Bacteriophages presence in nature and their role in the natural selection of bacterial populations

Distinct oral DNA viral signatures in rheumatoid arthritis: a Pilot study

Background

Despite evidence linking viruses and oral microbiome to rheumatoid arthritis (RA), limited whole genome sequencing research has been conducted on the oral virome (a viral component of the microbiome) of untreated RA patients. This pilot research seeks to address this knowledge gap by comparing the oral virome of untreated rheumatoid arthritis patients (RAs) and healthy individuals (HCs).

Method

Whole genome DNA sequence of saliva samples from 45 participants including 21 RAs and 24 age and gender matched HCs was obtained from the BioProject: PRJEB6997. Metaphlan3 pipeline and LEfSe analysis were used for the viral signature detection. Wilcoxon pairwise test and ROC analysis were used to validate and predict signatures.

Results

RA exhibits higher alpha diversity compared to HCs. Callitrichine gammaherpesvirus 3, Human gammaherpesvirus 4 (EBV), Murid betaherpesvirus 8, and Suid alphaherpesvirus 1 were enriched in RAs, while Aotine betaherpesvirus 1 from the Cytomegalovirus genus was enriched in HCs. In addition, Saccharomyces cerevisiae killer virus M1 (ScV-M1) was found to be enriched in RAs, whereas bacteriophage Hk97virus (Siphoviridae) and Cd119virus (Myoviridae) were enriched in HCs.

Conclusion

This study identifies significant DNA oral viral signatures at species level as potential biomarkers for the early detection and diagnosis of rheumatoid arthritis.

Exploring the Bacteriophage Frontier: A Bibliometric Analysis of Clinical Trials Between 1965 and 2024

In recent years, the rise of antibiotic-resistant bacteria has posed a severe threat to global public health, necessitating innovative and alternative approaches to combat this escalating crisis. Bacteriophages, viruses that infect and replicate within bacteria, have emerged as promising candidates for therapeutic intervention against antibiotic-resistant pathogens. This study delves into the intricate landscape of bacteriophage research, unraveling the trends and impact of research in the field. The analysis considers the chronological evolution of research, identifying key contributors, collaborative networks, and thematic trends that have shaped the trajectory of this rapidly growing field. Out of 101717 search results in the PubMed database, 163 clinical trials were identified, revealing a dynamic landscape of research activity between 1965 and 2024. The annual scientific publication analysis unveiled fluctuations in the number of publications, indicating an overall increasing trend. Notably, 2011 emerged as a peak year, signifying heightened activity in bacteriophage research. Employing Lotka's law, the authors' productivity analysis illustrated an inherent imbalance in author contributions, with a majority contributing to a single clinical trial. Co-authorship analysis highlighted leading collaborators. Co-occurrence analysis of keywords unveiled thematic clusters, providing insights into the diverse aspects of bacteriophage research. A word cloud emphasized significant terms, while a thematic map categorized themes into various developmental stages. Antimicrobial Agents, Chemotherapy, and Poultry Science were the most relevant journals based on the number of publications. The analysis of countries' contributions revealed the United States as a leading contributor, with Switzerland and China following suit. Collaboration patterns suggested predominantly independent research, with potential for increased international partnerships in certain regions. Additionally, temporal analysis of authors, institutions, sources, and countries revealed productivity patterns, historical context, and research shifts. By scrutinizing a vast array of scientific literature, this investigation aims to provide a panoramic view of how the scientific community has explored the potential of bacteriophages in the context of antibiotic resistance.

Complete genome sequences and characteristics of mycobacteriophages Diminimus, Dulcita, Glaske16, and Koreni

Complete genome sequences of four novel mycobacteriophages, Diminimus, Dulcita, Glaske16, and Koreni, isolated from soil are presented. All these bacteriophages belong to subcluster M1, except Koreni that belongs to subcluster A4. Moreover, all have siphovirus morphologies, with genome sizes ranging from 51,055 to 81,156 bp.

