Jean-Luc Gala

Due to their highly polyphagous capacities, black soldier fly ( Hermetia illucens ) larvae (BSFL) are increasingly valued for their ability to convert organic waste into valuable biomass that can be used for a variety of purposes. These remarkable digestive capabilities are highly dependent on an extremely plastic gut microbiota. However, the distribution and functioning of bacterial communities in the various gut compartments - particularly in the hindgut - remain little understood. In this study, we used a metabarcoding approach based on 16S gene sequencing to investigate the effect of three carbohydrate-rich diets with distinct molecular compositions on the functional diversity of the BSFL gut microbiota. Our results showed that the midgut harbors a highly substrate-sensitive microbiota, with a high abundance of Actinomyces spp., regardless of the substrate. A bacterial diversity oriented toward fatty acid biosynthesis pathways is promoted by starch-rich environment, whereas a lignocellulosic substrate fosters a midgut microbiota dominated by Paenibacillus spp. In contrast, the hindgut exhibits a distinctly stable and homogeneous bacterial composition dominated by Dysgonomonas spp. Overall, our results provide clear evidence of a two-compartment microbial system, in which the midgut primarily serves as a substrate-adaptive primary degradation chamber, while the hindgut functions as a stable terminal compartment for the final processing of residual substrates and the recycling of nutrients. These findings contribute to our understanding of the functional diversity of the bacterial microbiota along the BSFL digestive tract, which is a key factor in explaining this insect’s remarkable polyphagous behavior and optimizing its use for industrial purposes. Importance: By converting various types of organic waste into protein- and lipid-rich larvae, black soldier fly (BSFL) larvae act as a flexible bio-factory driven by their digestive tract. Yet, the functional diversity of the BSFL gut microbiota remains poorly characterized across the compartments of the digestive tract, with the hindgut still a black box. Grasping these aspects is essential to elucidate how this bio-factory functions and to guide the production of larvae tailored to specific industrial needs. By examining how different carbohydrate-rich diets affect this functional diversity, our research provides clear evidence for a two-compartment microbial system: the midgut functioning as a substrate-adaptive primary degradation chamber, and the hindgut functioning as a stable terminal compartment that processes residual substrate and recycles nutrients, with the genus Dysgonomonas acting as a key taxon. Furthermore, our research identifies pivotal bacterial genera (including Actinomyces and Paenibacillus ) supporting BSFL polyphagy under carbohydrate-rich diets.

The research investigates synthetic hydroxytyrosol (HT) antiviral properties against enveloped and non-enveloped viruses using in silico and in vitro methods. Molecular docking and ADMET analyses suggested favorable interactions of HT with ceramide and sphingomyelin (binding energies of −6.0 and −5.9 kcal/mol, respectively). Favorable predicted pharmacokinetics and safety profiles were also observed. In vitro tests provided preliminary evidence of the dose- and time-dependent virucidal effect of HT against several enveloped viruses, including HSV-1, West Nile virus, SARS-CoV-2 and various influenza A subtypes, which resulted in substantial viral load decreases at 1000 µg/mL. The viral titer of the measles virus decreased by 4.62 log₁₀ units during the 2 h of exposure. No virucidal activity was observed against the non-enveloped bovine rotavirus. Overall, these findings suggest that hydroxytyrosol may represent a promising candidate for further investigation as a virucidal agent, particularly against enveloped viruses.

Background: bacterial pathogens and their toxins present analytical challenges for rapid and specific detection, contributing to over 600 million cases of illness annually and worsening antimicrobial resistance (AMR). Conventional detection methods are useful but limited. Single-domain antibodies (sdAbs) offer alternative recognition elements with unique biochemical and engineering benefits, enabling the development of nanobody-based immunoassays and biosensing platforms that provide fast, highly selective, and reliable detection of bacterial pathogens and toxins in both food and clinical environments. Objectives: this systematic review assesses the analytical and functional performance of nanobody-based immunoassays and sensing formats for detecting bacteria and toxins across food and clinical samples. Methods: following PRISMA guidelines, major scientific databases were used to gather research, resulting in 32 eligible studies published between 2011 and 2025. Results: data collected included assay platforms, target bacteria and toxins, limit of detection, sensitivity, specificity, matrix recovery, and practicality. Risk of bias was evaluated using an adapted QUADAS-2 framework. The review shows that nanobody-based immunoassays have achieved high performance, thermostability, compatibility with genetic engineering, and versatile assay design. When combined with advanced transduction and signal amplification strategies, these systems contribute to the development of highly sensitive and user-friendly bioanalytical platforms for detecting bacteria and toxins. Conclusions: however, most studies relied on spiked samples and lacked large-scale validation, emphasizing the need for standardized benchmarking and real-world testing.

