Review
Microbiology
Yingying Zhang, Ran Wang
Summary: The human gastrointestinal tract is inhabited by various microorganisms, such as bacteria, archaea, viruses, and eukaryotes. While the impact of bacteria on human health is well-studied, the role of viruses, particularly phages, is less understood. Phages are viruses that specifically infect bacteria and have a symbiotic relationship with their host. Although advances in sequencing technology have improved our understanding of the human gut phageome, there is still much uncharacteized data. Prior to investigating phage function, it is necessary to establish a comprehensive sequencing database and understand the impact of phage-bacteria interactions on human health.
FRONTIERS IN MICROBIOLOGY
(2023)
Editorial Material
Microbiology
Evelien M. Adriaenssens
Summary: The importance of bacteriophages has been increasingly recognized in the past 20 years, with research showing their significance in various environments globally. Genomic diversity surpasses morphological diversity, and the lack of a complete taxonomic framework results in the loss of crucial information.
Article
Microbiology
Mirjam Zund, Hans-Joachim Ruscheweyh, Christopher M. Field, Natalie Meyer, Miguelangel Cuenca, Daniel Hoces, Wolf-Dietrich Hardt, Shinichi Sunagawa
Summary: This study demonstrates the powerful approach of integrating experimental induction and bioinformatic analysis to accurately locate inducible prophages using high-throughput sequencing data and quantify their activity. The ability to generate such quantitative information will provide better insights into the factors determining phage activity and how prophage-bacteria interactions impact the microbiome and human health.
Review
Microbiology
Yujie Zhang, Somanshu Sharma, Logan Tom, Yen-Te Liao, Vivian C. H. Wu
Summary: This review summarizes the critical role of the gut phageome in mammalian health. It provides an overall profile of phages in the gastrointestinal tract and their dynamic roles in shaping the surrounding microorganisms. The impacts of the gut phageome on gastrointestinal fitness and the bacterial community, as well as the influence of diets on its composition, are highlighted. Additionally, the review discusses the recent reports on the role of the gut phageome in the association of mammalian health and diseases.
Article
Microbiology
Juan C. Burckhardt, Derrick H. Y. Chong, Nicola Pett, Carolina Tropini
Summary: This study detected and characterized novel inoviruses from gut commensals in the Enterocloster genus. The results demonstrate that human gut-associated bacteria can secrete inoviruses and begin to elucidate the environmental niche filled by inoviruses in commensal bacteria.
Article
Microbiology
Emma Guerin, Andrey N. Shkoporov, Stephen R. Stockdale, Joan Colom Comas, Ekaterina V. Khokhlova, Adam G. Clooney, Karen M. Daly, Lorraine A. Draper, Niamh Stephens, Dimitri Scholz, R. Paul Ross, Colin Hill
Summary: In this study, phi crAss002, the first representative of the proposed Alphacrassvirinae sub-family of CrAss-like phages, was successfully isolated and characterized. It can co-exist at very high levels in liquid culture with its host, Bacteroides xylanisolvens, without impacting bacterial numbers, which suggests a potentially stable and significant phage-host relationship for further research.
Article
Microbiology
Pierre Ledormand, Nathalie Desmasures, Cedric Midoux, Olivier Rue, Marion Dalmasso
Summary: This study investigated the presence of phages in cider and found a very low occurrence of both free lytic phage particles and putative prophages. The occurrence of putative prophages was higher in the cider from the industrial producer. This is the first report on the investigation of the phageome and prophages in a fermented beverage.
Article
Microbiology
Darren Buckley, Toshitaka Odamaki, Jinzhong Xiao, Jennifer Mahony, Douwe van Sinderen, Francesca Bottacini
Summary: The study investigated prophage-like elements and CRISPR-Cas viral immune systems in human-associated Bifidobacterium genomes. Analysis revealed similar prophages and CRISPR spacers across different strains and species, providing insight into the human-associated bifidobacterial phageome. Evidence of CRISPR-Cas immunity against bifidobacterial prophages suggests historical interactions and gene targets for phage immunity.
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
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)
Review
Gastroenterology & Hepatology
Tatiana Borodovich, Andrey N. Shkoporov, R. Paul Ross, Colin Hill
Summary: Horizontal gene transfer (HGT) plays a significant role in human health and disease, particularly in the spread of antibiotic resistance genes and pathogenic factors. The abundance of bacteriophages in the human gut suggests that phage transduction could be an important mode of HGT in the gut microbiome. This review provides an in-depth understanding of phage-mediated HGT mechanisms, detection methods, and potential implications for the human gut microbiome.
GASTROENTEROLOGY REPORT
(2022)
Review
Microbiology
Ciara A. Tobin, Colin Hill, Andrey N. Shkoporov
Summary: The gut microbiome consists of a dense and metabolically active community of microorganisms and viruses in the lower gastrointestinal tract. Bacteria and their viruses are the most abundant members of the gut microbiome. Investigating their biology and interactions is crucial for understanding their roles in human health and disease. This review summarizes recent advances in understanding the taxonomic structure and ecological functions of the gut phageome, discussing the impact of age, diet, and geography on its composition. It also evaluates the potential link between changes in the gut phageome and diseases such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer, highlighting the need for standardization in research methods.
