Review
Biochemical Research Methods
Sofia Dahlman, Laura Avellaneda-Franco, Jeremy J. Barr
Summary: This article summarizes the role and progress of phages in the gut, discussing related content of infancy, adulthood, and disease progression, as well as the latest advances in traditional phage therapy and the emerging field of whole virome transplantation.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Editorial Material
Microbiology
Andrea Du Toit
Summary: Gut bacteriophages can modulate cognitive function.
NATURE REVIEWS MICROBIOLOGY
(2022)
Review
Microbiology
Aisling Brady, Alonso Felipe-Ruiz, Francisca Gallego del Sol, Alberto Marina, Nuria Quiles-Puchalt, Jose R. Penades
Summary: This review examines the molecular mechanisms and genetic organization of lysis-lysogeny decision-making in Gram-positive phages, highlighting the impact of these decisions on bacterial communities and ecosystems. By elucidating the strategies used by phages in making lysis-lysogeny decisions, this research contributes to a better understanding of phage-host interactions, which is crucial for various studies including bacterial evolution, community diversification, and phage therapeutics.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)
Article
Microbiology
Dorothee Serian, Yury Churin, Jens Andre Hammerl, Manfred Rohde, Arne Jung, Anja Mueller, Min Yue, Corinna Kehrenberg
Summary: In this study, seven Bordetella avium phages were isolated and characterized, showing broad host range and strong bacteriolytic activity. These phages used lipopolysaccharides as host receptors and exhibited a myovirus structure. Although phenotypically thought to be lytic, these phages were found to undergo a lysogenic phase, but infection did not confer stable host superinfection immunity. These findings are important for potential phage therapy against avian bordetellosis.
MICROBIOLOGY SPECTRUM
(2023)
Review
Microbiology
Ana Mafalda Pinto, Maria Daniela Silva, Lorenzo M. Pastrana, Manuel Banobre-Lopez, Sanna Sillankorva
Summary: The review examines the current use of phages and lysins in treating bacterial infections in various systems, as well as the challenges they face and advancements in delivery vehicle utilization.
FEMS MICROBIOLOGY REVIEWS
(2021)
Review
Virology
Menghui Zhang, Tianyou Zhang, Meishun Yu, Yu-Lei Chen, Min Jin
Summary: This review systematically summarizes the effects of various factors affecting temperate phage life cycle decisions and their ecological implications.
Review
Microbiology
Ana Mafalda Pinto, Maria Daniela Silva, Lorenzo M. Pastrana, Manuel Banobre-Lopez, Sanna Sillankorva
Summary: The emergence of multidrug-resistant pathogens is driving the search for alternative therapeutic approaches like phage therapy and lysins. Encapsulation in delivery vehicles allows for targeted therapy, overcoming barriers that could inactivate or eliminate these antimicrobial agents. Research has progressed significantly in the use of phages and endolysins in treating bacterial infections, especially in the respiratory, digestive, and integumentary systems.
FEMS MICROBIOLOGY REVIEWS
(2021)
Review
Immunology
Michele Zuppi, Heather L. Hendrickson, Justin M. O'Sullivan, Tommi Vatanen
Summary: Phages are viruses that infect bacteria and are widely found in various environments. They are abundant in the human gut and may play an important role in modulating the gut ecosystem. Although the extent of their influence on the gut ecosystem is not fully understood, there is increasing evidence supporting their significance in the gut microbiome.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Immunology
Sara Federici, Samuel P. Nobs, Eran Elinav
Summary: Bacteriophages, as potential treatments against antibiotic-resistant bacterial infections, have gained renewed interest in utilizing them as therapeutic vectors and modulators of the human microbiome, with advancements in understanding their mechanisms through next-generation sequencing. The narrow host range, antibacterial repertoire, and ease of manipulation of phages offer promising possibilities for targeted modulation of pathogenic, commensal, and pathobiont microbiome members for impacting mammalian physiology and immunity.
