ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

Effects of bacteriophages on gut microbiome functionality

The gut microbiome, composed of bacteria, fungi, and viruses, plays a crucial role in maintaining the delicate balance of human health. Emerging evidence suggests that microbiome disruptions can have far-reaching implications, ranging from the development of inflammatory diseases and cancer to metabolic disorders. Bacteriophages, or "phages", are viruses that specifically infect bacterial cells, and their interactions with the gut microbiome are receiving increased attention. Despite the recently revived interest in the gut phageome, it is still considered the "dark matter" of the gut, with more than 80% of viral genomes remaining uncharacterized. Today, research is focused on understanding the mechanisms by which phages influence the gut microbiota and their potential applications. Bacteriophages may regulate the relative abundance of bacterial communities, affect bacterial functions in various ways, and modulate mammalian host immunity. This review explores how phages can regulate bacterial functionality, particularly in gut commensals and pathogens, emphasizing their role in gut health and disease.

Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages

Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defenses. Among the most abundant phages in the gut are the crAss-like phages that infect members of the order Bacteroidales, in particular, genus Bacteroides. In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairs in vitro using a multi-omics approach (transcriptomics, proteomics and metabolomics). These included three Bacteroides species paired with three crAss-like phages (Bacteroides intestinalis and фcrAss001, Bacteroides xylanisolvens and фcrAss002, and an acapsular mutant of Bacteroides thetaiotaomicron with DAC15), and Parabacteroides distasonis paired with the siphovirus фPDS1. We show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, and vice versa. An acapsular variant of B. thetaiotaomicron demonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation. This study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as фPDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.

Exploring deep learning in phage discovery and characterization

Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.

Fate of antibiotic resistance genes under different wastewater treatments and environmental conditions in an Algerian watershed

In recent decades, antibiotic resistance has become a major health threat. This study evaluates the efficiency of two wastewater treatment plants (WWTP), conventional activated sludge and advanced filtration-based Enviro-Septic, for removing antibiotic resistance genes (ARGs) and their prevalence in an Algerian watershed. Thirty-five wastewater and 122 river samples were collected. Sampling covered a 50 km transect, from a low-pollution site to a water reservoir, at six sites. The study analyzed different fecal indicators (E. coli (EC), spores of sulfite-reducing clostridia (SRC), somatic coliphages (SOMCPH)), CrAssphage (CrAssPH)), and three ARGs (blaTEM, tetW, and sul1). Mean concentrations in raw sewage from the conventional and Enviro-Septic WWTPs were ∼7.1 and 6.4 log10 (CFU/100 ml) for EC, 6.2 log10 (PFU or CFU)/100 ml for SOMCPH and SRC in both treatments, and ∼7.5 and 5.2 for CrAssPH, respectively. The conventional WWTP achieved reductions of ∼4 log10 for EC and SOMCPH, 3.5 log10 for CrAssPH, and 1 log10 for SRC. The Enviro-Septic system showed similar efficacy for EC and SRC but lower for SOMCPH (2.8 log10) and CrAssPH (2.5 log10). The mean concentrations (log10 GC/100 ml) of ARGs in raw sewage of the conventional and the Enviro-Septic WWTP were 8.6 and 7.3 for tetW, 9.4 and 8.1 for sul1, 8.4 and 6.3 for blaTEM, respectively. Both treatments achieved reductions of 2.9-3 log10 for all ARGs. All river samples tested positive for the three ARGs, with lower concentrations at less fecally polluted sites, showing a reduction of up to 4 log10. Strong correlations (p < 0.05) were observed between culturable indicators, CrAssPH, and ARGs (ρ 0.58-0.96), indicating a strong association between ARGs and human fecal contamination, although other environmental sources cannot be ruled out. This study provides insights into ARG dynamics and supports strategies to mitigate their spread, and protect public health.

Intestivirid Acquisition Increases Across Infancy in a Wild Primate Population

Intestivirids (order Crassvirales, family Intestiviridae), viruses that infect Bacteroidales bacteria in the mammalian gastrointestinal tract, have been identified as a highly abundant component of the healthy human virome that may shape patterns of human health and disease through direct action on the microbiome. While double-stranded DNA bacteriophages called crAssphages (Carjivirus communis) that infect bacteria in the Bacteroidales order have been identified in humans within the first month of life, the enormous variation in post-parturition infant environments and diets has inhibited a robust understanding of the physiological and environmental factors that govern acquisition patterns. We turned to a wild population of graminivorous nonhuman primates (geladas, Theropithecus gelada) under long-term study in the Simien Mountains National Park, Ethiopia, analysing faecal samples from infants and mothers in this population across the infancy period for richness and presence of crAssphage-like viruses (family Intestiviridae). Eight intestivirid genomes were identified based on terminal redundancy representing six unique variants (< 98% intergenomic similarity) closely related to the human crAssphage. The prevalence of intestivirids in gelada faecal samples begins to rise at about 10 months of age, peaks in the months surrounding weaning (~18 months), and somewhat decreases but maintains high levels into adulthood. We found a strong association between cumulative rainfall and intestivirid detection, with a higher likelihood accompanying wetter seasons with higher grass availability. In this population, the months prior to weaning have been found to be accompanied by a shift in the microbiome characterised by a decrease in glycan degrader Bacteroidales taxa and an increase in fermentative Bacteroidales taxa, and wetter seasons when the vast majority of the gelada diet comprises grasses are associated with an increase in fermentative Bacteroidales taxa. In the context of these microbiome shifts, our results suggest that the intestivirid-bacterial host relationship may interact with major developmental and seasonal dietary shifts in the mammalian host.

CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing

Viruses are the most abundant biological entities in all ecosystems of the world. Their ubiquity makes them suitable candidates for indicating fecal contamination in rivers. Recently, a group of Bacteroidetes bacteriophages named CrAssphages, which are highly abundant, sensitive, and specific to human feces, were studied as potential viral biomarkers for human fecal pollution in water bodies. In this study, we evaluated the presence, diversity, and abundance of viruses with a focus on crAssphages via metagenomic analysis in an Amazonian river and conducted correlation analyses on the basis of physicochemical and georeferencing data. Several significant differences in viral alpha diversity indexes were observed among the sample points, suggesting an accumulation of viral organisms in the river mouth, whereas beta diversity analysis revealed a significant divergence between replicates of the most downstream point (IT4) when compared to the rest of the samples, possibly due to increased human impact at this point. In terms of the presence of crAssphage, the analysis identified 61 crAssphage contigs distributed along the Itacaiúnas River. Moreover, our analysis revealed significant correlations between 19 crAssphage contigs and human population density, substantiating the use of these viruses as possible markers for human fecal pollution in the Itacaiúnas River. This study is the first to assess the presence of crAssphages in an Amazonian river, with results suggesting the potential use of these viruses as markers for human fecal pollution in the Amazon.

IMPORTANCE

The Amazon biome is one of the most diverse ecosystems in the world and contains the most vast river network; however, the continuous advance of urban centers toward aquatic bodies exacerbates the discharge of pollutants into these water bodies. Fecal contamination contributes significantly to water pollution, and the application of an improved fecal indicator is essential for evaluating water quality. In this study, we evaluated the presence, diversity, and abundance of crAssphages in an Amazonian river and performed correlation analysis on the basis of physicochemical and georeferencing data to test whether crAssphages are viable fecal pollution markers. Our analysis revealed both the presence of crAssphages and their correlation with physicochemical data and showed significant correlations between the relative abundance of crAssphages and human density. These results suggest the potential use of these viruses as markers for water quality assessment in Amazonian rivers.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.

The reliability of CrAssphage in human fecal pollution detection: A cross-regional MST marker assessment

Microbial Source Tracking (MST) markers play a key role in identifying sources of fecal contamination, particularly human-associated pollution, which is critical for public health. This study investigates the distribution and reliability of three MST markers (crAssphage, HMBif, and HF183) across various environmental contexts in Europe, Asia, and Africa. Samples were obtained from wastewater treatment plants (WWTPs) and rivers across different catchment areas, including sampling during extreme weather conditions such as heavy rainfall and drought. The concentrations of these MST markers were measured and compared with traditional fecal indicators. The obtained results indicate that crAssphage showed consistently the highest prevalence and concentrations in all regions and sample types, demonstrating its robustness as a marker of human fecal contamination. Population density and climatic conditions significantly influenced marker levels, with the highest concentrations found in highly populated areas with moderate climates. The impact of extreme weather events was different for each condition: heavy rainfall resulted in elevated MST marker concentrations, likely due to sediment resuspension, while drought led to more inconsistent results. Strong correlations were observed among the three MST markers and between these markers and conventional fecal indicators. This study underscores the value of crAssphage as a reliable and effective tool for tracking human fecal pollution and highlights the influence of environmental and climatic factors on MST marker behavior.

The role of bacteriophage in inflammatory bowel disease and its therapeutic potential

Inflammatory bowel disease (IBD) refers to a group of chronic inflammatory disorders impacting the gastrointestinal (GI) tract. It represents a significant public health challenge due to its rising global incidence and substantial impact on patients' quality of life. Emerging research suggests a pivotal role of the human microbiome in IBD pathogenesis. Bacteriophages, integral components of the human microbiome, are indicated to influence the disease onset, progression, and therapeutic strategies. Here, we review the effect of bacteriophages on the pathogenesis of IBD and, more specifically, on the gut bacteria, the systemic immunity, and the susceptibility genes. Additionally, we explore the potential therapeutic use of the bacteriophages to modify gut microbiota and improve the health outcomes of IBD patients. This review highlights the potential of therapeutic bacteriophages in regulating gut microbiota and modulating the immune response to improve health outcomes in IBD patients. Future studies on personalized bacteriophage therapy and its integration into clinical practice could advance treatment strategies for IBD.

Extreme diversity of phage amplification rates and phage-antibiotic interactions revealed by PHORCE

Growth rate plays a fundamental role in microbiology and serves as an important proxy for fitness in evolution. While high-throughput measurements of bacterial growth rates are easily performed in any microbiology laboratory, similar methods are lacking for bacteriophages. This gap hinders systematic comparisons of important phage phenotypes, such as their amplification rate in bacterial populations and their bactericidal effect, across different phages and environmental conditions. Here, we show that the amplification rate of lytic phages can be quantified by analyzing bacterial population growth and collapse dynamics under phage predation using a parsimonious mathematical model - an approach termed Phage-Host Observation for Rate estimation from Collapse Events (PHORCE). We found that the resulting phage amplification rate captures the bactericidal effect independent of initial phage and bacterial population sizes for fast-growing hosts and adsorption-limited phages. Using high-throughput PHORCE, we found that the amplification rates of Escherichia coli phages vary widely by more than three orders of magnitude. Furthermore, our approach suggests that phage-antibiotic interactions are predominantly determined by the antibiotic, and not by the phage. In particular, the ribosome-inhibiting antibiotic doxycycline generally showed antagonism with phage amplification, whereas the DNA-damaging antibiotic nitrofurantoin was synergistic. This framework provides a means to quantitatively characterize phage phenotypes and may facilitate future high-throughput phage screens for antibacterial applications.

Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts

Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.

Exploring the Immunological Role of the Microbial Composition of the Appendix and the Associated Risks of Appendectomies

The appendix, an integral part of the large intestine, may serve two purposes. First of all, it is a concentration of lymphoid tissue that resembles Peyer's patches. It is also the main location in the body for the creation of immunoglobulin A (IgA), which is essential for controlling intestinal flora's density and quality. Second, the appendix constitutes a special place for commensal bacteria in the body because of its location and form. Inflammation of the appendix, brought on by a variety of infectious agents, including bacteria, viruses, or parasites, is known as appendicitis. According to a number of studies, the consequences of appendectomies may be more subtle, and may relate to the emergence of heart disease, inflammatory bowel disease (IBD), and Parkinson's disease (PD), among other unexpected illnesses. A poorer prognosis for recurrent Clostridium difficile infection is also predicted by the absence of an appendix. Appendectomies result in gut dysbiosis, which consequently causes different disease outcomes. In this review, we compared the compositional differences between the appendix and gut microbiome, the immunological role of appendix and appendix microbiome (AM), and discussed how appendectomy is linked to different disease consequences.

Antibiotic-resistance genes and metals increase in polluted tropical rivers of the Baia da Ilha Grande, Rio de Janeiro, Brazil

Baia da Ilha Grande (BIG), Rio de Janeiro, Brazil, is one of the largest bays in the world. BIG is important because it serves as a route for the mining and oil industries and plays a vital role in mariculture activities. However, BIG has suffered significant impacts in recent years due to increased pollution and climate change, culminating in a local mariculture collapse. We examined the pollution levels of the bay. Biogeochemical, microbiological, and metagenomics analyses were conducted in ten rivers during the 2022 dry and rainy seasons. Combined data analyses showed that the bay's ten most significant rivers are polluted and classified into three decreasing levels of pollution groups (P1-P3). The P1 group (Centro, Japuíba, Jacuecanga) had the worst-case scenario for all pollution types, and the highest number of the nearby populations, nautical workshops and hospitals. Whereas the P2 (Jacarei, Perequeaçu and Taquari) and P3 (Frade, Bracuí, Mambucaba, São Roque) had relatively reduced pollution, as shown mainly by fecal bacteria. Metals, such as Al (>0.3 mg/L), Fe (>1.4 mg/L), Pb (>0.15 mg/L), and resistance genes (∼2 % metagenomic profile) were also more abundant in P1. High levels of metals and antibiotic resistance genes were a strong indication of pollution. The results from this study shed light on the health status of BIG rivers for further conservation programs and public policies to prevent rivers and marine biodiversity losses, and they serves as a warning on the urgent need to treat effluents in the region.

Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles

Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due to a limited understanding of their lysogenic-lytic cycle and the common lack of plaque formation in vitro. In this study, we investigated the hankyphage, a widespread transposable phage of prominent Bacteroides symbionts. Hankyphages spontaneously produced virions in laboratory conditions even in the absence of inducer, but virions did not show any evidence of infectivity. To increase virion production and raise the chances of observing infection events, we identified a master repressor of the hankyphage lytic cycle, RepCHP, whose silencing amplified hankyphage gene expression, and enhanced replicative transposition and virion production. However, attempts to infect or lysogenize new host cells with different capsular types remained unsuccessful. Transmission electron microscopy and capsid DNA sequencing revealed an abnormal virion morphology and incomplete DNA packaging of the hankyphage, suggesting that it cannot complete its assembly in laboratory conditions for reasons that are yet to be identified. Still, metavirome and phylogenetic analyses were suggestive of hankyphage horizontal transmission. We could also detect the activity of diversity-generating retroelements (DGRs) that mutagenize the hankyphage tail fiber, and likely contribute to its broad host range. This study sheds light on the life cycle of this abundant intestinal bacteriophage and highlights important gaps in our understanding of the factors required for the completion of its life cycle. Elucidating this puzzle will be critical to gain a better understanding of the hankyphage biology and ecological role.

Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses

Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. Here, we developed a computational tool, QuantMeta, to determine the absolute abundance of targets in metagenomes spiked with synthetic DNA standards. The tool establishes (i) entropy-based detection thresholds to confidently determine the presence of targets, and (ii) an approach to identify and correct read mapping or assembly errors and thus improve the quantification accuracy. Together this allows for an approach to confidently quantify absolute abundance of targets, be they microbial populations, genes, contigs, or metagenome-assembled genomes. We applied the approach to quantify single- and double-stranded DNA viruses in wastewater viral metagenomes, including pathogens and bacteriophages. Concentrations of total DNA viruses in wastewater influent and effluent were >108 copies/ml using QuantMeta. Human-associated DNA viruses were detected and quantifiable with QuantMeta thresholds, including polyomavirus, papillomavirus, and crAss-like phages, at concentrations similar to previous reports that utilized quantitative polymerase chain reaction (PCR)-based assays. Our results highlight the higher detection thresholds of quantitative metagenomics (approximately 500 copies/μl) as compared to PCR-based quantification (approximately 10 copies/μl) despite a sequencing depth of 200 million reads per sample. The QuantMeta approach, applicable to both viral and cellular metagenomes, advances quantitative metagenomics by improving the accuracy of measured target absolute abundances.

