Article
Multidisciplinary Sciences
Joshua M. Borin, Sarit Avrani, Jeffrey E. Barrick, Katherine L. Petrie, Justin R. Meyer
Summary: Training bacteriophages on target hosts before therapy can prolong suppression of antibiotic-resistant bacteria by delaying the evolution of resistance. Evolution of resistance to trained phages is more costly and requires multiple mutations, making them more effective in combating resistance. Transfer of genetic information from host genomes through recombination can enhance phage fitness and improve treatment outcomes, highlighting the potential of training in phage therapy development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Alexandra von Strempel, Anna S. Weiss, Johannes Wittmann, Marta Salvado Silva, Diana Ring, Esther Wortmann, Thomas Clavel, Laurent Debarbieux, Karin Kleigrewe, Barbel Stecher
Summary: Gut microbial communities play a protective role against major human gastrointestinal pathogens. Bacteriophages (phages) are commonly ingested and have the potential for microbiome engineering without adverse effects. However, the functional role of phages in the gastrointestinal microbiome is still unclear.
Review
Microbiology
Greater Kayode Oyejobi, Xiaoxu Zhang, Dongyan Xiong, Faith Ogolla, Heng Xue, Hongping Wei
Summary: Phage treatment shows potential for bacterial infections, but bacterial resistance to phage is a challenge. Research on phage resistance and coevolutionary dynamics between phage and bacteria is crucial for successful phage therapy.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Microbiology
Kaitlyn E. Kortright, Simon Doss-Gollin, Benjamin K. Chan, Paul E. Turner
Summary: This study found that selection for Escherichia coli to resist phage T6, phage U115, or albicidin often results in cross-resistance evolution, but these mutants did not exhibit measurable growth deficiencies. This suggests that when considering new antibacterial therapies, thorough investigation into the evolutionary consequences of the treatment should be conducted to avoid potential evolved trade-ups.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Olaya Rendueles, Jorge A. M. de Sousa, Eduardo P. C. Rocha
Summary: Many bacterial genomes carry prophages that can eliminate competitors, and bacteria can develop resistance through various mechanisms, such as surface receptor modification or lysogenization. The adaptation process of phage resistance involves both genetic and non-genetic changes. Our study showed that the frequency of capsulated cells in phage-sensitive populations increased over time, indicating the fine-tuning of capsule production as an adaptation to reduce phage absorption.
Article
Evolutionary Biology
Joshua M. Borin, Justin J. Lee, Krista R. Gerbino, Justin R. Meyer
Summary: The use of phage therapy has gained renewed interest due to the evolution and spread of antibiotic-resistant bacteria. Phages can be used in cocktails to target different modalities and improve treatment outcomes. However, the multipartite nature of cocktails may lead to unintended evolutionary and ecological outcomes.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Ecology
Daniel A. Schwartz, William R. Shoemaker, Andreea Magalie, Joshua S. Weitz, Jay T. Lennon
Summary: Dormancy is an adaptation to fluctuating environments that allows individuals to reduce metabolic activity. It can influence species interactions by providing a refuge and retaining phenotypic and genetic diversity. This study demonstrates that dormancy modifies antagonistic coevolution patterns and processes by generating a seed bank that retains diversity and dampens coevolution.
Article
Food Science & Technology
Amel Chaib, Cecile Philippe, Fety Jaomanjaka, Yasma Barchi, Florencia Oviedo-Hernandez, Olivier Claisse, Claire Le Marrec
Summary: Winemaking involves complex processes, including alcoholic and malolactic fermentations. While natural microbiota can conduct spontaneous malolactic fermentation (MLF), the use of selected bacteria starter cultures is preferred for a reliable fermentation. Factors such as high ethanol concentration and the presence of bacteriophages can inhibit MLF.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2022)
Review
Ecology
Saul Huitzil, Cristian Huepe, Maximino Aldana, Alejandro Frank
Summary: This review explores the role of the microbiome in evolution, emphasizing its importance in addressing evolutionary phenomena and the missing heritability problem. The article advocates for recognizing the microbiome as a source of evolutionary innovation and analyzes the relevant evidence and implications.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biology
Matthew C. Bond, Lucia Vidakovic, Praveen K. Singh, Knut Drescher, Carey D. Nadell
Summary: Bacteriophages can be trapped in the biofilm matrix, remaining viable and able to kill susceptible cells, even if colonizing cells are present prior to phage exposure. Colonizing cells gain phage protection by being enveloped in curli-producing clusters of resident biofilm cells if they are present on the biofilm long enough before phage exposure.