Principles, Methods, and Real-Time Applications of Bacteriophage-Based Pathogen Detection

Bacterial pathogens in water, food, and the environment are spreading diseases around the world. According to a World Health Organization (WHO) report, waterborne pathogens pose the most significant global health risks to living organisms, including humans and animals. Conventional bacterial detection approaches such as colony counting, microscopic analysis, biochemical analysis, and molecular analysis are expensive, time-consuming, less sensitive, and require a pre-enrichment step. However, the bacteriophage-based detection of pathogenic bacteria is a robust approach that utilizes bacteriophages, which are viruses that specifically target and infect bacteria, for rapid and accurate detection of targets. This review shed light on cutting-edge technologies about the novel structure of phages and the immobilization process on the surface of electrodes to detect targeted bacterial cells. Similarly, the purpose of this study was to provide a comprehensive assessment of bacteriophage-based biosensors utilized for pathogen detection, as well as their trends, outcomes, and problems. This review article summaries current phage-based pathogen detection strategies for the development of low-cost lab-on-chip (LOC) and point-of-care (POC) devices using electrochemical and optical methods such as surface-enhanced Raman spectroscopy (SERS).

The role of bacteriophages in shaping bacterial composition and diversity in the human gut

The microbiota of the gut has continued to co-evolve alongside their human hosts conferring considerable health benefits including the production of nutrients, drug metabolism, modulation of the immune system, and playing an antagonistic role against pathogen invasion of the gastrointestinal tract (GIT). The gut is said to provide a habitat for diverse groups of microorganisms where they all co-habit and interact with one another and with the immune system of humans. Phages are bacterial parasites that require the host metabolic system to replicate via the lytic or lysogenic cycle. The phage and bacterial populations are regarded as the most dominant in the gut ecosystem. As such, among the various microbial interactions, the phage-bacteria interactions, although complex, have been demonstrated to co-evolve over time using different mechanisms such as predation, lysogenic conversion, and phage induction, alongside counterdefense by the bacterial population. With the help of models and dynamics of phage-bacteria interactions, the complexity behind their survival in the gut ecosystem was demystified, and their roles in maintaining gut homeostasis and promoting the overall health of humans were elucidated. Although the treatment of various gastrointestinal infections has been demonstrated to be successful against multidrug-resistant causative agents, concerns about this technique are still very much alive among researchers owing to the potential for phages to evolve. Since a dearth of knowledge exists regarding the use of phages for therapeutic purposes, more studies involving experimental models and clinical trials are needed to widen the understanding of bacteria-phage interactions and their association with immunological responses in the gut of humans.

A metagenomic study of gut viral markers in amyloid-positive Alzheimer's disease patients

BACKGROUND

Mounting evidence suggests the involvement of viruses in the development and treatment of Alzheimer's disease (AD). However, there remains a significant research gap in metagenomic studies investigating the gut virome of AD patients, leaving gut viral dysbiosis in AD unexplored. This study aimed to fill this gap by conducting a metagenomics analysis of the gut virome in both amyloid-positive AD patients (Aβ + ADs) and healthy controls (HCs), with the objective of identifying viral signatures linked with AD.

METHOD

Whole-genome sequence (WGS) data from 65 human participants, including 30 Aβ + ADs and 35 HCs, was obtained from the database NCBI SRA (Bio Project: PRJEB47976). The Metaphlan3 pipeline and linear discriminant analysis effect size (LEfSe) analysis were utilized for the bioinformatics process and the detection of viral signatures, respectively. In addition, the Benjamini-Hochberg method was applied with a significance cutoff of 0.05 to evaluate the false discovery rate for all biomarkers identified by LEfSe. The CombiROC model was employed to determine the discriminatory power of the viral signatures identified by LEfSe.

RESULTS

Compared to HCs, the gut virome profiles of Aβ + ADs showed lower alpha diversity, indicating a lower bacteriophage richness. The Siphoviridae family was decreased in Aβ + ADs. Significant decreases of Lactococcus phages were found in Aβ + ADs, including bIL285, Lactococcus phage bIL286, Lactococcus phage bIL309, and Lactococcus phage BK5 T, Lactococcus phage BM13, Lactococcus phage P335 sensu lato, Lactococcus phage phiLC3, Lactococcus phage r1t, Lactococcus phage Tuc2009, Lactococcus phage ul36, and Lactococcus virus bIL67. The predictive combined model of these viral signatures obtained an area under the curve of 0.958 when discriminating Aβ + ADs from HCs.