ANNUAL REVIEW OF MICROBIOLOGY
(2023)
Article
Virology
Ana Georgina Cobian Guemes, Tram Le, Maria Isabel Rojas, Nicole E. Jacobson, Helena Villela, Katelyn Mcnair, Shr-Hau Hung, Lili Han, Lance Boling, Jessica Claire Octavio, Lorena Dominguez, Vito Adrian Cantu, Sinead Archdeacon, Alejandro A. Vega, Michelle A. An, Hamza Hajama, Gregory Burkeen, Robert A. Edwards, Douglas J. Conrad, Forest Rohwer, Anca M. Segall, Mao Ye
Summary: This study reports the detection of antibiotic-resistant bacteria Achromobacter species in the airways of patients with Cystic Fibrosis, as well as the discovery of lytic phages with potential therapeutic value. The results of the study showed that most Achromobacter strains were susceptible to the phages isolated in the study, and the method of phage production met the safety standards for human administration. This study provides a comprehensive framework for the treatment of Achromobacter infections in Cystic Fibrosis.
Review
Food Science & Technology
Pierre Ledormand, Nathalie Desmasures, Marion Dalmasso
Summary: This review focuses on the current knowledge of phage communities in fermented foods and beverages, highlighting the lack of available data and the need for further research in this area.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2021)
Review
Microbiology
L. Fernandez, A. C. Duarte, A. Rodriguez, P. Garcia
Summary: Amid the global antibiotic resistance crisis, phages are increasingly seen as promising antimicrobial agents against multidrug-resistant bacteria, playing a key role in bacterial communities and maintaining a "healthy" status quo. They can be used as target-specific antimicrobials against pathogenic bacteria, without harming beneficial microbiota, and have the potential to treat diseases caused by bacterial dysbiosis. While there are concerns about potential negative impacts, such as immunogenicity and spread of resistance genes, phages are generally considered beneficial microbes that should not be overlooked for their risks.
BENEFICIAL MICROBES
(2021)
Article
Virology
Mohamed S. H. Hassan, Ahmed Ali, Motamed Elsayed Mahmoud, Danah Altakrouni, Shahnas M. Najimudeen, Mohamed Faizal Abdul-Careem
Summary: This study compared the efficacy of different vaccination programs against Canadian DMV/1639 IBV and found that the autogenous inactivated DMV/1639 vaccine was more effective in reducing viral loads and boosting virus neutralization titers. Both vaccination programs provided significant protection against pathological effects.
Article
Virology
Wanda Christ, Jonas Klingstrom, Janne Tynell
Summary: The integrated stress response (ISR) is activated in response to SARS-CoV-2 infection, triggering translational arrest and inhibiting stress granule formation. However, the stress-responsive transcription factors ATF4 and CHOP are not induced. Different SARS-CoV-2 variants show variant-specific differences in ISR activation, suggesting potential impacts on pathogenesis and treatment strategies.
Article
Virology
Xiao Han, Hankun Xu, Yifan Weng, Rong Chen, Jidong Xu, Tong Cao, Renjie Sun, Ying Shan, Fang He, Weihuan Fang, Xiaoliang Li
Summary: Classical swine fever virus (CSFV) can inhibit the host innate immunity by decreasing the level of high mobility group box 1 (HMGB1), and CSFV Npro can evade host antiviral immune response through upregulating HMGB1 acetylation.
Article
Virology
Sunjian Lyu, Fulei Xiong, Tianpeng Qi, Weifeng Shen, Qi Guo, Mingming Han, Li Liu, Weishao Bu, Julin Yuan, Bao Lou
Summary: This study identified and characterized a novel temperate A. hydrophila phage, P05B, which has strong lytic ability and stability across different temperatures and pH values.
Article
Virology
Siyuan Liu, Wei Chen, Raphael Nyaruaba, Shunlong Wang, Cihan Yang, Qun Wu, Ying Liu, Puyu Liu, Fei Wang, Jingling Wang, Zhiming Yuan, Dingwei Sun, Han Xia
Summary: Specific, sensitive, and reliable RT-qPCR assays for the detection of OYAV and EBIV have been successfully developed in this study. These assays hold great promise for their potential application in clinical and field samples in the future.
Article
Virology
Rui Wang, Qiang Sun, Jinbo Xiao, Congcong Wang, Xiaoliang Li, Jichen Li, Yang Song, Huanhuan Lu, Ying Liu, Shuangli Zhu, Zhijun Liu, Yong Zhang
Summary: Coxsackievirus A6 (CVA6) has emerged as an important agent causing hand, foot, and mouth disease (HFMD). Mutations in residue 64 of the virus have been found to increase resistance to ribavirin and decrease sensitivity to guanidine hydrochloride. This mutation also leads to increased replication fidelity and reduced pathogenicity. These findings provide a foundation for the development of a safe and effective live attenuated CVA6 vaccine.
