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Baurain, D.

Publications and source records attributed to Baurain, D..

14 recordsLinked to original sources
bioRxiv2026

Hyoid barbels as a key innovation triggering goatfish adaptive radiation

Key innovations can unlock ecological opportunities and redirect the evolutionary trajectory of entire lineages, yet few traits have been shown to trigger both hallmarks of a genuine adaptive radiation, rapid speciation and pronounced ecomorphological divergence, within a single lineage. This is especially true among coral reef fishes, where trophic novelties are routinely proposed as drivers of diversity but rarely tested against both criteria. Here, we show that goatfishes (Mullidae), a reef fish family having chemosensory hyoid barbels, meet this standard. First, macroevolutionary analyses of speciation dynamics reveal that goatfishes diversified at a markedly elevated rate relative to other Syngnathiformes. Using the most comprehensive phylogeny of the family to date, combining ultraconserved elements and mitochondrial data for 76 of the 103 recognized species, alongside the largest phenotypic dataset assembled for the group, we find that this elevated rate has been sustained since the family's origin roughly 25 million years ago, rather than declining as ecological opportunity became filled. Head shape, the trait most closely tied to the foraging strategy enabled by hyoid barbels, diverged rapidly among genera early in the family's history and has remained conserved ever since, while body shape and barbel microstructure evolved conservatively and pigmentation diversified later through repeated convergence. By opening access to previously untapped benthic prey resources and triggering a lasting burst of diversification, hyoid barbels emerge as a key innovation that reshaped the evolutionary trajectory of an entire reef fish lineage.

evolutionary biology↗
bioRxiv2025

Horizontal Gene Transfers Underpin Ribose Heterotrophy and Central Carbon Metabolism Remodeling in Gloeobacteraceae

Gloeobacterales has long been considered a "living fossil" cyanobacterial order, owing to its lack of thylakoid membranes and basal phylogenetic position. However, our study reveals that Gloeobacterales actively integrate horizontally transferred genes into their core metabolism. In Gloeobacteraceae--one of the two families within the order--these genes encode a complete ribose ATP synthase binding cassette (ABC) importer and downstream enzymes, enabling the heterotrophic uptake of external ribose and its assimilation into central carbon metabolism, along with photosynthesis, indicative of photomixotrophy. Beyond ribose utilization, their central carbon metabolism exhibits a mosaic architecture shaped by the integration of foreign genes into the Calvin-Benson-Bassham cycle, the pentose phosphate pathway, and the Embden-Meyerhof-Parnas pathway. Uniquely, these genes appear to have been acquired through multiple independent transfer events, as reflected by their dispersed genomic locations and diverse bacterial donors, including other cyanobacteria and Pseudomonadota. These findings contradict the long-standing view of Gloeobacterales as metabolically primitive relics. Instead, Gloeobacterales is likely a dynamic lineage that continues to adapt and evolve through metabolic innovation and the assimilation of foreign genes into its genomes.

evolutionary biology↗
bioRxiv2025

Host-specific adaptation and fitness trade-off of Barley Yellow Dwarf Viruses suggested by experimental evolution through aphid inoculation on multiple Poaceae species

Yellow dwarf viruses are damaging viruses infecting cereals. They are able to infect a wide range of host plants belonging to the Poaceae family. The ban of neonicotinoids in Europe has resulted in an increasing disease incidence and triggered the need to better understand their emergence and spread. The ability of a Barley yellow dwarf virus (BYDV) population to adapt to different hosts has never been studied. We performed an experimental evolution of two BYDV species (BYDV-PAS and BYDV-PAV) to study their adaptation to four Poaceae species (wheat, oat, two-row barley, and six-row barley). After four months of evolution (4 passages from plant to plant), the replicative fitness of the final viral populations was estimated, and the complete viral genomes were sequenced by high-throughput sequencing in pools of BYDV populations. Wildly divergent evolutionary trajectories were obtained, with stable or increased fitness, up to extinctions of viral populations within and among plant species. To understand these results, the composition of viral populations was analysed in detail using single nucleotide polymorphism (SNP) calling, clustering, and haplotype reconstruction methods. Interestingly, adaptation to oat and barley was mainly explained by a combination of BYDV-PAV haplotypes showing specific mutations. In contrast, adaptation to wheat was mainly explained by a combination of BYDV-PAS haplotypes harbouring specific mutations. Moreover, these local adaptations were associated to an adaptation cost in other hosts for some viral populations. The presence of adaptation costs in controlled but realistic conditions opens the door for evaluating practices such as crop mixtures or rotations on fields, as a means to mitigate the impact of BYDV. Author summaryThe use of genetically uniform plant resistant varieties in traditional agriculture creates unique environments that facilitate the rapid emergence of highly virulent pathogen populations. In natural ecosystems, host spatial and temporal heterogeneity help limit the outbreak of epidemics. As a result, disease management strategies such as crop mixtures and rotations have been proposed to reduce the selection pressure exerted on pathogen populations and prevent the emergence of "super-infectious" pathogens. These strategies would be particularly relevant against Barley yellow dwarf virus (BYDV), the virus causing the greatest economic losses on cereals, as insecticides controlling the disease are banned in Europe and few resistance genes are currently available. However, the effectiveness of these strategies against BYDV remains to be demonstrated. By experimentally evolving a natural BYDV population on different cereal species through natural transmission (e.g. vector instead of mechanical inoculation), we showed that different combinations of mutations and haplotypes enable the virus to adapt to different cereal species. Moreover, for some viral populations, the combination promoting adaptation to one host resulted in maladaptation in another host. These host-specific adaptations are key elements in the establishment of crop mixtures and rotations in the field. Our results generated in controlled but realistic conditions demonstrate for the first time that these cultural practices could be effective against these viruses.

