Phage strategies facilitate bacterial coexistence under environmental variability

Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as “Killing the Winner”, “Piggyback the loser” (PtL) or “Piggyback the Winner” (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed ‘in silico’ experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.

DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach

Background Prokaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing virulent and temperate phage–derived sequences in metavirome data is important for elucidating their different roles in interactions with bacterial hosts and regulation of microbial communities. However, there is no experimental or computational approach to effectively classify their sequences in culture-independent metavirome. We present a new computational method, DeePhage, which can directly and rapidly judge each read or contig as a virulent or temperate phage–derived fragment. Findings DeePhage uses a “one-hot” encoding form to represent DNA sequences in detail. Sequence signatures are detected via a convolutional neural network to obtain valuable local features. The accuracy of DeePhage on 5-fold cross-validation reaches as high as 89%, nearly 10% and 30% higher than that of 2 similar tools, PhagePred and PHACTS. On real metavirome, DeePhage correctly predicts the highest proportion of contigs when using BLAST as annotation, without apparent preferences. Besides, DeePhage reduces running time vs PhagePred and PHACTS by 245 and 810 times, respectively, under the same computational configuration. By direct detection of the temperate viral fragments from metagenome and metavirome, we furthermore propose a new strategy to explore phage transformations in the microbial community. The ability to detect such transformations provides us a new insight into the potential treatment for human disease. Conclusions DeePhage is a novel tool developed to rapidly and efficiently identify 2 kinds of phage fragments especially for metagenomics analysis. DeePhage is freely available via http://cqb.pku.edu.cn/ZhuLab/DeePhage or https://github.com/shufangwu/DeePhage.

Molecular Basis of Lysis–Lysogeny Decisions in Gram-Positive Phages

Temperate bacteriophages (phages) are viruses of bacteria. Upon infection of a susceptible host, a temperate phage can establish either a lytic cycle that kills the host or a lysogenic cycle as a stable prophage. The life cycle pursued by an infecting temperate phage can have a significant impact not only on the individual host bacterium at the cellular level but also on bacterial communities and evolution in the ecosystem. Thus, understanding the decision processes of temperate phages is crucial. This review delves into the molecular mechanisms behind lysis–lysogeny decision-making in Gram-positive phages. We discuss a variety of molecular mechanisms and the genetic organization of these well-understood systems. By elucidating the strategies used by phages to make lysis–lysogeny decisions, we can improve our understanding of phage–host interactions, which is crucial for a variety of studies including bacterial evolution, community and ecosystem diversification, and phage therapeutics. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A temperate phage 5W infecting multidrug-resistant Acinetobacter baumannii

We isolated 5W, a temperate phage that infects multidrug-resistant Acinetobacter baumannii from pond water, using an enrichment method that involves the addition of host bacteria. 5W is a long-tailed phage with a narrow host range lysed four of 19 A. baumannii clinical isolates tested, and complete lysis was observed for A. baumannii clinical isolate Ab1. 5W adsorbed rapidly to its Ab1 host and > 80% adsorption was observed after 2 min of mixing. The one-step growth curve showed that 5W has a 20 min latent period and a ~ 100 min rise period, with a burse size of ~ 180 PFU/cell. 5W contains a dsDNA genome 43,032 bp in length, with 61 open reading frames and a GC content of 39.85%. The genome lacks any known virulence and drug resistance genes, but encodes an N-acetyl-β-D-muramidase with numerous positively charged amino acids at its C-terminus that belongs to the GH_108 family. The M/S subunits of the restriction endonuclease are inserted in the lysogenic gene cluster. The first and second halves of the 5W genome are highly homologous with prophages phiABCR01-03 and phiABCR01-02 in the A. baumannii ABCR01 genome, respectively, which suggests that 5W may be a product of recombination between the two prophages.

Mining bacterial NGS data vastly expands the complete genomes of temperate phages

Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to the lysogenicity of these phages, which curb the identification and characterization of temperate phages. Existing in silico tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes. In this study, by a novel computational method mining both the integrated active prophages and their spontaneously induced forms (temperate phages), we obtained 192,326 complete temperate phage genomes from bacterial next-generation sequencing (NGS) data, hence expanded the existing number of complete temperate phage genomes by more than 100-fold. The reliability of our method was validated by wet-lab experiments. The experiments demonstrated that our method can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites (attP and attB sites), outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the evolution of microbes by 1) cross-infecting different bacterial host species; 2) transferring antibiotic resistance and virulence genes; and 3) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensive complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.

Complete Genome Sequences of the Methicillin-Resistant Strain Staphylococcus aureus 17Gst354 and Its Prophage Staphylococcus Phage vB_StaphS-IVBph354

We report the complete 2,783,931-bp circular genome sequence of the human methicillin-resistant strain Staphylococcus aureus 17Gst354, isolated from a nasal swab. The strain possessed an additional 4,397-bp plasmid. Moreover, we induced and sequenced its temperate phage Staphylococcus phage vB_StaphS-IVBph354, which has a circular genome of 41,970 bp.

Manual resolution of virome dark matter uncovers hundreds of viral families in the infant gut

The gut microbiome (GM) is shaped through infancy and plays a major role in determining susceptibility to chronic diseases later in life. Bacteriophages (phage) are known to modulate bacterial populations in numerous ecosystems, including the gut. However, virome data is difficult to analyse because it mostly consists of unknown viruses, i.e. viral dark matter. Here, we manually resolved the viral dark matter in the largest human virome study published to date. Fecal viromes from a cohort of 647 infants at 1 year of age were deeply sequenced and analysed through successive rounds of clustering and curation. This uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clusters. Most of the defined viral families and orders were novel and belonged to the Caudoviricetes viral class. Bacterial hosts were predicted for 79% of the viral species using CRISPR spacers in metagenomes from the same fecal samples. While Bacteroides-infecting Crassphages were present, novel viral families were more predominant, including phages infecting Clostridiales and Bifidobacterium. Phage lifestyles were determined for more than three thousand caudoviral species. Lifestyles were homogeneous at the family level for 149 caudiviral families. 32 families were found to be virulent, while 117 families were temperate. Virulent phage families were more abundant but temperate phage families were more diverse and widespread. Together, the viral families found in this study represent a major expansion of current bacteriophage taxonomy, and the sequences have been put online for use and validation by the community.

Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea

Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22–32 °C degrees), high salinity (37.5–41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 106 viruses mL−1 and 1.9 to 3.2 × 105 bacteria mL−1, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny.