Review
Biochemistry & Molecular Biology
Nathan I. Wisnoski, Jay T. Lennon
Summary: Movement is crucial for the fitness and survival of organisms. It plays a role in resource acquisition, predator avoidance, genetic exchange, and response to stressful environments. However, the relationship between individual movement and microbial diversity is not well understood. Movement ecology provides a framework to study the causes and consequences of microbial movements by integrating insights from cell biology, ecology, and evolution.
TRENDS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Steffanie A. Strathdee, Graham F. Hatfull, Vivek K. Mutalik, Robert T. Schooley
Summary: Increasing antimicrobial resistance rates have prompted a resurgence in bacteriophage research as an alternative therapy. The ideal therapeutic phage should possess lytic properties, efficiently kill the bacterial host, and be well-characterized to ensure safety. This article reviews the current state of phage therapy, including biological mechanisms, clinical applications, challenges, and future directions involving naturally occurring and genetically modified or synthetic phages.
Article
Microbiology
Wenyuan Zhou, Yajie Li, Xuechao Xu, Shengqi Rao, Hua Wen, Yeiling Han, Aiping Deng, Zhenwen Zhang, Zhenquan Yang, Guoqiang Zhu
Summary: Prophages in Staphylococcus aureus genome play a role in genetic diversity and survival strategies, but their interactions and genetic diversity with lytic phages and hosts are unclear. Through genome analysis, 579 intact and 1,389 incomplete prophages were identified in 493 S. aureus isolates. Compared to lytic phages, the intact and incomplete prophages harbored antimicrobial resistance and virulence factor genes. The shared gene pool and recombination events between prophages and lytic phages contribute to genetic diversity and coevolution.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alan Fecchio, Henrique Batalha-Filho, Janice H. Dispoto, Jeffrey A. Bell, Jason D. Weckstein
Summary: Amazonia serves as the main source of diversity for haemosporidian parasites in South America, but our understanding of their biogeographical processes and contributions from different areas of endemism is incomplete. This study investigates the spatiotemporal evolution of Plasmodium and Parahaemoproteus parasites and finds that dispersal is the main driver of Plasmodium diversification, while duplication is more frequent in Parahaemoproteus. The results show that the Inambari area is the primary source of Plasmodium diversity on Marajó Island, but the island receives more Parahaemoproteus lineages from Cerrado habitats than any Amazonian area. The unique dispersal patterns and host-shifting ability of each parasite genus may have facilitated their diversification across Amazonia, with deep evolutionary history potentially constraining their colonization of Marajó Island.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Breno H. Almeida, Maria L. S. Medeiros, Ana C. D. S. Bezerra, Michele D. C. Silva
Summary: This study reported the nematicidal effect of a lectin preparation isolated from Artocarpus heterophyllus seeds on larvae and adults of Haemonchus contortus. The results showed that the lectin preparation significantly reduced the motility index of H. contortus, indicating its potential for being utilized in the development of natural nematicides.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Microbiology
Amanda Carroll-Portillo, Kellin N. Rumsey, Cody A. Braun, Derek M. Lin, Cristina N. Coffman, Joe A. Alcock, Sudha B. Singh, Henry C. Lin
Summary: The ability of phage to regulate bacterial populations within the gastrointestinal microbiome offers potential for prophylactic and therapeutic applications. This study investigated the influence of mucin concentration and agitation on phage predation, using two lytic coliphage. Results showed that the interaction between phage and bacteria is influenced by environmental factors, with higher mucin concentration and agitation inhibiting phage predation at low multiplicities of infection, but not at high multiplicities of infection.
Article
Multidisciplinary Sciences
Ahmed M. Ibrahim
Summary: Cooperation is crucial for all domains of life, but it can be easily exploited by cheats. To support cooperation, evolutionary biologists search for mechanisms that can maintain it. Research shows that cooperation can emerge and be maintained when there is sufficient interaction among cooperators. However, conditional defector strategies can disrupt these mechanisms and take over the population.
SCIENTIFIC REPORTS
(2022)
Article
Virology
Nathaniel C. Esteves, Steffen Porwollik, Michael McClelland, Birgit E. Scharf
Summary: The study identified the impact of different gene deletion regions on the infectivity of flagellotropic phage chi, showing that multi-gene deletions affecting the efflux system reduced infection, deletion of the tig gene reduced infection, and deletion of genes involved in antioxidant synthesis reduced infectivity.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chujin Ruan, Josep Ramoneda, Guram Gogia, Gang Wang, David R. Johnson
Summary: Fungal hyphae-mediated dispersal plays an important role in regulating bacterial diversity during range expansion.
Article
Multidisciplinary Sciences
Martin Lukacisin, Adriana Espinosa-Cantu, Tobias Bollenbach
Summary: Introns mediate inducible phenotypic heterogeneity and provide a fitness advantage in yeast, enhancing survival and growth under stress and starvation conditions.
Article
Ecology
Theresa Jautzus, Jordi van Gestel, Akos T. Kovacs
Summary: Bacteria form cell collectives on surfaces in nature and secrete molecules that affect surface competition in different ways, such as surfactin acting as a common good and BslA and EPS acting locally.
Article
Biology
Emeric Bouin, Guillaume Legendre, Yuan Lou, Nichole Slover
Summary: The study suggests that in a two-dimensional heterogeneous environment, the best strategy for populations is to move in one direction only, especially towards the direction with smaller variation in resource distribution. This finding aligns with classical results on the evolution of slow dispersal.