evolutionary biology↗
bioRxiv2025

A Unique LHCE Light-Harvesting protein Family is involved in Photosystem I and II Far-Red Absorption in Euglena gracilis

Photosynthetic organisms have evolved diverse strategies to adapt to fluctuating light conditions, balancing efficient light capture with photoprotection. In green algae and land plants, this involves specialized light-harvesting complexes (LHCs), non-photochemical quenching, and state transitions driven by dynamic remodeling of antenna proteins associated with Photosystems (PS) I and II. Euglena gracilis, a flagellate with a secondary green plastid, represents a distantly related lineage whose light-harvesting regulation remains poorly understood. Although spectral shifts under different light regimes have been observed, their molecular basis was unknown. Here, through integrated phylogenomic, proteomic, structural, and spectroscopic analyses, we identify a novel chlorophyll a far-red-absorbing antenna complex in E. gracilis, composed of a species-specific Lhce protein family. This antenna forms a pentameric complex under low light and transiently associates with PSII during far-red light exposure. It is structurally and functionally distinct from canonical LHCII{square} trimers and absent in Viridiplantae. Additionally, PSI in E. gracilis is surrounded by an expanded Lhce/LhcbM belt around a minimal core. These findings reveal a unique mechanism for regulating PS antenna size in E. gracilis, distinct from known models in plants and green algae, and highlight an alternative evolutionary strategy for light acclimation in organisms with secondary plastids. HighlightEuglena gracilis features a unique, lineage-specific LhcE antenna system that dynamically associates with PSII and expands PSI light harvesting, revealing an alternative strategy for light acclimation in secondary plastids.

plant biology↗
bioRxiv2024

Identification and Characterization of Archaeal Pseudomurein Biosynthesis Genes through Pangenomics

The peptidoglycan (PG; or murein) is a mesh-like structure, which is made of glycan polymers connected by short peptides and surrounds the cell membrane of nearly all bacterial species. In contrast, there is no PG counterpart that would be universally found in Archaea, but rather various polymers that are specific to some lineages. Methanopyrales and Methanobacteriales are two orders of Euryarchaeota that harbor pseudomurein (PM), a structural analogue of the bacterial PG. Owing to the differences between PG and PM biosynthesis, some have argued that the origin of both polymers is not connected. However, recents studies have revealed that the genomes of PM-containing Archaea encode homologues of the bacterial genes involved in PG biosynthesis, even though neither their specific functions nor the relationships within the corresponding inter-domain phylogenies have been investigated so far. In this work, we devised a pangenomic bioinformatic pipeline to identify proteins for PM biosynthesis in Archaea without prior genetic knowledge. The taxonomic distribution and evolutionary relationships of the candidate proteins were studied in detail in Archaea and Bacteria through HMM sequence mining and phylogenetic inference of the Mur domain-containing family, the ATP-grasp superfamily and the MraY-like family. Our results show that archaeal muramyl ligases are of bacterial origin, but diversified through a mixture of horizontal gene transfers and gene duplications. However, in the ATP-grasp and MraY-like families, the archaeal members were not found to originate from Bacteria. Our pangenomic approach further identified five new genes potentially involved in PM synthesis and that would deserve functional characterization.

