Biology subjects

Adriaenssens, E. M.

Publications and source records attributed to Adriaenssens, E. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Defining the ESKAPE pathogen prophage repertoire with PHORAGER

Prophages are major drivers of bacterial evolution, mediating horizontal gene transfer and lysogenic conversion to alter host phenotypes. Nevertheless, identifying prophages within bacterial genomes remains challenging due to their heterogeneity and similarity to other mobile genetic elements. Here we present PHORAGER (Prophage Hunting, vOtu Retrieval, Annotation and Genomic ExploRation), a scalable Nextflow pipeline for the standardised identification and quality assessment of prophages from bacterial genomes. PHORAGER incorporates bacterial genome pre-processing, consolidation of predictions from multiple mining tools, annotation-based filtering to reduce false positives, and generation of ready-to-analyse summary tables. We validated PHORAGER using 30,824 publicly available ESKAPE pathogen genomes. PHORAGER recovered more high-quality prophages than individual mining tools alone, and through extensive quality assessments removed a substantial number of false-positive predictions. In total 23,132 putative prophages were identified, the majority belonging to the class Caudoviricetes, and exhibiting a high degree of host-specificity. Putative antimicrobial resistance genes were detected in 0.48% of prophages, whereas virulence factors were most abundant in S. aureus prophages. ESKAPE prophages also frequently encoded anti-phage defence systems. PHORAGER is freely available as open-source software and the ESKAPE prophage collection generated in this study provides a reusable resource for further investigations. GRAPHICAL ABTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/742953v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1ce582org.highwire.dtl.DTLVardef@11fc004org.highwire.dtl.DTLVardef@17765f5org.highwire.dtl.DTLVardef@1c6f0ff_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Bacteriophage genomics: What has five years of INPHARED taught us?

Bacteriophages are key drivers of microbial ecology and evolution, and the rapid expansion of phage sequencing has created sustained demand for curated reference genome databases. We released the INfrastructure for a PHAge REference Database (INPHARED) in January 2021 to provide quality-controlled metadata for complete phage genomes from cultured isolates. Here, we compare the 2021 and 2026 snapshots, spanning a five-year period that included a substantial overhaul of bacterial virus taxonomy by the ICTV. The database has approximately doubled, from 14,244 to 28,777 genomes, yet the proportion representing novel species-level diversity has declined, indicating that redundant sequencing is outpacing new discovery. Host bias persists despite the addition of 97 new host genera. We have incorporated genome quality assessments, lifestyle predictions, and defence and anti-defence system annotations, providing an updated resource and a snapshot of the current state of phage genomics.

microbiology↗

bioRxiv2026

The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study

The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA, and analysed the bacterial and viral portion from samples obtained over time. Each donor had a unique bacterial composition which diverged with time. When comparing phage treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92, and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences to typical members of the virome, and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model. Impact statementBacteriophages are increasingly investigated and tested for their efficacy in treating infections and are a key component in fight against antimicrobial resistant bacterial infections. Because of their specificity, it has become almost a dogma to state that they do not alter the gut microbiome. We have now tested this in an in vitro study using a commercially available cocktail and real human faecal microbiota. We show minimal effects on the composition of the healthy microbiota with an individual-specific effect on Escherichia coli caused by productive infection of one phage in the cocktail.

microbiology↗

bioRxiv2025

Scalable and systematic hierarchical virus taxonomy with vConTACT3

Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes with multiple evolutionary origins, and lack of a universal barcode gene. While virus ecogenomics has expanded access to and understanding of the virosphere, available classification tools poorly scale to modern discovery-based datasets, lack taxonomic resolution, and/or are unable to classify novel sequence space. Here we develop, benchmark, and release vConTACT3, a machine learning-based tool that improves scalability and accuracy, adds extensive user-requested features, expands classification to both eukaryote and prokaryote viruses for 4/6 officially recognized realms, and establishes accurate hierarchical taxonomy from genus to order. Application to 48,069 public virus genomes provided new taxonomy assignments for thousands of taxa, revealed support for fewer taxonomic ranks than currently available, and systematically identified taxonomically problematic areas across the virosphere.

bioinformatics↗

bioRxiv2025

Bacteriophage diversity declines with COPD severity in the respiratory microbiome

Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterised the lung virome by re-analysing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. Whilst viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Phages infecting anaerobic oral bacteria showed disproportionately lower abundance--Porphyromonas phages were 40-fold less abundant despite only 4-fold lower bacterial abundance--whilst pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonised patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognised feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.