JOURNAL OF MATHEMATICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Tatsuaki Kurata, Chayan Kumar Saha, Jessica A. Buttress, Toomas Mets, Tetiana Brodiazhenko, Kathryn J. Turnbull, Ololade F. Awoyomi, Sofia Raquel Alves Oliveira, Steffi Jimmy, Karin Ernits, Maxence Delannoy, Karina Persson, Tanel Tenson, Henrik Strahl, Vasili Hauryliuk, Gemma C. Atkinson
Summary: Toxin-antitoxin gene pairs are widespread in microorganisms and bacteriophages, acting as regulatory switches. A computational tool called FlaGs was used to analyze the conservation of genomic neighborhoods and uncover previously unknown diversity in TA operons. The poorly characterized antitoxin domain DUF4065 was found to be widely distributed and capable of neutralizing toxins with multiple different folds. Experimental validation confirmed the neutralizing activity of nine PanA-neutralized TA pairs, including a novel nucleotide cyclase toxin. Panacea-containing antitoxins were found to form complexes with their cognate toxins, indicating a direct neutralization mechanism. Directed evolution also demonstrated the evolutionary plasticity of the PanA antitoxin domain.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Curtis M. Lively, Julie Xu, Frida Ben-Ami
Summary: The study found that there may be a strong positive correlation between host genetic diversity and infection prevalence for intermediate values of parasite virulence and fecundity. However, in field populations, the correlation can be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the main force maintaining host diversity. Correlational analyses of field populations might therefore underestimate the role of parasites in maintaining host diversity.
Article
Biology
Jenna A. Moore-Ott, Selena Chiu, Daniel B. Amchin, Tapomoy Bhattacharjee, Sujit S. Datta
Summary: Bacteria are present everywhere in our daily lives, either as mobile planktonic cells or as immobilized surface-attached biofilms. Understanding the conditions under which bacteria transition between these different states is crucial. This study develops a biophysical model to predict and control biofilm formation based on factors such as cell concentration, motility, nutrient diffusion, chemotactic sensing, and autoinducer production.
Article
Parasitology
Benjamin J. Z. Quigley, Sam P. Brown, Helen C. Leggett, Pauline D. Scanlan, Angus Buckling
Article
Ecology
Meaghan Castledine, Angus Buckling, Daniel Padfield
JOURNAL OF EVOLUTIONARY BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Pawel Sierocinski, Florian Bayer, Gabriel Yvon-Durocher, Melia Burdon, Tobias Grosskopf, Mark Alston, David Swarbreck, Phil J. Hobbs, Orkun S. Soyer, Angus Buckling
Article
Biology
Lauri Mikonranta, Angus Buckling, Matti Jalasvuori, Ben Raymond
Article
Microbiology
Lisa van Sluijs, Stineke van Houte, John van Der Oost, Stan J. J. Brouns, Angus Buckling, Edze R. Westra
FEMS MICROBIOLOGY LETTERS
(2019)
Article
Ecology
Miguel A. Fortuna, Matthew A. Barbour, Luis Zaman, Alex R. Hall, Angus Buckling, Jordi Bascompte
Article
Biology
Elze Hesse, Daniel Padfield, Florian Bayer, Eleanor M. van Veen, Christopher G. Bryan, Angus Buckling
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2019)
Article
Biology
Tatiana Dimitriu, Lauren Marchant, Angus Buckling, Ben Raymond
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2019)
Article
Multidisciplinary Sciences
Anastasia V. Wass, George Butler, Tiffany B. Taylor, Philip R. Dash, Louise J. Johnson
ROYAL SOCIETY OPEN SCIENCE
(2020)
Article
Multidisciplinary Sciences
James S. Horton, Louise M. Flanagan, Robert W. Jackson, Nicholas K. Priest, Tiffany B. Taylor
Summary: Mutational hotspots can determine evolutionary outcomes and make evolution repeatable. Experiments in bacteria reveal that a powerfully deterministic genetic hotspot can be built and broken by a handful of silent mutations, highlighting an underappreciated role for silent genetic variation in determining adaptive outcomes.
NATURE COMMUNICATIONS
(2021)
Review
Microbiology
Tiffany B. Taylor, Matthew J. Shepherd, Robert W. Jackson, Mark W. Silby
Summary: At the gene level, mutation is the raw material for natural selection, while at the gene regulatory network (GRN) level, crosstalk provides opportunities for genetic innovation and adaptation. Various genetic and environmental features can increase the potential for crosstalk and rewiring of GRNs, which can be selected if they provide fitness benefits. This article identifies factors that facilitate crosstalk and rewiring, and discusses the impact of GRN features on evolution.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
M. J. Shepherd, J. S. Horton, T. B. Taylor
Summary: This study reveals the importance of genomic features in facilitating the formation of mutational hotspots, including genomic location, local nucleotide sequence, gene strandedness, and the presence of mismatch repair proteins.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Louise M. Flanagan, James S. Horton, Tiffany B. Taylor
Summary: The observed mutational spectrum of adaptive outcomes can be constrained by factors such as mutational biases and complex environments. In this study, we investigated the impact of nutrient environments on the evolution of motility in Pseudomonas fluorescens and found that the mutational spectrum and phenotype strength were influenced by the nutrient environment.
Article
Biochemistry & Molecular Biology
Matthew J. Shepherd, Aidan P. Pierce, Tiffany B. Taylor
Summary: The survival of a population during environmental shifts depends on the rate of phenotypic adaptation keeping up with changing conditions. This study explores the rewiring of gene regulatory network connections to facilitate novel interactions and transcription factor innovation. The research identifies three key properties that enable transcription factor innovation: high activation, high expression, and pre-existing low-level affinity for novel target genes. The ease of acquiring these properties is constrained by the preexisting GRN architecture.
Article
Ecology
Elze Hesse, Siobhan O'Brien, Nicolas Tromas, Florian Bayer, Adela M. Lujan, Eleanor M. van Veen, Dave J. Hodgson, Angus Buckling