Viral infections impose a significant burden on global public health and the economy. This study examines the current state of CRISPR-Cas system research, focusing on their applications in viral detection and their evolution over recent years. A bibliometric analysis and systematic review were conducted using articles published between 2019 and 2024, retrieved from Web of Science, Scopus, and PubMed databases. Out of 2713 identified articles, 194 were included in the analysis. The findings reveal substantial growth in scientific output related to CRISPR-Cas systems, with the United States leading in research and development in this field. The rapid increase in CRISPR-Cas research during this period underscores its immense potential to transform viral diagnostics. With advantages such as speed, precision, and suitability for deployment in resource-limited settings, CRISPR-Cas systems outperform many traditional diagnostic methods. The concerted efforts of scientists worldwide further highlight the promising future of this technology. CRISPR-Cas systems are emerging as a powerful alternative, offering the possibility of expedited and accessible point-of-care testing and paving the way for more equitable and effective diagnostics on a global scale.

Whole-genome sequencing using high-throughput sequencing is essential for identifying and characterising chromosomes and plasmids in nosocomial and environmental bacterial pathogens, including those with bioterrorism potential. To expedite outbreaks investigations, including accidental or intentional bacterial release, without compromising sequencing quality, we evaluated a more time-efficient, user-friendly, and cost-effective approach, using minimal DNA (~ 1 ng) from a single bacterial colony. Four DNA extraction methods were compared: the automated nucleic acid extractor (EZ1 Advanced, Qiagen) with or without DNA purification using AMPure® beads (EZ1 vs. EZ1-AMP), and two rapid and inexpensive methods: heat shock lysis (HS), and glass bead disruption (GBD). Additionally, we evaluated four library preparation kits: Illumina DNA Prep (DN), Illumina Nextera XT (XT), Roche KAPA HyperPlus (KP), and NEBNext® Ultra™ II FS DNA Library Prep Kit (NN). Whole-genome sequencing performance was evaluated on Bacillus cereus (B. cereus), Staphylococcus epidermidis (S. epidermidis), and Enterobacter cloacae (E. cloacae) ATCC strains. Key performance indicators included sequencing depth evenness across chromosome and plasmids (accounting for GC bias), genome assembly quality measured by contig number, N50, genome fraction, and percentage of mismatches. Key performance indicators confirmed that DNA and library preparation methods significantly influenced WGS quality. GBD enabled efficient sequencing across all three bacterial species, while HS proved inadequate for spore-forming bacteria B. cereus. DN, KP, and NN produced high-quality results with low GC bias, whereas XT exhibited significant GC bias and lower quality for bacteria with low GC content. This study highlights the importance of selecting suitable DNA and sequencing library preparation methods based on bacterial cell wall composition and GC content for optimal HTS outcomes.

Stakeholder training is essential for handling unexpected crises swiftly, safely, and effectively. Functional and tabletop exercises simulate potential public health crises using complex scenarios with realistic data. These scenarios are designed by integrating datasets that represent populations exposed to a pandemic pathogen, combining pathogen genomic data generated through high-throughput sequencing (HTS) together with patient epidemiological, clinical, and demographic information. However, data sharing between EU member states faces challenges due to disparities in data collection practices, standardisation, legal frameworks, privacy, security regulations, and resource allocation. In the Horizon 2020 PANDEM-2 project, we developed a multi-parametric training tool that links pathogen genomic data and metadata, enabling training managers to enhance datasets and customise scenarios for more accurate simulations. The tool is available as an R package: https://github.com/maous1/Pandem2simulator and as a Shiny application: https://uclouvain-ctma.Shinyapps.io/Multi-parametricSimulator/ , facilitating rapid scenario simulations. A structured training procedure, complete with video tutorials and exercises, was shown to be effective and user-friendly during a training session with twenty PANDEM-2 participants. In conclusion, this tool enhances training for pandemics and public health crises preparedness by integrating complex pathogen genomic data and patient contextual metadata into training simulations. The increased realism of these scenarios significantly improves emergency responder readiness, regardless of the biological incident’s nature, whether natural, accidental, or intentional.

Stakeholder training is essential for handling unexpected crises swiftly, safely, and effectively. Functional and tabletop exercises simulate potential public health crises using complex scenarios with realistic data. These scenarios are designed by integrating datasets that represent populations exposed to a pandemic pathogen, combining pathogen genomic data generated through high-throughput sequencing (HTS) together with patient epidemiological, clinical, and demographic information. However, data sharing between EU member states faces challenges due to disparities in data collection practices, standardisation, legal frameworks, privacy, security regulations, and resource allocation. In the H2020 PANDEM-2 project, we developed a multi-parametric training tool that links pathogen genomic data and metadata, enabling training managers to enhance datasets and customise scenarios for more accurate simulations. The tool is available as an R package: https://github.com/maous1/Pandem2simulator and as a Shiny application: https://uclouvain-ctma.Shinyapps.io/Multi-parametricSimulator/, facilitating rapid scenario simulations. A structured training procedure, complete with video tutorials and exercises, was shown to be effective and user-friendly during a training session with twenty PANDEM-2 participants. In conclusion, this tool enhances training for pandemics and public health crises preparedness by integrating complex pathogen genomic data and patient contextual metadata into training simulations. The increased realism of these scenarios significantly improves emergency responder readiness, regardless of the biological incident's nature, whether natural, accidental, or intentional.