Sustained in situ protein production and release in the mammalian gut by an engineered bacteriophage

Oral administration of biologic drugs is challenging because of the degradative activity of the upper gastrointestinal tract. Strategies that use engineered microbes to produce biologics in the lower gastrointestinal tract are limited by competition with resident commensal bacteria. Here we demonstrate the engineering of bacteriophage (phage) that infect resident commensals to express heterologous proteins released during cell lysis. Working with the virulent T4 phage, which targets resident, nonpathogenic Escherichia coli, we first identify T4-specific promoters with maximal protein expression and minimal impact on T4 phage titers. We engineer T4 phage to express a serine protease inhibitor of a pro-inflammatory enzyme with increased activity in ulcerative colitis and observe reduced enzyme activity in a mouse model of colitis. We also apply the approach to reduce weight gain and inflammation in mouse models of diet-induced obesity. This work highlights an application of virulent phages in the mammalian gut as engineerable vectors to release therapeutics from resident gut bacteria.

Evaluation of plasmid pBI143 for its optimal concentration methods, seasonal impact, and potential as a normalization parameter in wastewater-based epidemiology

Plasmid pBI143, abundant in the human gut, is a promising human-specific fecal marker. However, studies on its optimal concentration methods, seasonal variations, and potential as a normalization parameter for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), remain limited. Among the three concentration methods compared, polyethylene glycol (PEG) precipitation and centrifugation demonstrated comparable efficiencies (9.3 ± 0.6 and 9.2 ± 0.6 log10 copies/L, respectively; n = 8 each), outperforming membrane filtration (8.0 ± 0.6 log10 copies/L; n = 8). PEG precipitation was further applied to quantify pBI143, together with other human-specific fecal markers (crAssphage and pepper mild mottle virus (PMMoV)), in 52 wastewater samples collected weekly over a one year from a wastewater treatment plant in Yamanashi Prefecture, Japan, by quantitative polymerase chain reaction. The higher pBI143 concentrations (9.6 ± 0.5 log10 copies/L) compared to PMMoV (8.2 ± 0.2 log10 copies/L) and crAssphage (8.0 ± 0.2 log10 copies/L) highlighted its potential as a robust marker for human fecal contamination. Unlike PMMoV and crAssphage that remained stable across seasons, pBI143 showed seasonal fluctuations, especially during summer and autumn, suggesting its greater sensitivity to environmental conditions. The study evaluated the suitability of pBI143, crAssphage, and PMMoV for normalizing SARS-CoV-2 concentrations in wastewater; however, non-normalized SARS-CoV-2 concentrations showed the highest correlation with COVID-19 cases (ρ = 0.74), whereas normalization reduced this correlation (PMMoV-normalized, ρ = 0.72; crAssphage-normalized, ρ = 0.70; and pBI143-normalized, ρ = 0.50), likely due to differences in the persistence and structural properties of the markers, indicating that these markers are less effective for SARS-CoV-2 normalization. This study underscores the promising utility of pBI143 in wastewater surveillance but highlights the need for further research across diverse regions to validate its applicability.

Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements

Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.

Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks

The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.

Alterations in fecal bacteriome virome interplay and microbiota-derived dysfunction in patients with schizophrenia

Rising studies have consistently reported gut bacteriome alterations in schizophrenia (SCZ). However, little is known about the role of the gut virome on shaping the gut bacteriome in SCZ. Here in, we sequenced the fecal virome, bacteriome, and host peripheral metabolome in 49 SCZ patients and 49 health controls (HCs). We compared the gut bacterial community composition and specific abundant bacteria in SCZ patients and HCs. Specific gut viruses and host peripheral metabolites co-occurring with differential bacteria were identified using Multiple Co-inertia Analysis (MCIA). Additionally, we construct a latent serial mediation model (SMM) to investigate the effect of the gut virome on SCZ through the bacteriome and host metabolic profile. SCZ patients exhibited a decreased gut bacterial β-diversity compared to HCs, with seven differentially abundant bacteria, including Coprobacillaceae, Enterococcaceae etc. Gut viruses including Suoliviridae and Rountreeviridae, co-occur with these SCZ-related bacteria. We found that the viral-bacterial transkingdom correlations observed in HCs were dramatically lost in SCZ. The altered correlations profile observed in SCZ may impact microbiota-derived peripheral metabolites enriched in the bile acids pathway, eicosanoids pathway, and others, contributing to host immune dysfunction and inflammation. The SMM model suggested potential causal chains between gut viruses and SCZ, indicating that the effect of gut virome on SCZ is significantly mediated by bacteriome and metabolites. In conclusion, these findings provide a comprehensive perspective on the role of gut microbiota in the pathogenesis of SCZ. They reveal that patients with schizophrenia harbor an abnormal virome-bacteriome ecology, shedding light on the potential development of microbial therapeutics.

Modulating intestinal viruses: A potential avenue for improving metabolic diseases with unresolved challenges

The gut microbiome affects the occurrence and development of metabolic diseases, with a significant amount of research focused on intestinal bacteria. As an important part of the gut microbiome, gut viruses were studied recently, particularly through fecal virome transplantation (FVT), revealing manipulating the gut virus could reverse overweight and glucose intolerance in mice. And human cohort studies found gut virome changed significantly in patients with metabolic disease. By summarizing those studies, we compared the research and analytical methods, as well as the similarities and differences in their results, and analyzed the reasons for these discrepancies. FVT provided potential value to improve metabolic diseases, but the mechanisms involved and the effect of FVT on humans should be investigated further. The potential methods of regulating intestinal virome composition and the possible mechanisms of intestinal virome changes affecting metabolic diseases were also discussed.

