Review
Virology
Martyna Cieslik, Natalia Baginska, Ewa Jonczyk-Matysiak, Alicja Wegrzyn, Grzegorz Wegrzyn, Andrzej Gorski
Summary: Bacteriophages can limit bacterial growth and amplification, and also serve as modulators of mammalian immune responses, particularly temperate phages that influence processes such as phagocytosis of bacterial invaders and immune modulation of mammalian host cells.
Article
Microbiology
Sam Ford, Sara Moeskjaer, Peter Young, Rosa I. Santamaria, Ellie Harrison
Summary: Temperate phages in rhizobia, including a novel group identified in this study, have the potential to impact the ecological dynamics of bacterial communities. Genome comparisons among these phages revealed a high degree of gene conservation with a region of hypervariability containing hypothetical genes. These phages exhibit a history of active mobilization within and between Rhizobium species, as indicated by phylogenetic discordance between prophage and host phylogenies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Eugen Pfeifer, Remy A. Bonnin, Eduardo P. C. Rocha
Summary: Antibiotic resistance is rapidly spreading through horizontal transfer mediated by phage-plasmids, which carry a diverse range of clinically relevant antibiotic resistance genes and can transfer them across bacteria.
Article
Microbiology
Greater Kayode Oyejobi, Sunday Olabode Olaniyan, Nana-Aishat Yusuf, Deborah Adepeju Ojewande, Mobolaji Johnson Awopetu, Goodness Opeyemi Oyeniran, Fazal Mehmood Khan, Peter Alabi Dare, Maryam Kikelomo Adegbite-Badmus
Summary: Acinetobacter baumannii is an important nosocomial and opportunistic pathogen with high antibiotic resistance. New treatment approaches like the use of bacteriophage, phage-antibiotic combinations, and resistance-driven fitness losses are crucial for controlling its infections.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Microbiology
Miaomiao Wu, Yanpeng Zhu, Yuhui Yang, Yali Gong, Zongyue Chen, Binyou Liao, Yu Xiong, Xia Zhou, Yan Li
Summary: This study aimed to isolate and characterize novel oral phages using culture-omics method. A total of 75 bacterial strains were successfully isolated, revealing 14 potential new bacterial species. Additionally, a temperate phage targeting a specific oral commensal bacterium was isolated, indicating a potential role of oral phages in regulating oral microbiome and diseases.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Infectious Diseases
Addisu D. Teklemariam, Rashad R. Al-Hindi, Ishtiaq Qadri, Mona G. Alharbi, Wafaa S. Ramadan, Jumaa Ayubu, Ahmed M. Al-Hejin, Raghad F. Hakim, Fanar F. Hakim, Rahad F. Hakim, Loojen I. Alseraihi, Turki Alamri, Steve Harakeh
Summary: Bacteria and their predator bacteriophages engage in an ongoing arms race, employing various defense strategies. The bacterial immune arsenal towards phages is diverse and utilizes different components of the host machinery. These defense mechanisms include restriction-modification, mutations, receptor blocking, competitive inhibitors, extracellular matrix, assembly interference, abortive infection, toxin-antitoxin systems, bacterial retrons, and replication interference. Phages, in turn, develop defense mechanisms with small fitness cost to counteract these bacterial strategies. This review highlights the major bacterial defense systems and phage counterstrategies, suggesting potential research directions.
Article
Biochemistry & Molecular Biology
Yanze Mi, Yile He, Jinhui Mi, Yunfei Huang, Huahao Fan, Lihua Song, Xiaoping An, Shan Xu, Mengzhe Li, Yigang Tong
Summary: The emergence of phage-resistant bacterial strains poses challenges for phage therapy, but the resistant bacteria often come with adaptive trade-offs. This study investigates the impacts of phages targeting different bacterial receptors on the fitness of the bacterial population. The research findings suggest that phage-resistant bacteria may lose their resistance to antibiotics when countering with phages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Suzanne Humphrey, Alfred Fillol-Salom, Nuria Quiles-Puchalt, Rodrigo Ibarra-Chavez, Andreas F. Haag, John Chen, Jose R. Penades
Summary: It is commonly thought that horizontal transfer of most bacterial chromosomal genes is limited, in comparison with the frequent transfer of mobile genetic elements. Humphrey et al. show that, actually, phage-mediated lateral transduction of core chromosomal genes can be more efficient than the transfer of mobile genetic elements via conjugation or generalized transduction.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Ranjith Kumar Manoharan, Sathiyaraj Srinivasan, Gnanendra Shanmugam, Young-Ho Ahn
Summary: Wastewater treatment plants are hotspots of emerging antimicrobial genes and mobile genetic elements. Hospital wastewater influences the abundance of ARGs and MGEs in activated sludge.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2021)
Article
Environmental Sciences
Tianshu Feng, Qian Han, Wanghong Su, Qiaoling Yu, Jiawei Yang, Huan Li
Summary: In this study, 16S rRNA gene sequences and high-throughput quantitative PCR were used to investigate the microbial communities and antibiotic resistance genes (ARGs) in dust from different urban places. The results showed that dust contained various types and subtypes of ARGs, with different distributions in different public places and seasons. Microbes were identified as the primary driving factor for ARGs in dust, while dust physicochemical parameters had minimal impact.