microbiology↗

bioRxiv2025

Life-Stage Transitions Drive Distinct Gut Viral Communities in Dairy Cattle

Ruminant gut microbial communities profoundly influence host health and environmental impacts, yet their viral components remain poorly characterised across developmental transitions. Here, we analysed the dairy cow gut virome across four life stages--calf, heifer, dry adult, and lactating adult. Using hybrid sequencing, we assembled 30,321 viral operational taxonomic units, including 1,338 complete genomes representing mostly novel lineages. Virome composition shifted dramatically with life stage, transitioning from low-diversity, temperate-dominated communities in calves to high-diversity, lytic-dominated communities in adults. Virome transitions paralleled but showed distinct dynamics from bacterial community development, with viral and bacterial diversity negatively correlated during drying-off. Dry cows exhibited elevated viral loads relative to their bacterial hosts. We identified 26 viral sequences targeting the methanogen Methanobrevibacter, absent in calves but present in adults. These findings reveal the dynamic nature of ruminant gut viral communities and highlight phages potential regulatory role during critical life transitions.

microbiology↗

bioRxiv2025

Diverse Defence Systems and Prophages in Human-Associated Bifidobacterium Species Reveal "Arms Race" Dynamics

Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, viruses of bacteria, are drivers of gut bacterial composition in the human gut and could affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore the direct interactions occurring between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. A total of 1,086 bifidobacterial genomes were analysed in this study, revealing complex systems to prevent viral invasion. Despite their characteristically small genomes, Bifidobacterium strains harboured more than double the number of defence systems as most bacteria. In total, 34 defence system types and 56 subtypes were detected, including several different CRISPR-Cas systems with spacers that targeted almost three-quarters of bifidobacteria-derived prophages. We identified at least one prophage which met our stringent quality control measures in [~]63% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. Additionally, prophages were found to encode various anti-defence systems, such as anti-CRISPR genes and restriction modification resistance mechanisms. In summary, our investigation reveals "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages. ImportanceMembers of the Bifidobacterium genus are widely acknowledged as being highly important for human health, particularly in infants. To date, there have been a limited number of large-scale studies that have investigated the presence of prophages and anti-viral defence systems of Bifidobacterium strains from multiple human-associated species. Here, we have uncovered a complex set of anti-phage strategies encoded by Bifidobacterium strains. In addition, we have also identified a highly diverse phage mobilome present within the genomes of bifidobacteria across the genus, which also encode several unique systems for overcoming bacterial defences. Elucidating these co-evolutionary dynamics between phages and bifidobacteria may provide valuable insight into developing high-throughput methods for identifying next-generation probiotic or live biotherapeutic candidates, which may then be applied for the prevention and treatment of various diseases in humans.

microbiology↗

bioRxiv2024

GRAViTy-V2: a grounded viral taxonomy application

Taxonomic classification of viruses is essential for understanding their evolution and therefore their distribution, host interactions and pathogenic mechanisms. Classification methodologies usually rely on comparison of aligned sequence motifs in conserved genes, by genome organisation and gene complements, and at lower taxonomic ranks such as genus and species, through genome sequence identities. Building on our previous classification framework based on a novel whole-genome analysis method, we here describe Genome Relationships Applied to Viral Taxonomy Version 2 (GRAViTy-V2), which encompasses a greatly expanded range of features and numerous optimisations, packaged as an application that may be used as an alignment-free general-purpose virus classification tool. Using 28 datasets derived from the International Society on Taxonomy of Viruses 2022 taxonomy proposals, GRAViTy-V2 output was compared against human expert-curated classifications used for assignments in the 2023 round of ICTV taxonomy changes. GRAViTy-V2 produced taxonomies equivalent to manually-curated versions down to the family level and in almost all cases, to genus and species levels. However, discrepancies with our results primarily arose through various human and automated sequence annotation errors and erroneous annotations of coding sequences used in their original classification. Analysis times ranged from 1-506 min (median 3.59) on datasets with 17-1004 genomes and mean genome length of 3,000-1,000,000 bases, on a standard consumer-grade laptop. We discuss how the output from GRAViTY-V2 outputs allows for a full analysis of why taxonomic classifications were proposed, the value of the program for quality control of genetic comparisons, and how to optimise the speed of classification through proper use of GRAViTy-V2s workflow management system.

bioinformatics↗

bioRxiv2024

Rapid and Accurate Estimation of Genetic Relatedness Between Millions of Viral Genome Pairs Using MANIAC