CELLULAR & MOLECULAR IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Leena Putzeys, Maarten Boon, Eveline-Marie Lammens, Konstantin Kuznedelov, Konstantin Severinov, Rob Lavigne
Summary: RNA sequencing is widely used to study the transcription of phage-infected bacteria. However, short-read RNA sequencing methods often fail to capture the boundaries of transcripts, making it challenging to discover key transcription events and operon structures. In this study, ONT-cappable-seq, a long-read RNA sequencing technique, was developed to enable comprehensive analysis of prokaryotic transcripts.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Fatima Aysha Hussain, Javier Dubert, Joseph Elsherbini, Mikayla Murphy, David VanInsberghe, Philip Arevalo, Kathryn Kauffman, Bruno Kotska Rodino-Janeiro, Hannah Gavin, Annika Gomez, Anna Lopatina, Frederique Le Roux, Martin F. Polz
Summary: In marine Vibrio, phage resistance evolves rapidly and leads to differential susceptibility among bacterial strains. This resistance is cumulative, with each bacterial genome carrying multiple defense elements. The fast evolution of these elements decouples phage resistance from other genomic features.
Review
Oncology
Md. Sharifull Islam, Jie Fan, Fan Pan
Summary: Cancer is a devastating disease with a high mortality rate, and existing treatment options have limitations. Phages, which infect bacteria but not eukaryotic cells, have emerged as a promising alternative therapy for cancer due to their specificity and ease of genetic modification. Engineered phages can target cancer cells while sparing healthy ones, and also act as nanocarriers for delivering therapeutic agents. Phage-based vaccines have shown potential in stimulating the immune system and presenting antigens to B-cells and T-cells. This review explores the recent advances and challenges in phage therapy for cancer, highlighting its versatile tools and vaccine potential.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nikita Zrelovs, Juris Jansons, Tatjana Kazaka, Andris Kazaks, Andris Dislers
Summary: Pantoea spp. found in various environmental sources can benefit or harm plants, and some species are known human pathogens. This study isolated a strain of P. agglomerans from a dead Latvian grasshopper, and used it to retrieve three different lytic phages, including one with unusual morphology. Genome sequencing confirmed their characteristics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
James B. Winans, Benjamin R. Wucher, Carey D. Nadell
Summary: This study investigates how the cellular scale architecture of model 2-species biofilms affects cell-cell and cell-phage interactions, and its influence on the community dynamics of bacteria and phages.
News Item
Biotechnology & Applied Microbiology
Ben Johnson
Summary: Biotech companies are urgently testing bacteriophages, either naturally occurring or equipped with CRISPR-Cas, to selectively eliminate drug-resistant bacteria while preserving the integrity of the microbiome.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Catherine O'Reilly, Paula M. O'Connor, Orla O'Sullivan, Mary C. Rea, Colin Hill, R. Paul Ross
Summary: The study demonstrates that nisin can selectively deplete C. difficile in a faecal microbial environment at concentrations of 50-500 mu M, with minimal impact on the composition of the microbiota. This opens up the potential for using nisin as a therapeutic for clostridial gut infections.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Tais M. Kuniyoshi, Paula M. O'Connor, Elaine Lawton, Dinesh Thapa, Beatriz Mesa-Pereira, Sara Abulu, Colin Hill, R. Paul Ross, Ricardo P. S. Oliveira, Paul D. Cotter
Summary: This study demonstrates the effective anti-Listeria activity of the broader spectrum oxidation-resistant PA-1 variant M31L and penocin A in a human gut environment.
Article
Microbiology
Colin Buttimer, Francesca Bottacini, Andrey N. Shkoporov, Lorraine A. Draper, Paul Ross, Colin Hill
Summary: The study identified seven novel strains of Eggerthella lenta and conducted comparative and pangenome analyses to investigate the diversity of prophages associated with this species, revealing a complex relationship between the bacterium and diverse prophages.
