Biology subjects

Pillonel, T.

Publications and source records attributed to Pillonel, T..

7 recordsLinked to original sources

bioRxiv2026

Microbial community profiles of the snake cloaca in the presence and absence of Chlamydiota

Chlamydiota are obligate intracellular bacteria detected in snake cloacal microbiota, yet their biological significance remains poorly understood. Members range from recognised pathogens, such as Chlamydia serpentis, to potential environmental symbionts, raising questions about whether they represent transient contaminants, persistent colonisers, or subclinical infectious agents. Despite the cloaca serving as a primary site of chlamydial shedding in snakes, its interaction with the broader cloacal microbiota remains unexplored. Following pan-Chlamydiota PCR screening of 137 captive snakes across five collections, 52 samples (caenophidian snakes) (27 Chlamydiota-positive, 25 Chlamydiota-negative) were retained after V3-V4 16S rRNA sequencing and quality filtering. Presence of Chlamydiota was not associated with significant differences in alpha diversity or overall community composition, though it was related to greater within-community compositional heterogeneity. Differential abundance and multivariate analyses identified several enriched and depleted genera, with Lachnospiraceae and Copromonas consistently negatively associated with Chlamydiota across all three methods. Co-occurrence network analysis recovered more associations and a higher proportion of positive edges in the presence of Chlamydiota, with an expansion of anaerobic taxa. Inferred functional composition did not differ globally between groups; however, elastic net stability selection identified subtle pathway-specific differences, including enrichment of proteolytic and mycobacterial pathways in infected snakes. Our findings suggest subtle infection-associated community shifts that do not fully conform to established mammalian paradigms in which Chlamydia species behave either as gastrointestinal commensals or as cervicovaginal pathogens, highlighting the need for multi-omics approaches in larger cohorts of caenophidian and henophidian wild and captive snakes to better characterise the mechanistic basis and generalisability of these associations.

microbiology↗

bioRxiv2026

Comparative analysis of cloacal microbiota in Henophidia (non-venomous) and Caenophidia (venomous) snakes

The evolutionary divergence between Henophidia (non-venomous) and Caenophidia (venomous) snakes has produced distinct cranial morphologies, digestive strategies, and presence of specialised venom systems in Caenophidia, yet the extent to which these long-standing diverging trajectories have shaped cloacal microbiota assembly remains poorly understood. We characterised cloacal microbiota in 70 captive snakes (52 Caenophidia, 18 Henophidia) by 16S rRNA amplicon sequencing. Beta diversity was tested by PERMANOVA, differential abundance by ANCOM-BC2, community types by Dirichlet Multinomial Mixture modelling (DMM), and microbial interactions by SparCC co-occurrence networks. Predicted functional potential (PICRUSt2) was analysed by ALDEx2 differential abundance testing and elastic net feature selection. Henophidia exhibited significantly higher bacterial richness and greater compositional variability than Caenophidia. Community composition showed clade-associated differences (PERMANOVA) and partitioned into two distinct DMM community types. The Henophidia network was 11.9-fold denser and more modular, with Burkholderiaceae as a keystone hub, whereas the Caenophidia network was sparse. Henophidia showed predicted enrichment in C1 metabolic pathways (ethylmalonyl-CoA, formaldehyde assimilation I, glycine betaine degradation I, methylaspartate cycle), aromatic compound catabolism, and nitrogen recycling, whilst Caenophidia showed enrichment in allantoin and glucuronate degradation. This multi-method analysis suggests Burkholderiaceae as a candidate keystone taxon in Henophidia and indicates that phylogenetic clade is a major contributor to cloacal microbiota structure. The lower richness in Caenophidia raises a testable hypothesis that broad-spectrum antimicrobial activity of their venom components may selectively filter susceptible microbial lineages, motivating future shotgun metagenomic studies in wild populations of snakes.

ecology↗

bioRxiv2025

Engraftment of donor phageome via fecal microbiota transplantation in recurrent C. difficile infection: a prospective observational study

1The high efficacy of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI) is often attributed to the restoration of the bacterial community. However, factors beyond bacteria, such as bacteriophages (phages), may also play a critical role in FMTs success. We aimed to evaluate the preservation of the phage community (phageome) along the FMT production process following Good Manufacturing Practices (GMP) at the Lausanne University Hospital (CHUV), and the engraftment of the phages in patients receiving FMT to treat rCDI. Samples from one donor were used to test the need for amplification and to compare spin-column versus magnetic bead purification. Then, sixteen samples, from four donations of a second healthy donor, were collected at various production stages - fresh, frozen, homogenized, and encapsulated - for phageome analysis. The phage community profiles of three patients before, at 14, and 60 days after FMT were examined to evaluate donor phage engraftment. Phages were detected in all sample types, and samples clustered by donation, indicating that the pre-processing steps did not significantly alter the phage profile. The recipients phageome prior to FMT was characterized by low diversity, each recipient being dominated by a different phage. In contrast, the profile 14 days post-FMT demonstrated the engraftment of donor-derived phages, which persisted at 60 days. Most were predicted to be temperate phages of the Caudoviricetes class infecting members of the Clostridia bacterial class, and Lachnospiraceae and Oscillospiraceae bacterial families. Our findings suggest that the CHUV production process for oral FMT capsules preserves the phage community and that donor phages successfully engraft in recipients. Further larger-scale studies and intervention trials will help elucidate the mechanisms underlying the potential of phages in FMTs efficacy.

microbiology↗

bioRxiv2025

zAMP and zAMPExplorer: Reproducible Scalable Amplicon-based Metagenomics Analysis and Visualization

