Biology subjects

Bearzatto, B.

Publications and source records attributed to Bearzatto, B..

7 recordsLinked to original sources

bioRxiv2026

The two-component microbial system of the black soldier fly larvae (BSFL) gut: a plastic microbiota in the midgut, but a stable one in the hindgut

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.

microbiology↗

bioRxiv2023

Sodium myo-inositol cotransporter-1, SMIT1, promotes cardiac hypertrophy and fibrosis in pressure overloaded mouse hearts

AimsRecent clinical studies have reported that myo-inositol is consistently elevated in plasma of patients with heart failure (HF), yet its role in cardiac dysfunction remains poorly understood. Myo-inositol is specifically transported into cells by the sodium-myo-inositol co-transporter-1 (SMIT1), a member of the sodium-glucose co-transporter (SGLT) family expressed in the heart. While myo-inositol is essential for phosphoinositide signaling, osmoregulation, and metabolic homeostasis, dysregulation of SMIT1-mediated myo-inositol transport may contribute to key pathological mechanisms in HF. This study aims to elucidate the role of SMIT1 in the failing heart, especially during left ventricular remodeling that precedes it. Methods and resultsWe used a mouse model of pressure overload induced by transverse aortic constriction in wild-type (WT) mice and mice lacking SMIT1 (Smit1-/-), and primary cultured cardiomyocytes. By combining molecular, structural and functional studies, RNA-sequencing, and calcium measurements, we demonstrate the contribution of myo-inositol and SMIT1 to pathological hypertrophy and the progression towards HF. We found that in comparison to WT controls, Smit1-/- mice were protected against aortic banding induced systolic dysfunction, cardiac fibrosis and hypertrophy. This hypertrophic response was driven by SMIT1 expression in cardiomyocytes, where it favors intracellular myo-inositol and Na+ entry, leading to inositol 1,4,5-trisphosphate (IP3)- and Ca2+-dependent pro-hypertrophic signaling. Following hemodynamic stress, deletion of SMIT1 significantly altered IP3/calcium effectors, including Carabin, which modulates cardiac hypertrophy through inhibition of the calcineurin/NFAT and Ras/ERK1/2 pathways. ConclusionsThis work provides important insights into the role of myo-inositol and SMIT1 in cardiomyocytes. We demonstrate that SMIT1 is a key driver of pathological hypertrophy by inducing an IP3/Ca2+-dependent pro-hypertrophic transcriptional reprogramming in cardiomyocytes. These findings identify SMIT1 as a promising therapeutic target for preventing or treating pathological cardiac hypertrophy and HF.

cell biology↗

bioRxiv2023

Genomic characterization of multidrug-resistant extended spectrum β-lactamase-producing Klebsiella pneumoniae from clinical samples of a tertiary hospital in South Kivu Province, eastern Democratic Republic of Congo

Multidrug-resistant (MDR) and Extended Spectrum {beta}-Lactamase (ESBL)-producing extraintestinal K. pneumoniae are associated with increased morbidity and mortality. This study aimed to characterize the resistance and virulence profiles of extra-intestinal MDR ESBL-producing K. pneumoniae associated with infections at a tertiary hospital in South-Kivu province, DRC. Whole-genome sequencing (WGS) was carried out on 37 K. pneumoniae isolates displaying MDR, and ESBL-producing phenotype. The assembled genomes were analysed for phylogeny, virulence factors and antimicrobial resistance genes determinants. These isolates were compared to sub-Saharan counterparts. K. pneumoniae isolates displayed a high genetic variability with up to 16 sequence types (ST). AMR was widespread against {beta}-lactamases (including third and fourth-generation cephalosporins, but not carbapenems), aminoglycosides, ciprofloxacin, tetracycline, erythromycin, nitrofurantoin, and cotrimoxazole. The blaCTXM-15 gene was the most common {beta}-lactamase gene among K. pneumoniae isolates. No carbapenemase gene was found. ARG for aminoglycosides, quinolones, phenicols, tetracyclines, sulfonamides, nitrofurantoin were widely distributed among the isolates. Nine isolates had the colistin-resistant R256G substitution in the pmrB efflux pump gene without displaying reduced susceptibility to colistin. Despite carrying virulence genes, none had hypervirulence genes. Our results highlight the genetic diversity of MDR ESBL-producing K. pneumoniae isolates, and underscore the importance of monitoring simultaneously the evolution of phenotypic and genotypic AMR in Bukavu and DRC, while calling for caution in administering colistin and carbapenem to patients.

