of chloroviruses.
JOURNAL OF VIROLOGY
(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)
Article
Biochemistry & Molecular Biology
Gaurav G. G. Shimpi, Bastian Bentlage
Summary: In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.
Article
Microbiology
Gaurav Agarwal, Ronald D. Gitaitis, Bhabesh Dutta
Summary: This study revealed the genomic structure and evolution pattern of Psi through whole genome sequencing and phylogenetic analysis, identifying pathogenicity genes of Psi in onions. Horizontal gene transfer analysis demonstrated gene transfer between different Pantoea species, with frequent gene transfer events observed between the two pathovars of Psi.
Article
Biotechnology & Applied Microbiology
Sushanta Deb
Summary: This study comprehensively analyzes the genome of type strains of the Bifidobacterium genus and reveals the association between pan-genome evolution and metabolic function divergence. It also demonstrates that horizontal gene transfer, genome expansion, and reduction events contribute to the divergence of metabolic functions in the Bifidobacterium genus. Furthermore, a genome-based search identifies potential probiotic type species that could benefit nutrient-deficient individuals.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(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)
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
Microbiology
Gaurav Agarwal, Divya Choudhary, Shaun P. Stice, Brendon K. Myers, Ronald D. Gitaitis, Stephanus N. Venter, Brian H. Kvitko, Bhabesh Dutta
Summary: The study identified chromosomal and plasmid gene clusters as well as novel genes associated with pathogenicity in Pantoea ananatis through a comprehensive pan-genome wide association study. These genes play a role in the development of center rot disease in onions.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Evolutionary Biology
Joshua T. Smith, Cheryl P. Andam
Summary: Members of the genus Staphylococcus have been historically classified into coagulase-positive and coagulase-negative based on the presence of the coagulase protein. While horizontal gene transfer has been well-studied in CoPS species like Staphylococcus aureus, this study sheds light on the importance of these processes in CoNS evolution. CoNS species serve as reservoirs of transferrable genes associated with antimicrobial resistance, with certain species acting as hubs of gene flow and genetic diversity for the entire genus.
GENOME BIOLOGY AND EVOLUTION
(2021)
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
Biochemistry & Molecular Biology
Minkyu Park, Ali Sarkhosh, Violeta Tsolova, Islam El-Sharkawy
Summary: Horizontally transferred transposable elements play a significant role in plant genome evolution by generating additional TE subfamilies and causing differential proliferation in host genomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biology
Emilie Aubin, Moaine El Baidouri, Olivier Panaud
Summary: Plants maintain species integrity through vertical transmission of genetic information during reproduction, but recent reports have shown that horizontal gene transfers are common in nature, involving all organisms including plants. The advent of next-generation sequencing technologies has provided new perspectives for studying HGTs.
Article
Multidisciplinary Sciences
You Che, Yu Yang, Xiaoqing Xu, Karel Brinda, Martin F. Polz, William P. Hanage, Tong Zhang
Summary: The study found that plasmid-borne antimicrobial resistance genes are mainly enriched in conjugative plasmids. Scientists reported the discovery of a massive insertion sequence-associated antimicrobial resistance gene transfer network, suggesting a general evolutionary mechanism for horizontal gene transfer mediated by the interaction between conjugative plasmids and ISs. Experimental results confirmed the importance of these interactions in aiding the horizontal transfer and expanding the genetic range of antimicrobial resistance genes within complex microbial communities.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Xu Pan, Xin Li, Jie Sun, Zhiying Xiong, Haoyu Hu, Shangwei Ning, Hui Zhi
Summary: This study reveals that DNA methylation can drive tissue-specific enhancer basal transcription and target gene expression in human cancers. By integrating methylome, transcriptome, and 3D genomic data, enhancer methylation triplets were identified and regulatory patterns within them were dissected. Cancer-specific core TFs regulated by enhancers were observed to shape enhancer methylation forming enhancer methylation-driven CRCs (emCRCs).
Article
Virology
Marli Vlok, Adrian J. Gibbs, Curtis A. Suttle
Article
Microbiology
Christoph M. Deeg, Tan T. Le, Matthias M. Zimmer, Curtis A. Suttle
JOURNAL OF BACTERIOLOGY
(2020)
Article
Evolutionary Biology
Ben J. G. Sutherland, Claire Rycroft, Anne-Laure Ferchaud, Rob Saunders, Li Li, Sheng Liu, Amy M. Chan, Sarah P. Otto, Curtis A. Suttle, Kristina M. Miller
EVOLUTIONARY APPLICATIONS
(2020)
Article
Virology
Gideon J. Mordecai, Emiliano Di Cicco, Oliver P. Gunther, Angela D. Schulze, Karia H. Kaukinen, Shaorong Li, Amy Tabata, Tobi J. Ming, Hugh W. Ferguson, Curtis A. Suttle, Kristina M. Miller
Summary: This study identified several viral pathogens in farmed Atlantic and Chinook salmon, including two previously uncharacterized viruses and three putative novel viruses through the application of salmon host transcriptional biomarkers and metatranscriptomic sequencing. High-throughput RT-PCR screening of over 9,000 farmed and wild salmon revealed the widespread presence of these viruses, with some showing a broad host range. Additionally, in situ hybridization showed differing cell tropism for each virus tested, highlighting the importance of continual surveillance of emerging viruses for the management of aquaculture and wild resources.
Article
Biotechnology & Applied Microbiology
Julia A. Gustavsen, Curtis A. Suttle
Summary: This study revealed that the composition of marine viral assemblages undergoes significant changes over time and is laggedly correlated with the resemblance of potential hosts, indicating the influence of viruses on host communities. The dominant clusters of phylogenetically related viruses shift over time, reflecting ecological dynamics within these clusters. The temporal shuffling of viral genotypes primarily occurs within a few subsets of related individuals, suggesting a common structure in natural viral assemblages.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Ruba Abdulrahman Ashy, Curtis A. Suttle, Susana Agusti
Summary: Research in the Red Sea showed that despite being perceived as stable, warm, and saline, relatively modest changes in seasonal conditions led to significant fluctuations in the diversity of lysogeny.
Article
Microbiology
Kevin Xu Zhong, Anna Cho, Christoph M. Deeg, Amy M. Chan, Curtis A. Suttle
Summary: CRISPR-Cas Selective Amplicon Sequencing (CCSAS) is an efficient method for characterizing eukaryotic microbiomes, cutting host 18S rRNA gene sequences while leaving protistan and fungal sequences intact; CCSAS revealed a diverse community of eukaryotic microbes in oyster spat with minimal contamination from host sequences and designed taxon-specific sgRNA for around 16,000 metazoan and plant taxa, making CCSAS widely applicable for understudied eukaryotic microbiomes.
Article
Environmental Sciences
Gema L. Batanero, Andy J. Green, Juan A. Amat, Marion Vittecoq, Curtis A. Suttle, Isabel Reche
Summary: Coastal wetlands are valuable aquatic ecosystems with high productivity that provide important services, but are at risk of salinization due to predicted rise of sea level and freshwater extractions. Salinization may shift microbial activity from heterotrophic bacterial-dominated processes towards archaeal-dominated processes, influenced by factors like nitrogen concentration, salinity, and virus abundance. More research is needed to accurately predict future scenarios in coastal wetlands.
Article
Ecology
Kevin Xu Zhong, Jennifer F. Wirth, Amy M. Chan, Curtis A. Suttle
Summary: Microbial lysis plays a significant role in the dynamic changes of marine microbial communities. The study found that high relative lysis rates are associated with copiotrophic bacteria, while low lysis rates are more common in abundant taxa.
Article
Microbiology
Jan F. Finke, Colleen T. E. Kellogg, Curtis A. Suttle
Summary: Deep6 is a deep learning model that accurately classifies short metatranscriptomic sequences into prokaryotes, eukaryotes, or viral realms, without the need for reference or alignment. The average accuracies range from 0.87 to 0.97, depending on the length of the sequences.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Kevin Xu Zhong, Amy M. Chan, Anwar Al-Qattan, Yueang Li, Curtis A. Suttle
Summary: Vibrio natriegens strain PWH3a, isolated from the Texas Gulf Coast, is a model organism in marine microbiology with two circular chromosomes, 4,650 coding sequences, 34 rRNA, 4 noncoding RNA (ncRNA), 131 tRNA genes, and one Mu-like prophage sequence.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Tianyi E. Chang, Brian P. V. H. Hunt, Junya E. Hirai, Curtis H. Suttle
Summary: Sea lice, major ectoparasites of fish, have significant impacts on both wild and farmed fish. This study analyzed transcriptomes and small RNAs of sea lice, and identified 32 previously unknown RNA viruses. These findings greatly expand our knowledge of viral diversity in copepods and provide evidence of virus transmission between arthropods and other eukaryotes over evolutionary time.
Review
Microbiology
Alastair J. Roberts, Curtis A. Suttle
Summary: The diversity of viruses in crustacean zooplankton is enormous, including members of all realms of RNA viruses and single- and double-stranded DNA viruses. Viral infection is likely responsible for a significant portion of unexplained non-consumptive mortality in this group, affecting food webs and biogeochemical cycling. Additionally, zooplankton can transmit economically devastating viruses of finfish and other crustaceans.
