Biology subjects

Enault, F.

Publications and source records attributed to Enault, F..

10 recordsLinked to original sources

bioRxiv2026

Improving viral protein clustering using both diversified protein profiles and structural information

Viruses are abundant, ancestral and potentially fast-evolving biological entities. As a result, their encoded proteins are diverse and identifying homologous relationships between sequences is as important for phylogeny and functional annotation as it is challenging. Traditional methods group viral proteins by sequence similarity, build HMM profiles for each protein family, and cluster further via profile comparisons. Here, we present an improved framework where HMM sensitivity is boosted by enriching reference virus HMM profiles with tens of millions of metagenomic sequences. This increases diversity within most protein families, raising the diversity index from less than 2 for 92.7% of clusters to a median value of 6. This enrichment of the profiles more than triples the number of homologies detected compared to the raw profiles. First-step clusters are then grouped more effectively using these relationships and further unified via structural predictions and comparisons. The sequence-enrichment strategy excels at linking small proteins, while structures better connect highly structured ones like tail and head proteins. Applied to 1.42 million proteins, our method yields 56,560 families--far fewer than 200,018 (sequence-based) or 135,048 (raw HMM)--revealing that prior approaches vastly overestimated viral protein diversity. The strategy of enriching the diversity of sequences of interest with external sequences, combined with the complementary use of structural information, highlights deep evolutionary links, offering a more accurate picture of viral protein evolution.

bioinformatics↗

bioRxiv2025

Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment

Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of protein sequences. Consequently, the majority of functions carried by phage proteins remain elusive. Current tools to comprehensively identify phage protein functions from their sequence either lack sensitivity (those relying on homology for instance) or specificity (assigning a single coarse grain function to a protein). Here, we introduce Empathi, a protein-embedding-based classifier that assigns functions in a hierarchical manner - from general functional categories such as "structural" and "DNA-associated" proteins to more specific ones including "nucleases", "tail appendages" and "endolysins" to name only a few. These categories were specifically tailored for phage protein functions and organized such that molecular-level functions are respected in each category, making it well suited for training machine learning classifiers based on protein embeddings. We show on a dataset of cultured phage genomes that Empathi significantly outperforms homology-based methods, tripling the number of annotated homologous groups. On the EnVhog database, the most recent and extensive database of metagenomically-sourced phage proteins, Empathi doubled the annotated fraction of protein families from 16% to 33%. On complete genomes taken from new viromes, almost twice as many proteins are annotated using our method, predictions are consistent when compared to existing tools and Empathi predictions are highly colocalized. In addition, by leveraging Empathis ability to assign multiple labels to the same protein, it is possible to identify multifunctional proteins such as virion-associated lysins. Having a more global view of the repertoire of functions a phage possesses will assuredly help to understand them and their interactions with bacteria better.

bioinformatics↗

bioRxiv2024

Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments

The discovery of Jumbo phages and giant viruses of microeukaryotes has transformed our perception of the virosphere. Metagenomic and metatranscriptomic data further highlight their diversity and ecological impact. Nevertheless, sequence-based approaches fail to take into account the morphological diversity of non-cultivated viruses, resulting in our fragmented understanding of their nature and role in the environment. Here, we combined flow cytometry and electron microscopy to uncover both previously unsuspected morphological diversity as well as significant abundances of large viruses in aquatic environments. We discovered four new viral morphotypes, all of which were associated with microeukaryotes. We also obtained insights into the multi-year dynamics of the abundances of both giant microeukaryotic viruses and Jumbo phages. This work deepens our understanding of large viruses and reveals their key role as regulators of microbial communities.

ecology↗

bioRxiv2024

EnVhog: an extended view of the viral protein space on Earth

Over the last twenty years, hundreds of metagenomic studies have generated millions of viral genomic sequences from a wide variety of ecosystems. Despite this, the overall genetic diversity of viruses remains elusive, both in terms of the number of protein families they encode and the diversity of these families. Indeed, even if it is recognized that the organization of the viral protein sequence space requires sensitive homology detection methods, such methods have never been applied at a large scale. To produce a more realistic and comprehensive view of the protein diversity in the viral world, we have (i) collected thousands of viromes and identified viral contigs and proteins within them, (ii) retrieved viral proteins available in different public databases, and (iii) applied sensitive similarity searches to cluster all these proteins into families and (iv) annotated the protein clusters produced. More than 46 million deduplicated proteins were clustered into less than 2.3 million protein families. After further removing genomic sequences likely of cellular origin using an iterative procedure, the remaining 2,203,457 clusters were coined enVhogs (for environmental Viral homologous groups). Their multiple sequence alignments have been transformed into HMMs to constitute the EnVhog database. Even if only a small proportion of enVhogs were annotated (15.9 %), they encompass almost half of the protein dataset (44.8 %). Applied to the annotation of four recently published viromes from diverse environments (sulfuric soil, grassland, surface seawater and human gut), enVhog HMMs doubled the number of viral sequences characterized, and increased by 54%-74% the number of proteins functionally annotated. EnVhogDB, the largest comprehensive compilation of viral protein information to date, is a resource that will thus further help to determine the functions of proteins encoded in newly sequenced viral genomes, and help to improve the accuracy of viral sequence detection tools. EnVhog database is available at http://envhog.u-ga.fr/envhog.