microbiology↗
bioRxiv2022

Origin and Evolution of Pseudomurein Biosynthetic Gene Clusters

The peptidoglycan (PG; or murein) is a mesh-like structure, which is made of glycan polymers connected by short peptides and surrounds the cell membrane of nearly all bacterial species. In contrast, there is no PG counterpart that would be universally found in Archaea, but rather various polymers that are specific to some lineages. Methanopyrales and Methanobacteriales are two orders of Euryarchaeota that harbor pseudomurein (PM) in their cell-wall, a structural analogue of the bacterial PG. Owing to the differences between PG and PM biosynthesis, some have argued that the origin of both polymers is not connected. However, recents studies have revealed that the genomes of PM-containing Archaea encode homologues of the bacterial genes involved in PG biosynthesis, even though neither their specific functions nor the relationships within the corresponding inter-domain phylogenies have been investigated so far. In this work, we devised a bioinformatic pipeline to identify all potential proteins for PM biosynthesis in Archaea without relying on a candidate gene approach. After an in silico characterization of their functional domains, the taxonomic distribution and evolutionary relationships of the collected proteins were studied in detail in Archaea and Bacteria through HMM similarity searches and phylogenetic inference of the Mur domain-containing family, the ATP-grasp superfamily and the MraY-like family. Our results notably show that the extant archaeal muramyl ligases are ultimately of bacterial origin, but likely diversified through a mixture of horizontal gene transfer and gene duplication. Moreover, structural modeling of these enzymes allowed us to propose a tentative function for each of them in pentapeptide elongation. While our work clarifies the genetic determinants behind PM biosynthesis in Archaea, it also raises the question of the architecture of the cell wall in the last universal common ancestor.

microbiology↗
bioRxiv2022

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics .

BackgroundMicrobial culture collections play a key role in taxonomy by studying the diversity of their accessions and providing well characterized strains to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms (BCCM) were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (i.e. yeasts). FindingsThis public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenetic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. Technical detailsNextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. TestingThe toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early-branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. ConclusionThe GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be useful for other applications, as shown by our case study on Gloeobacterales.

bioinformatics↗
bioRxiv2022

An extended reservoir of class-D beta-lactamases in non-clinical bacterial strains

Bacterial genes coding for antibiotic resistance represent a major issue in the fight against bacterial pathogens. Among those, genes encoding beta-lactamases target penicillin and related compounds such as carbapenems, which are critical for human health. Beta-lactamases are classified into classes A, B, C and D, based on their amino acid sequence. Class D enzymes are also known as OXA beta-lactamases, due to the ability of the first enzymes described in this class to hydrolyze oxacillin. While hundreds of class D beta-lactamases with different activity profiles have been isolated from clinical strains, their nomenclature remains very uninformative. In this work, we have carried out a comprehensive survey of a reference database of 80,490 genomes and identified 24,916 OXA-domain containing proteins. These were deduplicated and their representative sequences clustered into 45 non-singleton groups derived from a phylogenetic tree of 1413 OXA-domain sequences, including five clusters that include the C-terminal domain of the BlaR membrane receptors. Interestingly, 801 known class D beta-lactamases fell into only 18 clusters. To probe the unknown diversity of the class, we selected ten protein sequences in ten uncharacterized clusters and studied the activity profile of the corresponding enzymes. A beta-lactamase activity could be detected for seven of them. Three enzymes were active against oxacillin and two against imipenem. These results indicate that, as already reported, environmental bacteria constitute a large reservoir of resistance genes that can be transferred to clinical strains, whether through plasmid exchange or hitchhiking with the help of transposase genes. ImportanceThe transmission of genes coding for resistance factors from environmental to nosocomial strains is a major component in the development of bacterial resistance towards antibiotics. Our survey of class D beta-lactamase genes in genomic databases highlighted the high sequence diversity of the enzymes that are able to recognize and/or hydrolyze beta-lactam antibiotics. Among those, we could also identify new beta-lactamases that are able to hydrolyze carbapenems, one of the last resort antibiotic families used in human chemotherapy. Therefore, it can be expected that the use of this antibiotic family will fuel the emergence of new beta-lactamases into clinically relevant strains.

microbiology↗
bioRxiv2021

ORPER: a workflow for constrained SSU rRNA phylogenies

The continuous increase of sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects evermore complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow "ORPER" (containerized in Singularity), which allows determining the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.

bioinformatics↗
bioRxiv2021

Lower statistical support with larger datasets: insights from the Ochrophyta radiation