ENVIRONMENTAL POLLUTION
(2022)
Review
Multidisciplinary Sciences
Olesia I. North, Eric D. Brown
Summary: Antibiotic resistance has become dangerously high worldwide, with a lack of new antibiotics available for clinicians. Combining phages with antibiotics shows promise in suppressing and even reversing resistance evolution in bacteria, highlighting the importance of further understanding their interactions in complex clinical environments.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Chao Wang, Yuqin Song, Na Tang, Gang Zhang, Sebastien Olivier Leclercq, Jie Feng
Summary: This study identified 27 highly prevalent antibiotic resistance genes shared between human and pig intestinal microbiota, with 11 of them having identifiable mobile genetic context. The comparison of mobile genetic elements and associated antibiotic resistance genes revealed varied contributions depending on the host, suggesting different genetic elements are involved in dissemination within human and pig populations. These findings deepen our understanding of antibiotic resistance gene dissemination among and between human and pig gut microbiota.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Engineering, Environmental
Jieya Zhou, Hao Wu, Lihu Shi, Xuming Wang, Yunpeng Shen, Shulei Tian, Lian Hou
Summary: Antibiotic fermentation residue (AFR) is a significant concern for pharmaceutical companies as improper disposal can lead to the transfer of antibiotic resistance in the environment. This study explored the resource recycling strategy for AFR through the production of bio-organic fertilizers using different drying methods. The concentrations of antibiotics in the fertilizers, wastewater, and exhaust gas were measured, and the soil bacterial community was analyzed. Antibiotic resistance genes and mobile genetic elements were also detected. The results show the promising potential of AFR recycling as a management solution for pharmaceutical waste.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Diana Morais, Luis Tanoeiro, Andreia T. Marques, Tiago Goncalves, Aida Duarte, Antonio Pedro Alves Matos, Joana S. Vital, Maria Eugenia Meirinhos Cruz, Manuela Colla Carvalheiro, Elsa Anes, Jorge M. B. Vitor, Maria Manuela Gaspar, Filipa F. Vale
Summary: Pseudomonas aeruginosa is a major threat to human and animal health due to its resistance to multiple antibiotics. Encapsulation of lysins in liposomes can be an effective strategy against this Gram-negative bacterium. This study identified and analyzed lysins from prophages in P. aeruginosa genomes and successfully encapsulated them in liposomes, resulting in a significant reduction in cell viability and lysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Ying Han, Haodong Wang, Jiayue Wu, Yikai Hu, Hexin Wen, Zijian Yang, Hao Wu
Summary: Hydrogen peroxide (H2O2) and aeration were found to be effective in removing antibiotic resistance genes (ARGs) from mariculture sediments. The H2O2 group showed a 3.8-32.3% reduction in ARG abundance compared to the aeration group, and this reduction was associated with decreased bacterial population and diversity. Path modeling analysis revealed that the reduction of mobile genetic elements (MGEs) played an important role in ARG removal in the H2O2 group, while changes in bacterial community composition determined ARG reductions in the aeration group.
ENVIRONMENTAL POLLUTION
(2023)
Article
Evolutionary Biology
Anna M. Bischofberger, Katia R. Pfrunder Cardozo, Michael Baumgartner, Alex R. Hall
Summary: Researchers found that bacteria increased their honey resistance by mutating genes involved in antibacterial activity of honey when adapting to different types of honey. However, they did not observe cross-resistance or collateral sensitivity against antibiotics from six different classes due to honey adaptation.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Ecology
Andrew D. Letten, Michael Baumgartner, Katia R. Pfrunder-Cardozo, Jonathan M. Levine, Alex R. Hall
Summary: The competitive suppression of antibiotic-resistant strains is strongly influenced by the composition of the microbiome, with the source community playing a more significant role than antibiotic exposure. While antibiotics can disrupt community composition, the suppression of resistant strains can still be maintained despite these changes.