genetics↗

bioRxiv2022

The di-symbiotic systems in the aphids Sipha maydis and Peryphillus lyropictus provide a contrasting picture of recent co-obligate nutritional endosymbiosis in aphids

Dependence on multiple nutritional bacterial symbionts forming a metabolic unit has repeatedly evolved in many insect species that feed on nutritionally unbalanced diets such as plant sap. This is the case for aphids of the subfamilies Lachninae and Chaitophorinae, which have evolved di-symbiotic systems in which the ancient obligate nutritional symbiont Buchnera aphidicola is metabolically complemented by an additional nutritional symbiont acquired more recently. Deciphering how different symbionts integrate both metabolically and anatomically in such systems is crucial to understanding how complex nutritional symbiotic systems function and evolve. In this study, we sequenced and analyzed the genomes of the symbionts B. aphidicola and Serratia symbiotica associated with the Chaitophorinae aphids Sipha maydis and Periphyllus lyropictus. Our results show that, in these two species, B. aphidicola and S. symbiotica complement each other metabolically (and their hosts) for the biosynthesis of essential amino acids and vitamins but with distinct metabolic reactions supported by each symbiont depending on the host species. Furthermore, the S. symbiotica symbiont associated with S. maydis appears to be strictly compartmentalized into the specialized host cells housing symbionts in aphids, the bacteriocytes, whereas the S. symbiotica symbiont associated with P. lyropictus exhibits a highly invasive phenotype, presumably because it is capable of expressing a larger set of virulence factors, including a complete flagellum for bacterial motility. Such contrasting levels of metabolic and anatomical integration for two S. symbiotica symbionts that were recently acquired as nutritional co-obligate partners reflect distinct coevolutionary processes specific to each association.

microbiology↗

bioRxiv2021

On the many advantages of using the VariantExperiment class to store, exchange and analyze SARS-CoV-2 genomic data and associated metadata

On Friday, 19 March 2021, WHO organized a virtual global workshop highlighting the need for a globally coordinated plan to increase SARS-CoV-2 genetic sequencing capacities to detect SARS-CoV-2 mutations and variants, and to monitor virus genomic evolution worldwide. One week later, in another virtual meeting, it focused on sero epidemiology for SARS-CoV-2 variants of concern and variants of interest. Efficient monitoring of the virus relies on the storage, handling and sharing of the genomic data and the associated metadata. In this manuscript, we demonstrate how the Bioconductor VariantExperiment class addresses these needs, offering a robust and efficient solution to the requirements laid out by the WHO.

bioinformatics↗

bioRxiv2019

Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017)

BackgroundOver the past recent years, Vibrio cholerae has been associated with outbreaks in Sub Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their potential spread to bordering countries.\n\nMethods/Principal findingsPhenotypic analysis and whole genome sequencing (WGS) were carried out on 78 clinical isolates of V. cholerae associated with cholera in eastern provinces of DRC between 2014 and 2017. SNP-based phylogenomic data show that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T)10 in East Africa. These isolates clustered in two sub-clades corresponding to Multiple Locus Sequence Types (MLST) profiles ST69 and the newly assigned ST515, the latter displaying a higher genetic diversity. Both sub-clades showed a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin and phylogenetically related to V. cholerae isolates associated with cholera outbreaks in western Tanzania, whereas ST515 isolates were disseminated along the Albertine Rift and closely related to isolates in South Sudan, Uganda, Tanzania and Zambia. Other V. cholerae isolates (5/78) were non-O1/non-O139 without any CTX prophage and no phylogenetic relationship with already characterized non-O1/non-O139 isolates.\n\nConclusions/SignificanceCurrent data confirm the association of both DRC O1 7PET (T)10 sub-clades ST69 and ST515 with recurrent outbreaks in eastern DRC and at regional level over the past 10 years. Interestingly, while ST69 is predominantly a locally endemic sequence type, ST515 became adaptable enough to expand across DRC neighboring countries.\n\nAuthors summaryCholera is a severe diarrheal disease caused by the Gram-negative bacterium Vibrio cholerae. After originating in Asia, the disease spread across sub-Saharan Africa, notably Democratic Republic of the Congo. The aim of our study was to assess the transmission pattern of V. cholerae strains prevailing in eastern DRC, and determine their genetic relatedness to strains from other African countries and other parts of the world. Between 2014 and 2017, we isolated V. cholerae from fecal samples of patients with acute diarrhea in eastern DRC, and subsequently examined the DNA of the bacteria. The results show that they all clustered in two genetic groups (ST69 and ST515) falling within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and T10 introduction event in East Africa. The genetic signature of ST515 may be involved in its adaptation to environmental conditions found in eastern DRC, and contribute to its extended geographic distribution. Indeed, unlike the locally endemic ST69, ST515 is spreading extensively through DRC cross-border countries such as South Sudan, Tanzania, Uganda and Zambia. This plainly justifies a regional strategy to strengthen the fight against cholera in eastern Africa.