A metagenome-wide study of the gut virome in chronic kidney disease

Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD+) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.

Persistence of crAssBcn phages in conditions of natural inactivation and disinfection process and their potential role as human source tracking markers

Due to their abundance in the human gut, human specificity, and global distribution, some crAss-like phages, including the original p-crAssphage, have been proposed as indicators of human fecal pollution suitable for microbial source tracking (MST). The prevalence of crAss-like phages in water, and consequently their usefulness as MST indicators, is determined by their ability to survive various inactivation and disinfection processes. Recently, we isolated new crAss-like phages (named crAssBcn phages) capable of infecting Bacteroides intestinalis and exhibiting a wide geographical distribution. Here, we assessed the infectivity and DNA integrity of three crAssBcn phages (ΦCrAssBcn6, 10, and 15) and ΦCrAss001, the first crAss-like phage isolated, at different pHs and temperatures, after UV and chlorine treatments, and under natural conditions. Their bacterial host, B. intestinalis and a siphovirus Bacteroides-infecting phage GA17-A were used as controls. Infectious crAssBcn phages remained stable for a month at 4, 22, and 37 °C, and at pH 7, but inactivated when exposed to pH 3. Infective crAssBcn phages decreased by 5 log10 after treatment with 10 ppm of chlorine for 1 min and after UV treatment at a fluence of 5.94 mJ/cm2. However, heat treatment at 60 and 70 °C resulted in only a moderate decrease (<1 log10 and almost 3 log10 units of reduction, respectively). Experiments under natural conditions in outdoor mesocosms revealed that inactivation rates for crAssBcn phages, as for the other microorganisms, were higher in summer (up to 6 log10) than in winter (<4 log10), suggesting a higher incidence of inactivation factors, such as sunlight and temperature, in the warmer months. B. intestinalis was significantly more prone to inactivation than phages in most conditions except for the irradiation treatment. In contrast, crAssBcn phage DNA remained stable, with minimal reduction under most of the tested conditions, except in the summer mesocosm and UV assays.

A roadmap of isolating and investigating bacteriophage infecting human gut anaerobes

Bacteriophages, viruses that infect bacteria, play a crucial role in manipulating the gut microbiome, with implications for human health and disease. Despite the vast amount of data available on the human gut virome, the number of cultured phages that infect human gut bacteria-particularly obligate anaerobes-remains strikingly limited. Here, we summarize the resources and basic characteristics of phages that infect the human gut obligate anaerobe. We review various methods for isolating these phages and suggest a strategy for their isolation. Additionally, we outline their impact on the field of viral biology, their interactions with bacteria and humans, and their potential for disease intervention. Finally, we discuss the value and prospects of research on these phages, providing a comprehensive 'Roadmap' that sheds light on the 'dark matter' of phages that infect human gut obligate anaerobes.

Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages

Background

Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defences. Among the most abundant phages in the gut are the crAss-like phages that infect members of the Bacteroidales, in particular Bacteroides. In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairs in vitro using a multi-omics approach (transcriptomics, proteomics and metabolomics). These included three Bacteroides species paired with three crAss-like phages (Bacteroides intestinalis and ϕcrAss001, Bacteroides xylanisolvens and ϕcrAss002, and an acapsular mutant of Bacteroides thetaiotaomicron with DAC15), and Parabacteroides distasonis paired with the siphovirus ϕPDS1.

Results

We show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, and vice versa. An acapsular variant of B. thetaiotaomicron demonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation.

Conclusions

This study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as ϕPDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.

Development of a novel crAss-like phage detection method with a broad spectrum for microbial source tracking

CrAssphage has been recognized as the most abundant and human-specific bacteriophage in the human gut. Consequently, crAssphage has been used as a microbial source tracking (MST) marker to monitor human fecal contamination. Many crAss-like phages (CLPs) have been recently discovered, expanding the classification into the new order Crassvirales. This study aims to assess CLP prevalence in South Korea and develop a detection system for MST applications. Thirteen CLPs were identified in six human fecal samples and categorized into seven genera via metagenomic analysis. The major head protein (MHP) displayed increased sequence similarity within each genus. Eight PCR primer candidates, designed from MHP sequences, were evaluated in animal and human feces. CLPs were absent in animal feces except for those from raccoons, which hosted genera VI, VIIa, and VIIb. CLPs were detected in 91.52% (54/59) of humans, with genus VI (38 out of 59) showing the highest prevalence, nearly double that of p-crAssphage in genus I (22 out of 59). This study highlights genus VI as a potent MST marker, broadening the detection range for CLPs. Human-specific and selectively targeted MST markers can significantly impact hygiene regulations, lowering public health costs through their application in screening liver, sewage, wastewater, and various environmental samples.