Average Nucleotide Identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimised for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference datasets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, here we introduce MANIAC, an efficient computational pipeline optimised for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIACs accuracy and scalability compared to existing approaches, even to datasets of hundreds-of-thousands of viral genomes. Applying MANIAC to a curated dataset of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap ([~]90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC=0.981), but that it works much better for virulent (PR-AUC=0.997) than temperate (PR-AUC=0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed under https://github.com/bioinf-mcb/MANIAC. ImportanceWe introduce a novel computational pipeline called MANIAC, designed to accurately assess Average Nucleotide Identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to datasets of over 100k genomes. Through the use of computer simulations and real data analyses, we show that MANIAC could ac- curately estimate genetic relatedness between pairs of viral genomes around 60-70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.

bioinformatics↗

bioRxiv2024

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.

microbiology↗

bioRxiv2023

Predicting stop codon reassignment improves functional annotation of bacteriophages

The majority of bacteriophage diversity remains uncharacterised, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokkagv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome medians) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased mean coding density from 66.8% to 90.0%, and from 69.0% to 89.8% for UHGV and INPHARED sequences. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.

bioinformatics↗

bioRxiv2023

Nanopore and Illumina Sequencing Reveal Different Viral Populations from Human Gut Samples

The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments including the human gut microbiome. However, the bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina was preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples. Impact StatementViral metagenomics, or viromics, has revolutionised our understanding of global viral diversity however long-read and hybrid approaches are not yet widespread in this field. Here, we compared the performance of Illumina short-read and Nanopore long-read assembly approaches for recovering fully resolved viral genomes from human faecal samples. We highlight Illuminas short-read sequencing for recovering fully resolved viral genomes, while acknowledging Oxford Nanopore Technologys long-read sequencing for capturing broader viral diversity. However, a hybrid approach, utilising both technologies, may mitigate the limitations of one technology alone. Data SummaryAll reads used in this study are available on European Nucleotide Archive (ENA) within the project PRJEB47625.

bioinformatics↗

bioRxiv2023

Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica

The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing and agriculture. In this study, we isolated twelve bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica were used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide, cellulose and BtuB. Lipopolysaccharide was identified as susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b that suggested that emergence of LPS mutations in culture with SPLA1a may represent a case of collateral sensitivity to SPLA5b. We show that combination therapy with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to monotherapy. Identification of host susceptibility and resistance genes and understanding infection dynamics is critical step in rationale design of phage cocktails against specific bacterial pathogens.

microbiology↗

bioRxiv2023

A hybrid and poly-polish workflow for the complete and accurate assembly of phage genomes: a case study of ten przondoviruses

Bacteriophages (phages) within the Przondovirus genus are T7-like podoviruses belonging to the Studiervirinae subfamily, within the Autographiviridae family and have a highly conserved genome organisation. The genome size of these phages ranges from 37 kb to 42 kb, encode 50-60 genes and are characterised by the presence of direct terminal repeats (DTRs) flanking the linear chromosome. These DTRs are often deleted during short-read-only and hybrid assemblies. Moreover, long-read-only assemblies are often littered with sequencing and/or assembly errors and require additional curation. Here, we present the isolation and characterisation of ten novel przondoviruses targeting Klebsiella spp. We describe HYPPA - a HYbrid and Poly-polish Phage Assembly workflow, which utilises long-read assemblies in combination with short-read sequencing to resolve phage DTRs and correcting errors, negating the need for laborious primer walking and Sanger sequencing validation. Our data demonstrate the importance of careful curation of phage assemblies before publication, and prior to using them for comparative genomics. IMPACT STATEMENTThe current workflows employed for phage genome assembly are often error-prone and can lead to many incomplete phage genomes being deposited within databases. This can create challenges when performing comparative genomics, and may also lead to incorrect taxonomic assignment. To overcome these challenges we proposed HYPPA, a workflow that can produce complete and high-quality phage genomes without the need for laborious lab-based validation. DATA SUMMARYPhage raw reads are available from the National Centre for Biotechnology Information Sequence Read Archive (NCBI-SRA) under the BioProject number PRJNA914245. Phage annotated genomes have been deposited at GenBank under the accessions OQ579023-OQ579032 (Table 1). Bacterial WGS data for clinical preterm infant samples have been deposited at GenBank under BioProject accession PRJNA471164 (Table S1). Bacterial raw reads for food samples are available from NCBI-SRA with individual accessions (SAMN33593347-SAMN33593351), and can be found under the BioProject number PRJNA941224 (Table S1). Strain-specific details for bacteria and publicly-available phages used in these analyses, along with accessions for the latter can be found in Table S1 and Table S6, respectively. The CL1-CL8 clinical Klebsiella strains (Table S1) were under a Materials Transfer Agreement, for which sequencing data and strain information is not available. O_TBL View this table: org.highwire.dtl.DTLVardef@8cae53org.highwire.dtl.DTLVardef@8e512org.highwire.dtl.DTLVardef@1f71a67org.highwire.dtl.DTLVardef@1e6947dorg.highwire.dtl.DTLVardef@11ebc58_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONPrzondoviruses within the collection to date and data relating to the closest database relative. C_TABLECAPTION C_TBL

microbiology↗

bioRxiv2022

MetaPhage: an automated pipeline for analyzing, annotating, and classifying bacteriophages in metagenomics sequencing data.