CONCLUSION

This is the first study to identify distinct viral signatures in the intestine that can be used to effectively distinguish individuals with AD from HCs.

Complete genome analysis of Tequatrovirus ufvareg1, a Tequatrovirus species inhibiting Escherichia coli O157:H7

Introduction

Bacteriophages infecting human pathogens have been considered potential biocontrol agents, and studying their genetic content is essential to their safe use in the food industry. Tequatrovirus ufvareg1 is a bacteriophage named UFV-AREG1, isolated from cowshed wastewater and previously tested for its ability to inhibit Escherichia coli O157:H7.

Methods

T. ufvareg1 was previously isolated using E. coli O157:H7 (ATCC 43895) as a bacterial host. The same strain was used for bacteriophage propagation and the one-step growth curve. The genome of the T. ufvareg1 was sequenced using 305 Illumina HiSeq, and the genome comparison was calculated by VIRIDIC and VIPTree.

Results

Here, we characterize its genome and compare it to other Tequatrovirus. T. ufvareg1 virions have an icosahedral head (114 x 86 nm) and a contracted tail (117 x 23 nm), with a latent period of 25 min, and an average burst size was 18 phage particles per infected E. coli cell. The genome of the bacteriophage T. ufvareg1 contains 268 coding DNA sequences (CDS) and ten tRNA genes distributed in both negative and positive strains. T. ufvareg1 genome also contains 40 promoters on its regulatory regions and two rho-independent terminators. T. ufvareg1 shares an average intergenomic similarity (VIRIDC) of 88.77% and an average genomic similarity score (VipTree) of 88.91% with eight four reference genomes for Tequatrovirus available in the NCBI RefSeq database. The pan-genomic analysis confirmed the high conservation of Tequatrovirus genomes. Among all CDS annotated in the T. ufvareg1 genome, there are 123 core genes, 38 softcore genes, 94 shell genes, and 13 cloud genes. None of 268 CDS was classified as being exclusive of T. ufvareg1.

Conclusion

The results in this paper, combined with other previously published findings, indicate that T. ufvareg1 bacteriophage is a potential candidate for food protection against E. coli O157:H7 in foods.

Bacteriophages in wastewater treatment: can they be an approach to optimize biological treatment processes?

In this paper, we explore the applications of bacteriophages and the advantages of using these viruses to control undesirable organisms in wastewater treatment plants. Based on this, this paper reviewed the literature on the subject by performing a bibliometric and scientometric analysis of articles published in peer-reviewed journals through 2021. We obtained 806 publications, of which 40% were published in the last 5 years, demonstrating an increase in interest in the subject. These articles analyzed, bacteriophages in treatment plants were strongly linked to bacteria such as Escherichia coli and related to disinfection, inactivation, sewage, and wastewater, in addition, biocontrol studies have gained prominence in recent years, particularly due to the resistance of microorganisms to antibiotics. Studies have shown that bacteriophages have great potential for application in treatment systems to control unwanted processes and act as valuable economic and environmental tools to improve the efficiency of various treatment technologies. Although these viruses have already been studied in various applications to optimize treatment plant processes, technology transfer remains a challenge due to the limitations of the technique-such as physicochemical factors related to the environment-and the complexity of biological systems. The research focusing on application strategies in conjunction with molecular biology techniques can expand this study area, enabling the discovery of new bacteriophages.