CrAss-like phages are suitable indicators of antibiotic resistance genes found in abundance in fecally polluted samples

Antibiotic resistance genes (ARGs) have been extensively observed in bacterial DNA, and more recently, in phage particles from various water sources and food items. The pivotal role played by ARG transmission in the proliferation of antibiotic resistance and emergence of new resistant strains calls for a thorough understanding of the underlying mechanisms. The aim of this study was to assess the suitability of the prototypical p-crAssphage, a proposed indicator of human fecal contamination, and the recently isolated crAssBcn phages, both belonging to the Crassvirales group, as potential indicators of ARGs. These crAss-like phages were evaluated alongside specific ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, blaVIM, blaOXA-48, qnrA, qnrS, tetW and sul1) within the total DNA and phage DNA fractions in water and food samples containing different levels of fecal pollution. In samples with high fecal load (>103 CFU/g or ml of E. coli or somatic coliphages), such as wastewater and sludge, positive correlations were found between both types of crAss-like phages and ARGs in both DNA fractions. The strongest correlation was observed between sul1 and crAssBcn phages (rho = 0.90) in sludge samples, followed by blaCTX-M-9 and p-crAssphage (rho = 0.86) in sewage samples, both in the phage DNA fraction. The use of crAssphage and crAssBcn as indicators of ARGs, considered to be emerging environmental contaminants of anthropogenic origin, is supported by their close association with the human gut. Monitoring ARGs can help to mitigate their dissemination and prevent the emergence of new resistant bacterial strains, thus safeguarding public health.

Stable coexistence between an archaeal virus and the dominant methanogen of the human gut

The human gut virome, which is mainly composed of bacteriophages, also includes viruses infecting archaea, yet their role remains poorly understood due to lack of isolates. Here, we characterize a temperate archaeal virus (MSTV1) infecting Methanobrevibacter smithii, the dominant methanogenic archaeon of the human gut. The MSTV1 genome is integrated in the host chromosome as a provirus which is sporadically induced, resulting in virion release. Using cryo-electron tomography, we capture several intracellular virion assembly intermediates and confirm that only a small fraction of the host population actively produces virions in vitro. Similar low frequency of induction is observed in a mouse colonization model, using mice harboring a stable consortium of 12 bacterial species (OMM12). Transcriptomic analysis suggests a regulatory lysogeny-lysis switch involving an interplay between viral proteins to maintain virus-host equilibrium, ensuring host survival and viral persistence. Thus, our study sheds light on archaeal virus-host interactions and highlights similarities with bacteriophages in establishing stable coexistence with their hosts in the gut.

Dietary Effects on the Gut Phageome

As knowledge of the gut microbiome has expanded our understanding of the symbiotic and dysbiotic relationships between the human host and its microbial constituents, the influence of gastrointestinal (GI) microbes both locally and beyond the intestine has become evident. Shifts in bacterial populations have now been associated with several conditions including Crohn's disease (CD), Ulcerative Colitis (UC), irritable bowel syndrome (IBS), Alzheimer's disease, Parkinson's Disease, liver diseases, obesity, metabolic syndrome, anxiety, depression, and cancers. As the bacteria in our gut thrive on the food we eat, diet plays a critical role in the functional aspects of our gut microbiome, influencing not only health but also the development of disease. While the bacterial microbiome in the context of disease is well studied, the associated gut phageome-bacteriophages living amongst and within our bacterial microbiome-is less well understood. With growing evidence that fluctuations in the phageome also correlate with dysbiosis, how diet influences this population needs to be better understood. This review surveys the current understanding of the effects of diet on the gut phageome.

CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker

CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.

Assessing phage-host population dynamics by reintroducing virulent viruses to synthetic microbiomes

Microbiomes feature complex interactions between diverse bacteria and bacteriophages. Synthetic microbiomes offer a powerful way to study these interactions; however, a major challenge is obtaining a representative bacteriophage population during the bacterial isolation process. We demonstrate that colony isolation reliably excludes virulent viruses from sample sources with low virion-to-bacteria ratios such as feces, creating "virulent virus-free" controls. When the virulent dsDNA virome is reintroduced to a 73-strain synthetic gut microbiome in a bioreactor model of the human colon, virulent viruses target susceptible strains without significantly altering community structure or metabolism. In addition, we detected signals of prophage induction that associate with virulent predation. Overall, our findings indicate that dilution-based isolation methods generate synthetic gut microbiomes that are heavily depleted, if not devoid, of virulent viruses and that such viruses, if reintroduced, have a targeted effect on community assembly, metabolism, and prophage replication.

Decoding huge phage diversity: a taxonomic classification of Lak megaphages

High-throughput sequencing for uncultivated viruses has accelerated the understanding of global viral diversity and uncovered viral genomes substantially larger than any that have so far been cultured. Notably, the Lak phages are an enigmatic group of viruses that present some of the largest known phage genomes identified in human and animal microbiomes, and are dissimilar to any cultivated viruses. Despite the wealth of viral diversity that exists within sequencing datasets, uncultivated viruses have rarely been used for taxonomic classification. We investigated the evolutionary relationships of 23 Lak phages and propose a taxonomy for their classification. Predicted protein analysis revealed the Lak phages formed a deeply branching monophyletic clade within the class Caudoviricetes which contained no other phage genomes. One of the interesting features of this clade is that all current members are characterised by an alternative genetic code. We propose the Lak phages belong to a new order, the 'Grandevirales'. Protein and nucleotide-based analyses support the creation of two families, three sub-families, and four genera within the order 'Grandevirales'. We anticipate that the proposed taxonomy of Lak megaphages will simplify the future classification of related viral genomes as they are uncovered. Continued efforts to classify divergent viruses are crucial to aid common analyses of viral genomes and metagenomes.

The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis

Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.

Genome Analysis of Epsilon CrAss-like Phages

CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.