genomics↗

bioRxiv2019

Backward compatibility of whole genome sequencing data with MLVA typing using a new MLVAtype shiny application: the example of Vibrio cholerae

Multiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks for subtyping pathogens causing foodborne and water-borne disease outbreaks. However, Whole Genome Sequencing (WGS) has recently emerged as the new more powerful reference for pathogen subtyping, making a data conversion method necessary which enables the users to compare the MLVA identified by either method. The MLVAType shiny application was designed to extract MLVA profiles from WGS data while ensuring backward compatibility with traditional MLVA typing methods.\n\nTo test and validate the MLVAType algorithm, WGS-derived MLVA profiles of nineteen Vibrio cholerae isolates from Democratic Republic of the Congo (n=9) and Uganda (n=10) were compared to MLVA profiles generated by microchip electrophoresis (Bioanalyzer Agilent 2100), GeneScan analysis, and Sanger sequencing as the reference method. Unlike amplicon-size derived MLVA profiles, results obtained by Sanger sequencing and WGS were totally concordant. However, the latter were affected by censored estimations whose percentage was inversely proportional to the k-mer parameter used during genome assembly. With a k-mer of 127, less than 15% estimation of V. cholerae VNTR was censored. Preventing censored estimation was only achievable when using a longer k-mer size (i.e. 175), which is not proposed in the SPAdes v.3.13.0 software.\n\nIn silico analysis showed that this limitation does not apply to other microbial species (e.g. Mycobacterium, Streptococcus, Staphylococcus, and Pseudomonas) characterized by smaller lengths of motif repeats. As NGS read lengths and qualities tend to increase with time, one may expect the increase of k-mer size in a near future. Using MLVAType application with a longer k-mer size will then efficiently retrieve MLVA profiles from WGS data while avoiding censored estimation irrespective of the microbial species.\n\nAuthor summaryNext Generation Sequencing (NGS) has emerged as a powerful high throughput genomic approach enabling the Whole Genome Sequence (WGS) of pathogens to be assembled in a relatively short time. A major advantage of WGS, compared to traditional genotypic identification and typing methods, is its ability to generate data that can be exploited in silico for multiple bacterial tests including accurate subtyping, determination of genetic relatedness, and characterization of virulence and antimicrobial resistance determinants. Accordingly, WGS is now rapidly replacing traditional methods like Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA) that has long been used in the public health sector for laboratory-based surveillance of pathogens and outbreak response. While these missions require maintenance of data comparability within networks, the lack of backward compatibility between WGS-derived and traditional MLVA methods is a well-recognized issue. As illustrated here with Vibrio cholerae isolates from DRC and Uganda, the MLVAType software application analyzes WGS data to generate MLVA profiles that are identical to those determined with traditional typing. Interestingly, this tool has also the potential to extract MLVA profiles from any bacterial genome that are characterized by a small number of tandem repeats, e.g. Streptococcus, Staphylococcus, Pseudomonas, and Mycobacterium species. This restriction can be lifted if subsequences of length k, called k-mers, are longer than what is currently proposed by genome assembly algorithm like SPAdes v.3.13.0.

bioinformatics↗