The COVID-19 pandemic posed significant challenges to public health, exposing first responders to high biosafety risks during medical assistance and containment efforts. The PANDEM-2 study aimed to address these critical biosafety issues by emphasising the importance of frequently updated, harmonised guidelines. This study reviewed scientific publications, lessons learned, and real-world experiences from the COVID-19 pandemic to identify biorisk gaps in three critical areas: (i) patient transportation and management, (ii) sample handling and testing, and (iii) data management and communication by laboratory staff. At the onset of the pandemic, first responders faced several challenges, including the rapid expansion of emergency medical services, conversion of non-medical structures, increased internal and cross-border transport of infected patients, frequent changes in biosafety protocols, and a shortage of personal protective equipment. In response, this study developed a versatile and easily adaptable toolkit, including biosafety guidance and recommendations linked to updated national and international online repositories. It establishes the groundwork for a minimum standard that can be tailored to various pandemic response scenarios, using monkeypox as a fictive test case. The toolkit enables rapid access to updated information via QR codes and mobile devices, improving biorisk response by providing an adaptable and standardised approach for caregivers involved in national and cross-border responses.

Between 2018 and 2024, we conducted systematic whole-genome sequencing and phylogenomic analysis on 263 V. cholerae O1 isolates from cholera patients across four provinces in the Democratic Republic of Congo (North-Kivu, South-Kivu, Tanganyika, and Kasai Oriental). These isolates were classified into the AFR10d and AFR10e sublineages of AFR10 lineage, originating from the third wave of the seventh El Tor cholera pandemic (7PET). Compared to the strains analysed between 2014 and 2017, both sublineages had few genetic changes in the core genome but recent isolates (2022-2024) had significant CTX prophage rearrangement. AFR10e spread across all four provinces, while AFR10d appeared to be extinct by the end of 2020. Since 2022, most V. cholerae O1 isolates exhibited significant CTX prophage rearrangements, including a tandem repeat of an environmental satellite phage RS1 downstream the ctxB toxin gene of the CTX-Φ-3 prophage on the large chromosome, as well as two or more arrayed copies of an environmental pre-CTX-Φ prophage precursor on the small chromosome. We used Illumina data for mapping and coverage estimation to identify isolates with unique CTX-Φ genomic features. Gene localization was then determined on MinION-derived assemblies, revealing an organization similar to that of non-O1 V. cholerae isolates found in Asia (O139 VC1374, and environmental O4 VCE232), but never described in V. cholerae O1 El Tor from the third wave. In conclusion, while the core genome of AFR10d and AFR10e showed minimal changes, significant alterations in the CTX-Φ and pre-CTX-Φ prophage content and organization were identified in AFR10e from 2022 onwards.

Between 2018 and 2022, we conducted whole-genome sequencing and phylogenomic analysis on 173 Vibrio cholerae bacteria (172 V. cholerae O1 and 1 V. cholerae non-O1/non-O139 isolates) from cholera patients across four provinces in the Democratic Republic of Congo (North-Kivu, South-Kivu, Tanganyika, and Kasai Oriental). All V. cholerae O1 isolates were classified into the AFR10d and AFR10e sublineages of AFR10 lineage, originating from the third wave of the seventh El Tor cholera pandemic (7PET). Compared to the strains analysed between 2014 and 2017, we observed only limited genetic changes in the core genome of both sublineages. However, AFR10e expanded across the four provinces, whereas AFR10d appeared to become extinct by the end of 2020. The V. cholerae isolates from 2022 exhibited significant rearrangement in the CTX prophage and associated phage satellites. Notably, this included the tandem repeat of a novel environmental satellite phage RS1 downstream the ctxB t oxin gene of the CTX-Φ-3 prophage on the large chromosome, and two tandemly arrayed copies of the pre-CTX-Φ prophage precursor on the small chromosome. In conclusion, while the core genome of V. cholerae O1 AFR10d and AFR10e sublineages showed minimal changes, significant alterations in the content and organisation of elements associated with the CTX-Φ and pre-CTX prophages were identified in AFR10e V. cholerae O1 isolated in 2022.