Article
Ecology
Henry Goehlich, Linda Sartoris, Kim-Sara Wagner, Carolin C. Wendling, Olivia Roth
Summary: The study found that broad-nosed pipefish are locally adapted to low salinity environments, but still retain phenotypic plasticity to cope with ancestral salinity levels and prevailing pathogens.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Microbiology
Fokko Smakman, Alex R. Hall
Summary: Dead bacterial cells can either support or inhibit the growth of other bacteria based on their lysis process and the surrounding environment. Adding lysate from dead bacteria can suppress the growth of Escherichia coli, particularly affecting genes involved in motility.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Biology
Claudia Igler, Lukas Schwyter, Daniel Gehrig, Carolin Charlotte Wendling
Summary: This study investigates the impact of prophages on the spread of conjugative plasmids and finds that prophages can limit the spread of plasmids. The inhibitory effect is strongly influenced by environmental conditions and bacterial genetic background.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Microbiology
Richard C. Allen, Katia R. Pfrunder-Cardozo, Alex R. Hall
Summary: The study found that local environmental conditions (such as pH, temperature, and bile salts) can influence collateral sensitivity of antibiotics against bacteria, potentially by promoting different sets of mutants during resistance evolution or modifying the expression of collateral effects for individual mutants.
Article
Biochemistry & Molecular Biology
Anna M. Bischofberger, Alex R. Hall
Summary: Humans interact with surfaces and microbial communities in the environment. The composition of bacterial communities on banknotes varies depending on the local collection environment, but shows no evidence of geographic structure.
Article
Genetics & Heredity
Jana S. Huisman, Fabienne Benz, Sarah J. N. Duxbury, J. Arjan G. M. de Visser, Alex R. Hall, Egil A. J. Fischer, Sebastian Bonhoeffer
Summary: This study compares commonly used methods for measuring plasmid conjugation rates and finds that these estimates are often dependent on factors such as measurement time, population densities, and initial ratios of donor to recipient populations. The study proposes a new method to estimate conjugation rates and provides analytical expressions for the valid parameter range. In addition, a user-friendly software package and web interface are provided for accurate and comparable measurement of plasmid conjugation rates.
Article
Genetics & Heredity
Anne Kupczok, Zachary M. Bailey, Dominik Refardt, Carolin C. Wendling
Summary: Lambdoid phages are related temperate phages that can infect gut bacteria. These phages have a mosaic genome structure and evolve by transferring genomic regions. The study identified groups of genes that are frequently co-transferred and observed that they tend to be near each other on the genome. These co-transferred genes are involved in related functions and play an important role in the evolution of the modular structure of these genomes.
MICROBIAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Henry Goehlich, Olivia Roth, Michael Sieber, Cynthia M. Chibani, Anja Poehlein, Jelena Rajkov, Heiko Liesegang, Carolin C. Wendling
Summary: Infections by filamentous phages can influence bacterial fitness, with the production of viral particles being energetically costly. Bacteria can evolve resistance if the costs outweigh the benefits, shortening phage epidemics. The impact of abiotic conditions on host resistance evolution is still unknown.
Article
Microbiology
Cynthia Maria Chibani, Robert Hertel, Meina Neumann-Schaal, Henry Goehlich, Kim Wagner, Boyke Bunk, Cathrin Sproeer, Jorg Overmann, Michael Hoppert, Silke Mareike Marten, Olivia Roth, Heiko Liesegang, Carolin C. Wendling
Summary: A new Vibrio strain, K08M4(T), was isolated from the broad-nosed pipefish Syngnathus typhle in the Kiel Fjord. The strain showed distinct phenotypic features and its complete genome sequence was analyzed.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Carolin C. Wendling
Summary: Prophages, latent viral elements in bacterial genomes, have diverse effects on bacterial ecology and evolution. This review summarizes the latest advancements in understanding how these effects are transmitted across multiple biological systems, potentially impacting ecosystem stability and functioning. Prophages have context-specific effects on higher-order interactions, ranging from contributions to global biogeochemical processes and mutualistic interactions to negative impacts on ecosystem engineers and potential cascading effects for multiple species. Future research should adopt an integrative approach to quantify the effects of prophages in complex ecosystems.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2023)
Article
Biology
Pedro Gomez, Alex R. Hall, Steve Paterson, Angus Buckling
Summary: Interactions between microbes can both constrain and enhance their adaptation to the environment. In a study with a commercial potting compost microbial community, the presence of the community did not constrain the adaptation of the soil bacterium Pseudomonas fluorescens SBW25, but some mutations that were beneficial in the abiotic environment were costly in the presence of the community. Whole-genome sequencing revealed clone-specific mutations supporting multiple genetic pathways to adaptation.