In the last decades, a great interest has emerged in the study and characterisation of the microbiota, especially the human gut microbiota, demonstrating that commensal microorganisms play a pivotal role in normal anatomical development and physiological function of the human body. To better understand the complex bacterial dynamics that characterize different environments, bacteriophage predation and gene transfer need to be considered as well, as they are important factors that may contribute to controlling the density, diversity, and network interactions among bacterial communities. To date, a variety of bacteriophage identification tools have been developed, differing on phage mining strategies, input files requested and results produced; however, new users approaching the bacteriophage analysis might struggle in untangling the variety of methods and comparing the different results produced. Here we present MetaPhage, a comprehensive reads-to-report pipeline that streamlines the use of multiple miners and generates an exhaustive report to both summarize and visualize the key findings and to enable further exploration of specific results with interactive filterable tables. The pipeline is implemented in Nextflow, a widely adopted workflow manager, that enables an optimized parallelization of the tasks on different premises, from local server to the cloud, and ensures reproducible results using containerized packages. MetaPhage is designed to allow scalability, reproducibility and to be easily expanded with new miners and methods, in a field that is constantly expanding. MetaPhage is freely available under a GPL-3.0 license at https://github.com/MattiaPandolfoVR/MetaPhage.

bioinformatics↗

bioRxiv2021

Diverse soil RNA viral communities have the potential to influence grassland ecosystems across multiple trophic levels

Grassland ecosystems form 30-40%1 of total land cover and provide essential ecosystem services, including food production, flood mitigation and carbon storage2. Their productivity is closely related to soil microbial communities3, yet the role of viruses within these critical ecosystems is currently undercharacterised4 and in particular, our knowledge of soil RNA viruses is significantly limited5. Here, we applied viromics6 to characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3,462 viral operational taxonomic units (vOTUs) and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited showed minimal similarity in viral community composition, but with >10-fold more vOTUs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses of viral sequences predicted broad host ranges including bacteria, plants, fungi, vertebrates and invertebrates, contrasting with soil DNA viromes which are typically dominated by bacteriophages7. RNA viral communities therefore likely have the ability to influence soil ecosystems across multiple trophic levels. Our study represents an important step towards the characterisation of terrestrial RNA viral communities and the intricate interactions with their hosts, which will provide a more holistic view of the biology of economically and ecologically important terrestrial ecosystems.

ecology↗

bioRxiv2021

Highly diverse flavobacterial phages isolated from North Sea spring blooms

It is generally recognized that phages have a modulating role in the marine environment. Therefore, we hypothesized that phages can be a mortality factor for the dense heterotrophic bacterial population succeeding in phytoplankton blooms. For the marine carbon cycle, spring phytoplankton blooms are important recurring events. In this study, we focused on Flavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms - Duplodnaviria and Monodnaviria. Taxonomic analysis allowed us to delineate ten new phage genera and seven new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating indicated that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years indicated that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.

microbiology↗

bioRxiv2021

Metagenomic investigation of the equine faecal microbiome reveals extensive taxonomic and functional diversity

BackgroundThe horse plays crucial roles across the globe, including in horseracing, as a working and companion animal and as a food animal. The horse hindgut microbiome makes a key contribution in turning a high fiber diet into body mass and horsepower. However, despite its importance, the horse hindgut microbiome remains largely undefined. Here, we applied culture-independent shotgun metagenomics to thoroughbred equine faecal samples to deliver novel insights into this complex microbial community. ResultsWe performed metagenomic sequencing on five equine faecal samples to construct 123 high- or medium-quality metagenome-assembled genomes from Bacteria and Archaea. In addition, we recovered nearly 200 bacteriophage genomes. We document surprising taxonomic and functional diversity, encompassing dozens of novel or unnamed bacterial genera and species, to which we have assigned new Candidatus names. Many of these genera are conserved across a range of mammalian gut microbiomes. ConclusionsOur metagenomic analyses provide new insights into the bacterial, archaeal and bacteriophage components of the horse gut microbiome. The resulting datasets provide a key resource for future high-resolution taxonomic and functional studies on the equine gut microbiome.

genomics↗