Capturing the environment of the Clostridioides difficile infection cycle

Clostridioides difficile (formerly Clostridium difficile) infection is a substantial health and economic burden worldwide. Great strides have been made over the past several years in characterizing the physiology of C. difficile infection, particularly regarding how gut microorganisms and their host work together to provide colonization resistance. As mammalian hosts and their indigenous gut microbiota have co-evolved, they have formed a complex yet stable relationship that prevents invading microorganisms from establishing themselves. In this Review, we discuss the latest advances in our understanding of C. difficile physiology that have contributed to its success as a pathogen, including its versatile survival factors and ability to adapt to unique niches. Using discoveries regarding microorganism-host and microorganism-microorganism interactions that constitute colonization resistance, we place C. difficile within the fiercely competitive gut environment. A comprehensive understanding of these relationships is required to continue the development of precision medicine-based treatments for C. difficile infection.

Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection

Resistance to bacteriophage infections protects bacteria in phage-replete environments, enabling them to survive and multiply in the presence of their viral predators. However, such resistance may confer costs for strains, reducing their ecological fitness as expressed as competitiveness for resources or virulence or both. There is limited knowledge about such costs paid by phage-resistant plant pathogenic bacteria in their natural habitats. This study analyzed the costs of phage resistance paid by the phytopathogenic pectinolytic bacterium Dickeya solani both in vitro and in potato (Solanum tuberosum L.) plants. Thirteen Tn5 mutants of D. solani IPO 2222 were identified that exhibited resistance to infection by lytic bacteriophage vB_Dsol_D5 (ΦD5). The genes disrupted in these mutants encoded proteins involved in the synthesis of bacterial envelope components (viz. LPS, EPS and capsule). Although phage resistance did not affect most of the phenotypes of ΦD5-resistant D. solani such as growth rate, production of effectors, swimming and swarming motility, use of various carbon and nitrogen sources and biofilm formation evaluated in vitro, all phage resistant mutants were significantly compromised in their ability to survive on leaf surfaces as well as to grow within and cause disease symptoms in potato plants.

Metabolomics application for the design of an optimal diet

Precision nutrition is an emerging branch of nutrition science that aims to use modern omics technologies (genomics, proteomics, and metabolomics) to assess an individual's response to specific foods or dietary patterns and thereby determine the most effective diet or lifestyle interventions to prevent or treat specific diseases. Metabolomics is vital to nearly every aspect of precision nutrition. It can be targeted or untargeted, and it has many applications. Indeed, it can be used to comprehensively characterize the thousands of chemicals in foods, identify food by-products in human biofluids or tissues, characterize nutrient deficiencies or excesses, monitor biochemical responses to dietary interventions, track long- or short-term dietary habits, and guide the development of nutritional therapies. Indeed, metabolomics can be coupled with genomics and proteomics to study and advance the field of precision nutrition. Integrating omics with epidemiological and clinical data will begin to define the beneficial effects of human food metabolites. In this review, we present the metabolome and its relationship to precision nutrition. Moreover, we describe the different techniques used in metabolomics and present how metabolomics has been applied to advance the field of precision nutrition by providing notable examples and cases.

Insights Into the Role of the Lung Virome During Respiratory Viral Infections

The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.

The Effect of Zero-Valent Iron Nanoparticles (nZVI) on Bacteriophages

Bacteriophages are viruses that attack and usually kill bacteria. Their appearance in the industrial facilities using bacteria to produce active compounds (e.g., drugs, food, cosmetics, etc.) causes considerable financial losses. Instances of bacteriophage resistance towards disinfectants and decontamination procedures (such as thermal inactivation and photocatalysis) have been reported. There is a pressing need to explore new ways of phage inactivation that are environmentally neutral, inexpensive, and more efficient. Here, we study the effect of zero-valent iron nanoparticles (nZVI) on four different bacteriophages (T4, T7, MS2, M13). The reduction of plaque-forming units (PFU) per mL varies from greater than 7log to around 0.5log depending on bacteriophages (M13 and T7, respectively). A comparison of the importance of oxidation of nZVI versus the release of Fe2+/Fe3+ ions is shown. The mechanism of action is proposed in connection to redox reactions, adsorption of virions on nZVI, and the effect of released iron ions. The nZVI constitutes a critical addition to available antiphagents (i.e., anti-bacteriophage agents).

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.