Intestinal Dysbiosis: Microbial Imbalance Impacts on Colorectal Cancer Initiation, Progression and Disease Mitigation

The human gastrointestinal tract houses a diverse range of microbial species that play an integral part in many biological functions. Several preclinical studies using germ-free mice models have demonstrated that the gut microbiome profoundly influences carcinogenesis and progression. Colorectal cancer appears to be associated with microbial dysbiosis involving certain bacterial species, including F. nucleatum, pks+ E. coli, and B. fragilis, with virome commensals also disrupted in patients. A dysbiosis toward these pro-carcinogenic species increases significantly in CRC patients, with reduced numbers of the preventative species Clostridium butyicum, Roseburia, and Bifidobacterium evident. There is also a correlation between Clostridium infection and CRC. F. nucleatum, in particular, is strongly associated with CRC where it is associated with therapeutic resistance and poor outcomes in patients. The carcinogenic mode of action of pathogenic bacteria in CRC is a result of genotoxicity, epigenetic alterations, ROS generation, and pro-inflammatory activity. The aim of this review is to discuss the microbial species and their impact on colorectal cancer in terms of disease initiation, progression, and metastasis. The potential of anticancer peptides as anticancer agents or adjuvants is also discussed, as novel treatment options are required to combat the high levels of resistance to current pharmaceutical options.

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle

The prototypic crAssphage (Carjivirus communis) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain its widespread success. Through genomic analyses and culturing, we find that crAssphage uses a phage-plasmid lifestyle to persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, we use a plaque-free culturing approach to measure crAssphage replication in culture with Phocaeicola vulgatus, Phocaeicola dorei, and Bacteroides stercoris, revealing a broad host range. We demonstrate that crAssphage persists with its hosts in culture without causing major cell lysis events or integrating into host chromosomes. The ability to switch between phage and plasmid lifestyles within a wide range of hosts contributes to the prolific nature of crAssphage in the human gut microbiome.

Assessment of crAssphage as a human fecal source tracking marker in the lower Great Lakes

CrAssphage or crAss-like phage ranks as the most abundant phage in the human gut and is present in human feces-contaminated environments. Due to its high human specificity and sensitivity, crAssphage is a potentially robust source tracking indicator that can distinguish human fecal contamination from agricultural or wildlife sources. Its suitability in the Great Lakes area, one of the world's most important water systems, has not been well tested. In this study, we tested a qPCR-based quantification method using two crAssphage marker genes (ORF18-mod and CPQ_064) at Toronto recreational beaches along with their adjacent river mouths. Our results showed a 71.4 % (CPQ_064) and 100 % (ORF18-mod) human sensitivity for CPQ_064 and ORF18-mod, and a 100 % human specificity for both marker genes. CrAssphage was present in 57.7 % or 71.2 % of environmental water samples, with concentrations ranging from 1.45 to 5.14 log10 gene copies per 100 mL water. Though concentrations of the two marker genes were strongly correlated, ORF18-mod features a higher human sensitivity and higher positive detection rates in environmental samples. Quantifiable crAssphage was mostly present in samples collected in June and July 2021 associated with higher rainfall. In addition, rivers had more frequent crAssphage presence and higher concentrations than their associated beaches, indicating more frequent and greater human fecal contamination in the rivers. However, crAssphage was more correlated with E. coli and Enterococcus at the beaches than in the rivers, suggesting human fecal sources may be more predominant in driving the increases in E. coli and Enterococcus at the beaches when impacted by river plumes.

Convergence of gut phage communities but not bacterial communities following wild mouse bacteriophage transplantation into captive house mice

Bacteriophages are abundant components of vertebrate gut microbial communities, impacting bacteriome dynamics, evolution, and directly interacting with the superhost. However, knowledge about gut phageomes and their interaction with bacteriomes in vertebrates under natural conditions is limited to humans and non-human primates. Widely used specific-pathogen-free (SPF) mouse models of host-microbiota interactions have altered gut bacteriomes compared to wild mice, and data on phageomes from wild or other non-SPF mice are lacking. We demonstrate divergent gut phageomes and bacteriomes in wild and captive non-SPF mice, with wild mice phageomes exhibiting higher alpha-diversity and interindividual variability. In both groups, phageome and bacteriome structuring mirrored each other, correlating at the individual level. Re-analysis of previous data from phageomes of SPF mice revealed their enrichment in Suoliviridae crAss-like phages compared to our non-SPF mice. Disrupted bacteriomes in mouse models can be treated by transplanting healthy phageomes, but the effects of phageome transplants on healthy adult gut microbiota are still unknown. We show that experimental transplantation of phageomes from wild to captive mice did not cause major shifts in recipient phageomes. However, the convergence of recipient-to-donor phageomes confirmed that wild phages can integrate into recipient communities. The differences in the subset of integrated phages between the two recipient mouse strains illustrate the context-dependent effects of phage transplantation. The transplantation did not impact recipient gut bacteriomes. This resilience of healthy adult gut microbiomes to the intervention has implications for phage allotransplantation safety.

Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection

The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.

Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut

The human gut microbiome plays a significant role in health and disease. The viral component (virome) is predominantly composed of bacteriophages (phages) and has received significantly less attention in comparison to the bacteriome. This knowledge gap is largely due to challenges associated with the isolation and characterization of novel gut phages, and bioinformatic hurdles such as the lack of a universal phage marker gene and the absence of sufficient numbers of homologs in viral databases. Here, we describe the isolation from human feces of a novel lytic phage with siphovirus morphology, φPDS1, infecting Parabacteroides distasonis APCS2/PD, and classified within a newly proposed Sagittacolavirus genus. In silico and biological characterization of this phage is presented in this study. Key to the isolation of φPDS1 was the antibiotic-driven selective enrichment of the bacterial host in a fecal fermenter. Despite producing plaques and lacking genes associated with lysogeny, φPDS1 demonstrates the ability to coexist in liquid culture for multiple days without affecting the abundance of its host. Multiple studies have shown that changes in Parabacteroides distasonis abundance can be linked to various disease states, rendering this novel phage-host pair and their interactions of particular interest.