SummaryTo enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria and archaea or ITS for fungi. zAMP is complemented by two modules, one to process databases to optimize taxonomy assignment, and the second to benchmark primers, databases and classifier performances. Coupled with zAMPExplorer, an interactive R Shiny application that provides an intuitive interface for quality control, diversity analysis, and statistical testing, this complete toolbox addresses both research and clinical needs for microbiota profiling. Availability and ImplementationComprehensive documentation and tutorials are provided alongside the source code of zAMP and zAMPExplorer software to facilitate installation and use. zAMP is implemented as a Snakemake workflow, ensuring reproducibility by running within Singularity or Docker containers, and is also easily installable via Bioconda. The zAMPExplorer application, designed for visualization and statistical analysis, can be installed using either a Docker image or from R-universe.

bioinformatics↗

bioRxiv2023

zDB: bacterial comparative genomics made easy

The analysis and comparison of genomes relies on different tools for tasks such as annotation, orthology prediction and phylogenetic inference. Most tools are specialized for a single task and additional efforts are necessary to integrate and visualize the results. To fill this gap, we developed zDB, an application that integrates an analysis pipeline and a visualization platform. Starting from annotated Genbank files, zDB identifies orthologs and infers a phylogeny for each orthogroup. A species phylogeny is also constructed from shared single-copy orthologs. The results can be enriched with Pfam protein domain prediction, COG and KEGG annotations and Swissprot homologs. The web application allows searching for specific genes or annotations, running Blast queries and comparing genomic regions and whole genomes. The metabolic capacities of organisms can be compared at either the module or pathway levels. Finally, users can run queries to examine the conservation of specific genes or annotations across a chosen subset of genomes and display the results as a list of genes, Venn diagram or heatmaps. Those features will make zDB useful for both bioinformaticians and researchers more accustomed to laboratory research. zDB is perfectly suited to process datasets with tens to hundred of genomes on a desktop machine. IMPORTANCEGenome comparison and analysis rely on many independent tools, leaving to scientists the burden to integrate and visualize their results for interpretation. To alleviate this burden, we have built zDB, a comparative genomics tool that includes both an analysis pipeline and a visualization platform. The analysis pipeline automates gene annotation, orthology prediction and phylogenetic inference, while the visualization platform allows scientists to easily explore the results in a web browser. Among other features, the interface allows users to visually compare whole genomes and targeted regions, assess the conservation of genes or metabolic pathways, perform Blast searches or look for specific annotations. Altogether, this tool will be useful for a broad range of applications in comparative studies between two to hundred genomes. Furthermore, it is designed to allow sharing datasets easily at local or international scale, thereby supporting exploratory analyses for non-bioinformaticians on the genome of their favorite organisms.

bioinformatics↗

bioRxiv2020

Characterization of the antimicrobial activity of the cell-penetrating peptide TAT-RasGAP317-326

Antibiotic resistance is an increasing threat for public health, underscoring the need for new antibacterial agents. Antimicrobial peptides (AMPs) represent an alternative to classical antibiotics. TAT-RasGAP317-326 is a recently described AMP effective against a broad range of bacteria, but little is known about the conditions that may influence its activity. Using RNA-sequencing and screening of mutant libraries, we show that Escherichia coli and Pseudomonas aeruginosa respond to TAT-RasGAP317-326 by regulating metabolic and stress response pathways, possibly implicating two-component systems. Our results also indicate that bacterial surface properties, in particular integrity of the lipopolysaccharide layer, influence peptide binding and entry. Finally, we found differences between bacterial species with respect to their rate of resistance emergence against this peptide. Our findings provide the basis for future investigation on the mode of action of this peptide and its potential clinical use as an antibacterial agent.

microbiology↗

bioRxiv2020

Substitution of nucleotide-sugar by trehalose-dependent glycogen synthesis pathways in Chlamydiales underlines an unusual requirement for storage polysaccharides within obligate intracellular bacteria

All obligate intracellular pathogens or symbionts of eukaryotes lack glycogen metabolism. Most members of the Chlamydiales order are exceptions to this rule as they contain the classical GlgA-GlgC-dependent pathway of glycogen metabolism that relies on the ADP-Glucose substrate. We surveyed the diversity of Chlamydiales and found glycogen metabolism to be universally present with the important exception of Criblamydiaceae and Waddliaceae families that had been previously reported to lack an active pathway. However, we now find elements of the more recently described GlgE maltose-1-P-dependent pathway in several protist-infecting Chlamydiales. In the case of Waddliaceae and Criblamydiaceae, the substitution of the classical pathway by this recently proposed GlgE pathway was essentially complete as evidenced by the loss of both GlgA and GlgC. Biochemical analysis of recombinant proteins expressed from Waddlia chondrophila and Estrella lausannensis established that both enzymes do polymerize glycogen from trehalose through the production of maltose-1-P by TreS-Mak and its incorporation into glycogens outer chains by GlgE. Unlike Mycobacteriaceae where GlgE-dependent polymerization is produced from both bacterial ADP-Glc and trehalose, glycogen synthesis seems to be entirely dependent on host supplied UDP-Glc and Glucose-6-P or on host supplied trehalose and maltooligosaccharides. These results are discussed in the light of a possible effector nature of these enzymes, of the chlamydial host specificity and of a possible function of glycogen in extracellular survival and infectivity of the chlamydial elementary bodies. They underline that contrarily to all other obligate intracellular bacteria, glycogen metabolism is indeed central to chlamydial replication and maintenance.

microbiology↗