bioinformatics↗

bioRxiv2023

Clouds, oases for airborne microbes. Differential metagenomics/ metatranscriptomics analyses of cloudy and clear atmospheric situations

Bacteria cells and fungal spores can aerosolize and remain suspended in the atmosphere for several days, exposed to water limitation, oxidation, and lack of nutrients. Using comparative metagenomics/metatranscriptomics, we show that clouds are associated with the activation of numerous metabolic functions in airborne microorganisms, including fungal spore germination. The whole phenomenon mirrors the rapid recovery of microbial activity in soils after rewetting by rain, known as the "Birch effect". Insufficient nutrient resources in cloud droplets cause a famine that recycling cellular structures could alleviate. The recovery of metabolic activity by microorganisms in clouds could favor surface invasion upon deposition, but it may also compromise further survival upon cloud evaporation. In any case, clouds appear as floating biologically active aquatic systems. One-Sentence SummaryClouds activate metabolic processes in airborne microorganisms

ecology↗

bioRxiv2022

Viral DNA SIP: the isotopic composition of virions is correlated with that of the substrate used for host growth

DNA Stable Isotope Probing is emerging as a powerful tool to study host-virus interactions. Indeed, since all viruses depend on a host for virion production, a link between the isotopic compositions of hosts and the virions they produce is expected. However, stable isotope probing applied to viral DNA has never been evaluated on simple biological models. Here, this method was tested on the bacteriophage T4 and its host Escherichia coli. To validate that E. coli cells cultivated using a substrate enriched in 13C isotope were resulting on the production of 13C-labeled T4 DNA. T4 DNA buoyant density in CsCl gradient was overall higher than the values predicted by a previously established empirical model, highlighting the need to adapt this type of models when analysing modified viral DNA. Moreover, our results show a strong correlation between the proportion of 13C6-D-glucose in the substrate used for host growth and the buoyant density of T4 DNA, validating the use of DNA SIP in viral ecology, to identify viruses infecting hosts with a specific metabolism.

microbiology↗

bioRxiv2022

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of ssDNA phages infecting marine and terrestrial Alphaproteobacteria

The Microviridae family represents one of the major clades of ssDNA phages. Their cultivated members are lytic and infect Proteobacteria, Bacteroidetes, and Chlamydiae. Prophages have been predicted in genomes from Bacteroidales, Hyphomicrobiales, and Enterobacteraceae and cluster within the "Alpavirinae", "Amoyvirinae" and Gokushovirinae. We have isolated "Ascunsovirus oldenburgi" ICBM5, a novel phage distantly related to known Microviridae. It infects Sulfitobacter dubius SH24-1b and uses both a lytic and a carrier-state life strategy. Using ICBM5 proteins as a query, we uncovered in publicly available resources 65 new microviridae prophages and episomes in bacterial genomes and retrieved 47 environmental viral genomes (EVGs) from various viromes. Genome clustering based on protein content and phylogenetic analysis showed that ICBM5, together with Rhizobium phages, new prophages, episomes, and EVGs cluster within two new phylogenetic clades, here tentatively assigned the rank of subfamily and named "Tainavirinae" and "Occultatumvirinae". They both infect Rhodobacterales. Occultatumviruses also infect Hyphomicrobiales, including nitrogen-fixing endosymbionts from cosmopolitan legumes. A biogeographical assessment showed that tainaviruses and occultatumviruses are spread worldwide, in terrestrial and marine environments. The new phage isolated here shed light onto new and diverse branches of the Microviridae tree, suggesting that much of the ssDNA phage diversity remains in the dark.

microbiology↗

bioRxiv2021

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 inflammatory diseases later in life. Bacteriophages (phages) 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. We uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clades. 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, including those 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 Caudoviricetes families, including 32 families that were found to be virulent, while 117 were temperate. Virulent phage families were more abundant but temperate ones were more diverse and widespread. Together, the viral families found in this study represent a major expansion of existing bacteriophage taxonomy.

microbiology↗

bioRxiv2020

Unveiling Crucivirus Diversity by Mining Metagenomic Data

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding ssDNA (CRESS-DNA) viruses that encode capsid proteins (CPs) that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of CP genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and ten CP-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins, and that the exchange of Rep protein domains between cruciviruses is rarer than gene exchange. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCEViruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and are viruses that appear to have multiple origins from prokaryotic plasmids. CRESS-DNA viruses such as the cruciviruses, have homologues of capsid proteins (CPs) encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

evolutionary biology↗

bioRxiv2017

Genomic, proteomic, and phylogenetic analysis of spounaviruses indicates paraphyly of the order Caudovirales

It is almost a cliche that tailed bacteriophages of the order Caudovirales are the most abundant and diverse viruses in the world. Yet, their taxonomy still consists of a single order with just three families: Myoviridae, Siphoviridae, and Podoviridae. Thousands of newly discovered phage genomes have recently challenged this morphology-based classification, revealing that tailed bacteriophages are genomically even more diverse than once thought. Here, we evaluate a range of methods for bacteriophage taxonomy by using a particularly challenging group as an example, the Bacillus phage SPO1-related viruses of the myovirid subfamily Spounavirinae. Exhaustive phylogenetic and phylogenomic analyses indicate that the spounavirins are consistent with the taxonomic rank of family and should be divided into at least five subfamilies. This work is a case study for virus genomic taxonomy and the first step in an impending massive reorganization of the tailed bacteriophage taxonomy.

microbiology↗