Anaerobiosis, a neglected factor in phage-bacteria interactions

IMPORTANCE

Many parameters affect phage-bacteria interaction. Some of these parameters depend on the environment in which the bacteria are present. Anaerobiosis effect on phage infection in facultative anaerobic bacteria has not yet been studied. The absence of oxygen triggers metabolic changes in facultative bacteria and this affects phage infection and viral life cycle. Understanding how an anaerobic environment can alter the behavior of phages during infection is relevant for the phage therapy success.

Comparison of viral concentration techniques for native fecal indicators and pathogens from wastewater

Viral pathogens are typically dilute in environmental waters, necessitating a concentration step prior to subsequent quantification or analysis. Historically, studies on viral concentration efficiency have been done by spiking known viruses into the sample; however, spike-in controls may not have the same behavior as "native" viruses exposed to environmental conditions. In this study, four concentration methods, including polyethylene glycol precipitation (PEG), skimmed milk flocculation (SMF), pH drop followed by filtration through a 0.45 μm filter (pH), and centrifugation using an Amicon filter (Amicon), were evaluated to concentrate native viral targets in wastewater. Viral targets included both indicators (crAssphage and pepper mild mottle virus) and pathogens (adenovirus, norovirus GII, human polyomavirus, and SARS-CoV-2) in addition to a bacterial marker (HF183). A non-native spike-in control was also added to compare native and spike-in recoveries. Recovery varied widely across targets and methods, ranging from 0.1 to 39.3 %. The Amicon method was the most broadly effective concentration for recovery efficiency. For the lowest-titer target, the PEG method resulted in the lowest number of non-detections, with 96.7 % positive detections for SARS-CoV-2, compared to 66.7 %, 80 %, and 76.7 % positive detections for SMF, pH, and Amicon, respectively. The non-native spike-ins chosen were only representative of a few native recovery trends, varying by both target and concentration method, and consistently under or over-estimated recovery. Overall, this study suggests the utility of including native targets in viral concentration evaluation and determining the efficiency of concentration methods for a specific target of interest.

Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile

IMPORTANCE

Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.

Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome.

Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage

Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.

Bacteriophages from faecal contamination are an important reservoir for AMR in aquatic environments

Bacteriophages have been shown to play an important role in harbouring and propagating antibiotic resistance genes (ARGs). Faecal matter contains high levels of phages, suggesting that faecal contamination of water bodies may lead to increased antimicrobial resistance (AMR) levels due to increased phage loading in aquatic environments. In this study, we assessed whether faecal pollution of three rivers (Rivers Liffey, Tolka, and Dodder) was responsible for increased levels of ARGs in phage particles using established phage-faecal markers, focusing on four ARGs (blaTEM, tet(O), qnrS, and sul1). We observed all four ARGs in phage fractions in all three rivers, with ARGs more frequently observed in agricultural and urban sampling sites compared to their source. These findings highlight the role of faecal pollution in environmental AMR and the impact of agricultural and urban activities on water quality. Furthermore, our results suggest the importance of including phages as indicators when assessing environmental AMR, as they serve as significant reservoirs of resistance genes in aquatic environments. This study provides important insights into the role of faecal pollution and phages in the prevalence of AMR in the environment and the need for their inclusion in future studies to provide a comprehensive understanding of environmental AMR.

Antiviral type III CRISPR signalling via conjugation of ATP and SAM

CRISPR systems are widespread in the prokaryotic world, providing adaptive immunity against mobile genetic elements1,2. Type III CRISPR systems, with the signature gene cas10, use CRISPR RNA to detect non-self RNA, activating the enzymatic Cas10 subunit to defend the cell against mobile genetic elements either directly, via the integral histidine-aspartate (HD) nuclease domain3-5 or indirectly, via synthesis of cyclic oligoadenylate second messengers to activate diverse ancillary effectors6-9. A subset of type III CRISPR systems encode an uncharacterized CorA-family membrane protein and an associated NrN family phosphodiesterase that are predicted to function in antiviral defence. Here we demonstrate that the CorA-associated type III-B (Cmr) CRISPR system from Bacteroides fragilis provides immunity against mobile genetic elements when expressed in Escherichia coli. However, B. fragilis Cmr does not synthesize cyclic oligoadenylate species on activation, instead generating S-adenosyl methionine (SAM)-AMP (SAM is also known as AdoMet) by conjugating ATP to SAM via a phosphodiester bond. Once synthesized, SAM-AMP binds to the CorA effector, presumably leading to cell dormancy or death by disruption of the membrane integrity. SAM-AMP is degraded by CRISPR-associated phosphodiesterases or a SAM-AMP lyase, potentially providing an 'off switch' analogous to cyclic oligoadenylate-specific ring nucleases10. SAM-AMP thus represents a new class of second messenger for antiviral signalling, which may function in different roles in diverse cellular contexts.

Microviruses: A World Beyond phiX174

Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.

Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. 'tikkala' strain Bc01, Kolpuevirus sp. 'frurule' strain Bc03, and 'Rudgehvirus jaberico' strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.