The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing ...computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.
Beeswax is a product of honeybees (
Apis mellifera
) and has been used extensively through time, especially as the primary component in medieval sealing wax for authenticating millions of documents. ...Today, these seals form large collections which, along with the historical information in the documents that the seals are attached to, could be a potential biomolecular archive for honeybees. Here, we investigate the possibility of obtaining biological information from medieval wax seals by performing a palynological and shotgun metagenomic analysis on eight medieval wax seal fragments. Our palynological results show that some pollen and fungal spores remain in the seals, albeit very little. Only one out of eight samples yielded enough DNA for sequencing. Moreover, only minor parts of the DNA reads could be taxonomically identified and were identified as plant and fungal DNA. These results demonstrate some potential for using wax seals as biological archives, but most importantly provides a framework for future studies, in addition to understanding further the degradation of seals as cultural heritage objects. We emphasize that future analyses should focus on other methodologies to retrieve data for historical context or alternatively improve molecular methods and screen sample collections broadly.
Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence in the human ...gut remains largely unknown. Here, we introduce the Gut Phage Database, a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalog of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.
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•Database containing 142,809 non-redundant gut phage genomes from 28,060 metagenomes•Host assignment reveals phage diversity and host range across gut bacteria isolates•Epidemiology analysis unveils 280 viral clusters that are globally distributed•The Gubaphage is a clade that infects several members of the Bacteroidales order
By mining human gut metagenomes and gut bacteria isolates, Camarillo-Guerrero et al. compile high-quality gut bacteriophage genomes into the Gut Phage Database (GPD) and analyze the diversity and worldwide distribution of phage.
Biosurfactants have emerged as a remarkable strategy for microbial enhanced oil recovery (MEOR) due to their amphipatic nature, superficial activity and low toxicity. On one hand, conventional ...biosurfactants for MEOR belong to the rhamnolipids group, which are surface-active compounds of glycolipid-type. On the other hand, transmembrane proteins have been studied in recent years and have shown good surface tension reduction potential. This work aimed to evaluate and compare the emulsification index (EI), oil displacement ability (ODA) and additional oil recovery (AOR) percentages of rhamnolipids produced by a native isolate Pseudomonas aeruginosa strain Pa4 and OmpA produced by Escherichia coli. The results confirmed a high recovery potential for both of the biosurfactants with the best superficial activity for P. aeruginosa rhamnolipid mixture (EI of 95% and ODA of 59.94 cm2) and the highest recovery for OmpA, obtaining an AOR of 12%.
•We compared rhamnolipids and transmembrane proteins for enhanced oil recovery.•Rhamnolipids showed a higher ODA and IE than OmpA. OmpA had the best performance related to AOR.•These biosurfactants have a different effect in the recovery process and outstanding activity for enhancing oil recovery.
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through ...metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
Virus-host interactions are regulated by complex coevolutionary dynamics. In
, phase-variable type I restriction-modification (R-M) systems are part of the core genome. We hypothesized that the ...ability of the R-M systems to switch between six target DNA specificities also has a key role in preventing the spread of bacteriophages. Using the streptococcal temperate bacteriophage SpSL1, we show that the variants of both the SpnIII and SpnIV R-M systems are able to restrict invading bacteriophage with an efficiency approximately proportional to the number of target sites in the bacteriophage genome. In addition to restriction of lytic replication, SpnIII also led to abortive infection in the majority of host cells. During lytic infection, transcriptional analysis found evidence of phage-host interaction through the strong upregulation of the
nucleotide biosynthesis regulon. During lysogeny, the phage had less of an effect on host gene regulation. This research demonstrates a novel combined bacteriophage restriction and abortive infection mechanism, highlighting the importance that the phase-variable type I R-M systems have in the multifunctional defense against bacteriophage infection in the respiratory pathogen
With antimicrobial drug resistance becoming an increasing burden on human health, much attention has been focused on the potential use of bacteriophages and their enzymes as therapeutics. However, the investigations into the physiology of the complex interactions of bacteriophages with their hosts have attracted far less attention, in comparison. This work describes the molecular characterization of the infectious cycle of a bacteriophage in the important human pathogen
and explores the intricate relationship between phase-variable host defense mechanisms and the virus. This is the first report showing how a phase-variable type I restriction-modification system is involved in bacteriophage restriction while it also provides an additional level of infection control through abortive infection.
Background:
Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a ...novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space.
Methods:
A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j
®
graph database.
Results:
PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank.
Conclusions:
PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.
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