Review
Gastroenterology & Hepatology
Hiba Shareefdeen, Colin Hill
Summary: This review discusses recent advances in viral metagenomics and its association with various diseases. The human intestinal virome, mainly composed of bacteriophages, is influenced by environmental factors and plays a dynamic role in host health and disease. Novel correlations have been found between the virome and diseases such as obesity, necrotizing enterocolitis, and severe acute respiratory syndrome coronavirus 2 infection. Further associations with cognition, diet, and geography highlight the complexity of the gut bacteria-virome relationship. Understanding the gut virome and its dynamics is crucial for future microbiome-based interventions, biomarker identification, and novel therapeutics.
CURRENT OPINION IN GASTROENTEROLOGY
(2022)
Review
Gastroenterology & Hepatology
Alexis Mosca, Ana Teresa Abreu Y. Abreu, Kok Ann Gwee, Gianluca Ianiro, Jan Tack, Thi Viet Ha Nguyen, Colin Hill
Summary: An optimally operating microbiome is important for various physiological functions, but disruptions can lead to the production of metabolites and toxins that contribute to different conditions. Probiotics have the potential to address these issues, but their use in vulnerable individuals may raise safety concerns and maintaining their viability poses challenges. As a result, interest in postbiotics is growing. Postbiotics, which consist of inactivated microbial cells or cell components, offer more stability and similar health benefits as probiotics. Emerging evidence shows the clinical benefits of postbiotics in prevalent conditions, making them a promising alternative to probiotics. Further research on the interaction mechanisms between postbiotics and commensal microorganisms will enhance our understanding of their potential clinical benefits and may lead to targeted postbiotic therapy.
Article
Infectious Diseases
Anna Desmond, Fiona O'Halloran, Lesley Cotter, Colin Hill, Des Field
Summary: Neonatal infections are a major cause of infant mortality and morbidity. The global incidence of multi-drug resistance in neonatal pathogens is increasing, highlighting the need for alternative treatment strategies. This study found that nisin and its derivatives show activity against multi-drug resistant strains of Streptococcus agalactiae and Staphylococcus capitis, and that combining nisin peptides with antibiotics can enhance their antimicrobial effects. These findings suggest that nisin and its derivatives have potential as alternative antimicrobial strategies to target neonatal pathogens.
Article
Biotechnology & Applied Microbiology
Thomas S. Postler, Luisa Rubino, Evelien M. Adriaenssens, Bas E. Dutilh, Balazs Harrach, Sandra Junglen, Andrew M. Kropinski, Mart Krupovic, Jiro Wada, Anya Crane, Jens H. Kuhn, Arcady Mushegian, Janis Rumnieks, Sead Sabanadzovic, Peter Simmonds, Arvind Varsani, F. Murilo Zerbini, Julie Callanan, Lorraine A. Draper, Colin Hill, Stephen R. Stockdale
Summary: The International Committee on Taxonomy of Viruses has adopted a binomial naming format for virus species, which is comparable with other biological taxonomies. Latinization of these names is optional, but it provides the advantage of cultural neutrality and compatibility with other taxonomies.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Oliver W. Bayfield, Andrey N. Shkoporov, Natalya Yutin, Ekaterina V. Khokhlova, Jake L. R. Smith, Dorothy E. D. P. Hawkins, Eugene V. Koonin, Colin Hill, Alfred A. Antson
Summary: CrAssphage and related crassviruses are the most abundant viruses in the human gut, with some individuals having up to 95% of viral sequences from these viruses. By reconstructing Bacteroides intestinalis virus fcrAss001 using cryo-electron microscopy, we gained insights into the structure and function of its proteins. The muzzle protein forms a new fold called the 'crass fold' and acts as a gatekeeper for controlling cargo release. Additionally, the fcrAss001 virus provides ample storage space for cargo proteins in both the capsid and the tail, with a mechanism for protein ejection involving partial unfolding during extrusion through the tail.