Article
Biotechnology & Applied Microbiology
Matthew R. Olm, Alexander Crits-Christoph, Keith Bouma-Gregson, Brian A. Firek, Michael J. Morowitz, Jillian F. Banfield
Summary: The program inStrain is used to study genetic diversity in microbial populations, particularly in fecal metagenomes of newborn premature infants. Results show that siblings share more microbial strains compared to unrelated infants, and infants born via cesarean section harbor bacteria with higher nucleotide diversity than vaginally delivered infants, potentially due to hospital acquisition. InStrain can be applied to analyze microdiversity and strain comparison in any metagenomic dataset.
NATURE BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Layla Hockerstedt, Elina Numminen, Ben Ashby, Mike Boots, Anna Norberg, Anna-Liisa Laine
Summary: This study found that isolated host populations are more affected by pathogen infection, while connected host populations have higher levels of resistance diversity. Spatial structure and host gene flow play important roles in the impacts of pathogens on hosts.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Bahman Panahi, Mohammad Majidi, Mohammad Amin Hejazi
Summary: This study utilized a genome-mining approach to investigate the diversity and occurrence of CRISPR-Cas systems in 83 L. brevis strains, as well as their targeted effects on phages and plasmids. The results showed that L. brevis strains frequently harbor multiple CRISPR systems, and different subtypes of CRISPR sequences undergo diverse evolutionary paths. The study revealed the potential of using CRISPR spacer polymorphism for genotyping lactobacillus strains and provided insights into the distribution, diversity, and functional impacts of CRISPR-Cas systems in L. brevis strains.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Casey O. Barkan, Shenshen Wang
Summary: Closely related microbial strains can stably coexist in natural systems, resulting in high levels of fine-scale biodiversity. The mechanisms that maintain this coexistence are not fully understood, but spatial heterogeneity and migration rate play important roles. In this study, a simple evolutionary model with heterogeneous selection pressure was used to investigate how migration rate affects biodiversity. The results show that the biodiversity-migration rate relationship is influenced by multiple phase transitions and critical slowing down, which can provide insights for detecting and altering extinction events.
Article
Microbiology
Daniel A. Schwartz, Josue A. Rodriguez-Ramos, Michael Shaffer, Rory M. Flynn, Rebecca A. Daly, Kelly C. Wrighton, Jay T. Lennon
Summary: Spore-forming bacteria are common in mammalian guts and affect host health and nutrition. Dormant spore production plays a crucial role in the colonization, persistence, and transmission of these bacteria. Recent studies have shown that phages can counteract dormancy-mediated defense mechanisms and alter the transitions between active and inactive states through the expression of phage-carried sporulation genes during infection. Identification of sporulation genes preferentially carried by phages that infect spore-forming bacteria can help in understanding the complex genetic network responsible for spore development.
Article
Chemistry, Analytical
Carlos Cardoso-Palacios, Ingela Lanekoff
JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY
(2016)
Article
Multidisciplinary Sciences
Xiaoze Li, Cecilia Johansson, Carlos Cardoso Palacios, Anki Mossberg, Soniya Dhanjal, Monika Bergvall, Stefan Schwartz
Article
Virology
Alexandra Ahlgren-Berg, Carlos Cardoso-Palacios, Jesper M. Eriksson, Sridhar Mandali, Wilhelmina Sehlen, Lina Sylwan, Elisabeth Haggard-Ljungquist
Article
Microbiology
Shazeeda Koonjan, Fredrik Seijsing, Callum J. Cooper, Anders S. Nilsson
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Microbiology
Shazeeda Koonjan, Callum J. Cooper, Anders S. Nilsson
Summary: ETEC strains are a significant cause of bacterial diarrheal illness, with potential treatment through bacteriophage therapy. Phage vB_EcoP_SU7, a rare Podoviridae member, exhibits an elongated head C3 morphotype. Despite limited host range and poor infection kinetics, it is unlikely to be used as a standalone therapeutic phage.
Review
Chemistry, Medicinal
Callum J. Cooper, Shazeeda Koonjan, Anders S. Nilsson
Article
Microbiology
Joakim L. Karlsson, Carlos Cardoso-Palacios, Anders S. Nilsson, Elisabeth Haggård-Ljungquist
JOURNAL OF BACTERIOLOGY
(2006)