It is commonly assumed that increasing the number of characters has the potential to resolving radiations. We studied photosynthetic stramenopiles (Ochrophyta) using alignments of heterogeneous size and origin (6,762 sites for mitochondrion, 21,692 sites for plastid and 209,105 sites for nucleus). While statistical support for the relationships between the six major Ochrophyta lineages increases when comparing the mitochondrion and plastid trees, it decreases in the nuclear tree. Statistical support is not simply related to the dataset size but also to the quantity of phylogenetic signal available at each position and our ability to extract it. Here, we show that proper signal extraction is difficult to attain, as demonstrated by conflicting results obtained when varying taxon sampling. Even though the use of a better fitting model improved signal extraction and reduced the observed conflicts, the plastid dataset provided higher statistical support for the ochrophyte radiation than the larger nucleus dataset. We propose that the higher support observed in the plastid tree is due to an acceleration of the evolutionary rate in one short deep internal branch, implying that more phylogenetic signal per position is available to resolve the Ochrophyta radiation in the plastid than in the nuclear dataset. Our work therefore suggests that, in order to resolve radiations, beyond the obvious use of datasets with more positions, we need to continue developing models of sequence evolution that better extract the phylogenetic signal and design methods to search for genes/characters that contain more signal specifically for short internal branches.

evolutionary biology↗
bioRxiv2018

Consensus assessment of the contamination level of publicly available cyanobacterial genomes

BACKGROUNDPublicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes.\n\nRESULTSAs reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods).\n\nCONCLUSIONSOur results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.

genomics↗
bioRxiv2018

Metagenomic assembly of new (sub)arctic Cyanobacteria and their associated microbiome from non-axenic cultures

Cyanobacteria form one of the most diversified phylum of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were likely associated to Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we deploy a metagenomic pipeline that enables the easy recovery of high-quality genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 15 arctic or subarctic strains, of which 14 early-branching organisms that will be useful for cyanobacterial phylogenomics. In parallel, we managed to assemble 31 co-cultivated bacteria from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.\n\nImportanceComplete genomes of cold-adapted Cyanobacteria are underrepresented in databases, due to the difficulty to grow them axenically. In this work, we report the genome sequencing of 12 (sub)arctic and 3 temperate Cyanobacteria, along with 21 Proteobacteria and 5 Bacteroidetes recovered from their microbiome. Following the use of a state-of-the-art metagenomic pipeline, 12 of our new cyanobacterial genome assemblies are of high-quality, which indicates that even non-axenic cultures can yield complete genomes suitable for phylogenomics and comparative genomics. From a methodological point of view, we investigate the fate of SSU rRNA (16S) genes during metagenomic binning and observe that multi-copy rRNA operons are lost because of higher sequencing coverage and divergent tetranucleotide frequencies. Moreover, we devised a measure of genomic identity to compare metagenomic bins of different completeness, which allowed us to show that Cyanobacteria-associated bacteria can be highly related in spite of considerable distance between collection points.

genomics↗
bioRxiv2017

Assessment Of The Potential Role Of Streptomyces In Cave Moonmilk Formation

Moonmilk is a karstic speleothem mainly composed of fine calcium carbonate crystals (CaCO3) with different textures ranging from pasty to hard, in which the contribution of biotic rock-building processes is presumed to involve indigenous microorganisms. The real bacterial input in the genesis of moonmilk is difficult to assess leading to controversial hypotheses explaining the origins and the mechanisms (biotic versus abiotic) involved. In this work we undertook a comprehensive approach in order to assess the potential role of filamentous bacteria, particularly a collection of moonmilk-originating Streptomyces, in the genesis of this speleothem. Scanning electron microscopy (SEM) confirmed that indigenous filamentous bacteria could indeed participate in moonmilk development by serving as nucleation sites for CaCO3 deposition. The metabolic activities involved in CaCO3 transformation were furthermore assessed in vitro among the collection of moonmilk Streptomyces, which revealed that peptides/amino acids ammonification, and to a lesser extend ureolysis, could be privileged metabolic pathways participating in carbonate precipitation by increasing the pH of the bacterial environment. Additionally, in silico search for the genes involved in biomineralization processes including ureolysis, dissimilatory nitrate reduction to ammonia, active calcium ion transport, and reversible hydration of CO2 allowed to identify genetic predispositions for carbonate precipitation in Streptomyces. Finally, their biomineralization abilities were confirmed by environmental SEM, which allowed to visualize the formation of abundant mineral deposits under laboratory conditions. Overall, our study provides novel evidences that filamentous Actinobacteria could be key protagonists in the genesis of moonmilk through a wide spectrum of biomineralization processes.

microbiology↗
bioRxiv2016

PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/.

bioinformatics↗