Article
Gastroenterology & Hepatology
Colin Buttimer, Ekaterina V. Khokhlova, Lisa Stein, Cara M. Hueston, Bianca Govi, Lorraine A. Draper, R. Paul Ross, Andrey N. Shkoporov, Colin Hill
Summary: This study isolates and characterizes six bacteriophages that can infect Ruminococcus gnavus, a gut microbe associated with inflammatory bowel disease. The phages have a temperate lifestyle and can coexist with the host bacterium without causing a significant reduction in its abundance. Analysis of gut virome data reveals a high abundance of these phages in individuals with IBD. This work provides insight into the interaction between phages and R. gnavus in the human gut microbiome.
Article
Gastroenterology & Hepatology
Daniel Merenstein, Bruno Pot, Gregory Leyer, Arthur C. Ouwehand, Geoffrey A. Preidis, Christopher A. Elkins, Colin Hill, Zachery T. Lewis, Andrea L. Shane, Niv Zmora, Mariya I. Petrova, Maria Carmen Collado, Lorenzo Morelli, Gina A. Montoya, Hania Szajewska, Daniel J. Tancredi, Mary Ellen Sanders
Summary: Probiotics are used by both healthy individuals and in clinical settings, but there are potential risks associated with their consumption. This has led to the need for concise recommendations on how to ensure the safe and effective use of new probiotic strains and products, especially in vulnerable populations.
Article
Microbiology
Ivan Sugrue, Daragh Hill, Paula M. O'Connor, Li Day, Catherine Stanton, Colin Hill, R. Paul Ross
Summary: This study describes a new variant of nisin, nisin E, produced by Streptococcus equinus strains isolated from sheep milk. The genome sequencing and analysis revealed similarities to nisin U, but with a unique rearrangement of the core peptide encoding gene. Nisin E showed antimicrobial activity against Lactobacillus, Bacillus, and Clostridiodes, and was immune to nisin U. The discovery of nisin E suggests its central role in the competitive nature of S. equinus.
Article
Microbiology
Neda Nezam-Abadi, Christopher J. R. Turkington, Lorraine A. Draper, Andrey N. Shkoporov, R. Paul Ross, Colin Hill
Summary: Here, we present the draft genome sequence of Legionella pneumophila subsp. pneumophila strain DSM 25199, a serogroup 1 strain with a genome size of 3,426,844 bp. The assembly consists of 24 contigs with an N-50 of 300,843 bp.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Chemistry, Medicinal
Shona Uniacke-Lowe, Fergus W. J. Collins, Colin Hill, R. Paul Ross
Summary: With the increase in antimicrobial resistance, the deep-sea fish microbiome can serve as a potential source of antimicrobials, including bacteriocins. In this study, bacterial isolates recovered from deep-sea fish were screened for antimicrobial activity and their genomic DNA was analyzed for bacteriocin and other antimicrobial metabolite genes. The study identified 147 candidate biosynthetic gene clusters, including 35 bacteriocin clusters, and discovered unique bacteriocin gene clusters encoding novel peptides. This dual approach provided insights into the bacteriocinogenic potential and antimicrobial molecules of the deep-sea isolates.
Article
Food Science & Technology
Friederike Uhlig, Alicja K. Warda, Cara M. Hueston, Lorraine A. Draper, Gilles Chauviere, Erik Eckhardt, Colin Hill, Niall P. Hyland
Summary: Lactobacillus LB, generated through fermentation, has beneficial effects on intestinal ion transport and motility, alleviating acute diarrhea and irritable bowel syndrome symptoms. Low-lactose Lactobacillus LB (LL-LB) increases baseline short-circuit current and is partially mediated by sodium-D-glucose transporter 1. Preparations produced from a single strain fermentate of L. fermentum have a stronger effect on baseline short-circuit current and carbachol-induced contractions compared to LL-LB.
JOURNAL OF FUNCTIONAL FOODS
(2023)
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)
