The association of prokaryotic antiviral systems and symbiotic phage communities in drinking water microbiomes

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.

New perspectives on bacterial chlorine resistance: Phages encoding chlorine resistance genes improve bacterial adaptation

Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about what role and mechanism phages play in the resistance of bacterial communities to chlorine disinfectants. Here, we investigated the changes in the abundance, activity and function of the bacterial-phage community under the effect of chlorine disinfectants in a 92-day running anaerobic-anoxic-oxic system, using metagenomics and metatranscriptomics sequencing. We found that transcriptional activities of both bacteria and phage are highly sensitive to chlorine disinfectants, although their relative abundance was not obviously altered. The increase in both phage diversity and the ratio of temperate to lytic phages' average activity indicated phages, especially temperate, could play a crucial role in the response to chlorine disinfectants. Interestingly, the phages that carry chlorine resistance genes (CRGs) were the drivers of the phage and microbial community when chlorine disinfectants were present, but they followed the dynamics of community in the absence of chlorine disinfectants. Based on the association bipartite network, we further found that phages directly mediated the horizontal transfer of CRGs among bacteria, facilitating the spread of CRGs in the bacterial community. Moreover, the 4 CRGs related to cell wall repair, redox balance regulation, and efflux pumps that were carried by the phages but lacking in the hosts suggest the potential compensatory effects of the phage for the chlorine resistance of their hosts. Our findings reveal the important role of phages in improving the resistance of bacterial communities to chlorine disinfectants, providing a new perspective on the co-evolution of phages and bacteria to adapt to environments.

Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

BACKGROUND

The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.

RESULTS

Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.

CONCLUSIONS

Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.

Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities

Bacteria have evolved various antiviral defense systems (DSs) to protect themselves, but how DSs respond to the variation of bacteriophages in complex bacterial communities and whether DSs function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge (AS) samples from two full-scale wastewater treatment plants over 6 years and found that DSs were widespread in AS, with 91.1% of metagenome-assembled genomes (MAGs) having more than one complete DS. The stability of the bacterial community was maintained under the fluctuations of the phage community, and DS abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of DSs to phage fluctuations. The rapid turnover of clustered regularly interspaced short palindromic repeat spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical MAGs showing significant differences in DS composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities and reveals the key roles of DSs in stabilizing bacterial community structure and function.

Making waves: Intelligent phage cocktail design, a pathway to precise microbial control in water systems

Current practices in water and wastewater treatment to control unwanted microbes have led to new problems, including health effects from disinfection byproducts, growth of opportunistic pathogens resistant to residual disinfectants (e.g., chlorine), and antibiotic resistance. These challenges are spurring interest in rethinking our practices of microbial control. Simultaneously, advances in molecular biology and computation power are driving renewed interest in using phages (viruses that infect bacteria) to precisely control microbial growth (aka, phage biocontrol). In this Making Waves article, I begin by reviewing the current state of research into phage cocktail design, emphasizing our limited understanding of the features of successful phage cocktails (combinations of multiple types of phages). I describe the state of modeling phage-bacteria interactions and underscore the need for increasing research efforts to predict phage cocktail success, a key gap slowing the application of phage biocontrol. I also detail how research must also focus on techniques for engineering more effective phages to offer a more rapid alternative to phage discovery from natural environments. In this way, phage cocktails comprised of phages with complementary infection strategies may be designed. The final area for increased research effort that I highlight is the need for phage cocktail design to account for possible unintended environmental effects, a risk that is increasingly acknowledged in phage ecology studies but mostly ignored by those developing phage biocontrol technologies. By focusing more research effort towards the areas necessary for intelligent phage cocktail design, we can accelerate the development of phage-based biocontrol in water systems and improve public health.

New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems

Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from nondisinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomovar) within this genus is detected in 75% of drinking water systems included in this study. We propose a name for this uncultured bacterium as "Raskinella chloraquaticus" and describe the genus as "Raskinella" (endorsed by SeqCode). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, is able to metabolize halogenated compounds, proliferates in a biofilm-based environment, and shows clear indications of disinfection-mediated selection.

Adaptive strategies and ecological roles of phages in habitats under physicochemical stress

Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.

Comprehensive Analysis of Antiphage Defense Mechanisms: Serovar-Specific Patterns

Leptospirosis is a major zoonotic disease caused by pathogenic spirochetes in the genus Leptospira, affecting over a million people annually and causing approximately 60,000 deaths. Leptospira interrogans, a key causative agent, likely possesses defense systems against bacteriophages (leptophages), yet these systems are not well understood. We analyzed 402 genomes of L. interrogans using the DefenseFinder tool to identify and characterize the antiphage defense systems. We detected 24 unique systems, with CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins), PrrC, Borvo, and Restriction-Modification (R-M) being the most prevalent. Notably, Cas were identified in all strains, indicating their central role in phage defense. Furthermore, there were variations in the antiphage system distribution across different serovars, suggesting unique evolutionary adaptations. For instance, Retron was found exclusively in the Canicola serovar, while prokaryotic Argonaute proteins (pAgo) were only detected in the Grippotyphosa serovar. These findings significantly enhance our understanding of Leptospira's antiphage defense mechanisms. They reveal the potential for the development of serovar-specific phage-based therapies and underscore the importance of further exploring these defense systems.

Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce

Introduction

Although the composition and succession of microbial communities in soy sauce fermentation have been well-characterized, the understanding of phage communities in soy sauce remains limited.

Methods

This study determined the diversity, taxonomic composition, and predicted function of phage communities and the phage-host interactions in two types of raw soy sauce (Cantonese-type fermentation, NJ; Japanese-type fermentation, PJ) using shotgun metagenomics.

Results and discussion

These two raw soy sauces showed differences in phage composition (121 viral operational taxonomic units (vOTUs) in NJ and 387 vOTUs in PJ), with a higher abundance of the family Siphoviridae (58.50%) in the NJ phage community and a higher abundance of Myoviridae (33.01%) in PJ. Auxiliary metabolic functional annotation analyses showed that phages in the raw soy sauces mostly encoded genes with unknown functions (accounting for 66.33% of COG profiles), but the NJ sample contained genes mostly annotated to conventional functions related to carbohydrate metabolism (0.74%) and lipid metabolism (0.84%), while the PJ sample presented a higher level of amino acid metabolism functions (0.12%). Thirty auxiliary metabolism genes (AMGs) were identified in phage genomes, which were associated with carbohydrate utilization, cysteine and methionine metabolism, and aspartic acid biosynthesis for the host. To identify phage-host interactions, 30 host genomes (affiliated with 22 genera) were also recruited from the metagenomic dataset. The phage-host interaction analysis revealed a wide range of phage hosts, for which a total of 57 phage contigs were associated with 17 host genomes, with Shewanella fodinae and Weissella cibaria infected by the most phages. This study provides a comprehensive understanding of the phage community composition, auxiliary metabolic functions, and interactions with hosts in two different types of raw soy sauce.