Article
Virology
Yao Xiong, Keran Ma, Xiao Zou, Yantao Liang, Kaiyang Zheng, Tiancong Wang, Hong Zhang, Yue Dong, Ziyue Wang, Yundan Liu, Hongbing Shao, Andrew Mcminn, Min Wang
Summary: This study isolated a novel virus, vB_VviC_ZQ26, infecting Vibrio cyclitrophicus from coastal waters near Qingdao, China. It was found that vB_VviC_ZQ26 belongs to a new vibriophage-specific family, Coheviridae, and is mainly found in temperate and tropical epipelagic zones.
Article
Virology
Xing Li, Zhiping Ye, Ewan P. Plant
Summary: By analyzing clinical and cultured samples using the same bioinformatic pipeline, it was found that 5' copyback DVGs are prevalent in human clinical samples but not in cultured samples. Furthermore, there are differences in DVG production and composition between in vivo and in vitro infections.
Article
Virology
Shreya Banerjee, Rakesh Sarkar, Arpita Mukherjee, Suvrotoa Mitra, Animesh Gope, Mamta Chawla-Sarkar
Summary: Rotavirus is a major cause of viral gastroenteritis in infants and continues to be a severe issue in underdeveloped nations. Recent research has shown that a long non-coding RNA called SLC7A11-AS1 is upregulated during rotavirus infection and plays a role in facilitating the virus's propagation by regulating intracellular glutathione and lipid peroxidation.
Article
Virology
Eiichi Hondo, Tetsufumi Katta, Ayato Sato, Naoya Kadofusa, Tomoki Ishibashi, Hiroshi Shimoda, Hirokazu Katoh, Atsuo Iida
Summary: Bat-borne emerging viruses, such as the Ebola virus and Nipah virus, pose a significant threat to public health. In this study, we identified micafungin as a potential antiviral drug against Pteropine orthoreovirus (PRV) and found that it inhibits viral release in human cells through activating the endoplasmic reticulum stress response pathway. This research provides valuable insights into the development of effective treatments for future virus pandemics.
Article
Virology
M. Joubert, N. van den Berg, J. Theron, V. Swart
Summary: This study investigated the host gene expression in asymptomatic avocado nursery trees infected with Avocado sunblotch viroid (ASBVd) using RNA sequencing. The results showed that 631 genes were differentially expressed during infection, with 63% upregulated. ASBVd infection significantly affected plant defence responses, phytohormone networks, gene expression pathways, secondary metabolism, cellular transport, as well as protein modification and degradation. This study provides insights into the molecular interactions underlying avsunviroid-host interactions.
Article
Virology
Wanling Zhang, Haiyan Yang, Zhengyun Liu, Shengyu Wang, Tianyang Chen, Hong Song, Yunbin Xu, Fajin Li, Guo Luo, Huan Wang
Summary: EV71 infection leads to changes in mitochondrial morphology and dynamics in human neuroblastoma cells, resulting in mitochondrial dysfunction that may contribute to nervous system dysfunction.
Article
Virology
Mikhail Oliveira Leastro, Elliot Watanabe Kitajima, Vicente Pallas, Jesus Angel Sanchez- Navarro
Summary: This study reports the construction and validation of an infectious cDNA clone of Citrus leprosis virus C (CiLV-C) based on an agroinfection system. Agro-injected Nicotiana benthamiana plants showed localized lesions similar to the natural infection process. The virus recovered from the infected plant tissue could be mechanically transmitted between plants. The CiLV-C reverse genetic system provides a powerful molecular tool for unraveling the peculiarities of the citrus leprosis pathosystem.
Article
Virology
Manel Essaidi-Laziosi, Francisco J. Perez-Rodriguez, Catia Alvarez, Pascale Sattonnet-Roche, Giulia Torriani, Meriem Bekliz, Kenneth Adea, Matthias Lenk, Tasnim Suliman, Wolfgang Preiser, Marcel A. Mueller, Christian Drosten, Laurent Kaiser, Isabella Eckerle
Summary: This study found that the Omicron variant has different replication characteristics compared to other variants of concern, being able to efficiently produce infectious virus in nasal cells but not lung cells. In addition, the Delta and Omicron variants showed increased infection efficiency in A549 cells. These findings suggest that the variants of concern have better adaptation to humans but do not have an extended host range.
Article
Virology
Martin Faye, Modeste Name Faye, Babacar Ndiaye, Moussa Moise Diagne, Safietou Sankhe, Ndeye Marieme Top, Amadou Diallo, Cheikh Loucoubar, Ndongo Dia, Amadou Alpha Sall, Ousmane Faye
Summary: Genomic surveillance in Senegal since March 2020 has detected the emergence of Omicron BA.4 and BA.5 sublineages in June 2022. Next-generation sequencing and phylogeny analysis of isolates from a cluster of cases in Northern Senegal in July 2022 revealed that the BA.4 cases originated from a XAS recombinant, marking the first reported sequence of this variant from Senegal. Continuous genomic surveillance of positive SARS-CoV-2 samples is crucial.