Baobab Index

Long-reads-whole genome sequencing was conducted using PacBio Sequel II Single-Molecule Real-Time platform, followed by genome assembly, phylogenetic analysis and functional annotation using different bioinformatics pipelines. The strains possess ~3.900,000 bp genome size and %GC ranging between 45%-46.7%, as expected in Overall, these findings emphasize the dynamic interplay between genomic conservation and flexibility within the

A viral metagenomic analysis of a 40 ml water sample from a small freshwater lake near Flagstaff, Arizona, USA, resulted in the identification of 295 circular viral genome sequences. Of these, 126 are members of

BRCA1 and BRCA2 gene mutations are major contributors to hereditary breast and ovarian cancer syndrome (HBOC). While mutation prevalence has been well-characterized in high-income countries, African populations remain underrepresented in genomics cancer research. Accurate prevalence data are essential for informing targeted screening, counselling, and personalized treatment strategies across the continent. To systematically assess the prevalence and geographic distribution of pathogenic BRCA1 and BRCA2 mutations in African populations affected by HBOC, and identify opportunities to enhance genetic testing and clinical integration. A systematic review and meta-analysis were conducted in accordance with PRISMA guidelines. PubMed, Scopus, Web of Science, and Embase were searched for studies published between January 2000 and June 2024. Studies were eligible if they reported germline BRCA1 or BRCA2 mutation data in African individuals with breast and/or ovarian cancer. Two reviewers independently screened studies, extracted data, and assessed methodological quality. Meta-analyses were performed using STATA 18 and RevMan, with fixed-effects models applied. Heterogeneity was evaluated using the I² statistic, and subgroup analyses were conducted based on gene type. A total of 52 studies from 19 African countries were included. Most studies originated from Morocco (28.4%), Tunisia (18.9%), South Africa (14.7%), and Nigeria (11.6%). Cross-sectional designs were most common (68.4%). Sanger sequencing was used in 45.3% of studies, followed by next-generation sequencing (31.6%). The overall pooled prevalence of pathogenic BRCA1/2 mutations was 9.0% (95% CI: 7.7-10.4%). Subgroup analyses showed a higher prevalence for BRCA1 mutations (10.5%, 95% CI: 8.3-13.0%) compared to BRCA2 (5.5%, 95% CI: 4.9-6.1%). Over half of the studies did not distinguish between the two genes, highlighting a need for standardized gene-specific reporting. There is a significant burden of pathogenic BRCA mutations in African HBOC populations, particularly BRCA1. However, gaps in geographic coverage and inconsistent reporting suggest the true burden may be underestimated. Expanding access to genetic testing, improving reporting standards, and integrating hereditary cancer screening into public health strategies are critical steps to advance precision oncology across Africa.

Acne is one of the most common dermatologic diseases in the world. It is due to the secretion of a high level of sebum that causes follicular hyperkeratinisation, alterations of the cutaneous microbiota, and inflammatory processes. One of the first-line treatments is still an antibiotic prescription, that inhibits bacterial growth and, as a consequence, lowers some of the other symptoms. Nevertheless, this high level of antibiotic prescription contributes to the increase of antibiotic resistance. Alternatives to antibiotics are thus highly required, as acne does not represent per se an infection. In the frame of the IRGAP (Interdisciplinary Research Group on Ancient Pharmacopeias) consortium, different preparations dedicated to cutaneous ailments have been identified based on ancient traditional uses, dating back to Antiquity or Middle Ages. Among them, the combination of Aloe vera and Myrrh was widely conserved over centuries. Even though this combination is no longer in use, we wondered why this combination was so widely conserved. We considered the use of this combination of ingredients to treat acne, a case study for which both plants are still used, but separately. The effects of both plant extracts were analyzed on the growth of different bacteria from the skin microbiota, cultivated alone or in co-culture conditions. As the skin is a rather heterologous environment, we further tested the robustness of our study by varying the experimental conditions. We further analyzed any complementary effects of these extracts on the inflammation process linked to acne. We showed that both plant extracts have complementary effects on micro-organisms and on macrophages. Indeed, while Myrrh extracts inhibited the growth of specific skin microbiota bacteria, Aloe vera gel extracts on the opposite, favored the growth of others: the two plants could act in a complementary way to restore a healthy microbiota. Another complementarity was also observed on macrophages: while Myrrh extracts showed an anti-inflammatory effect, Aloe vera gel extracts showed an antioxidant effect. Our results highlight the potential of the combination of Myrrh and Aloe vera to address both the dysbiosis of the skin microbiota and the inflammation associated with acne. Thus, this exploration of forgotten combinations from historical pharmacopoeias underscores the importance of revisiting past traditional knowledge as a source of innovation.

Although the physiological mechanisms underlying salt tolerance in wild barley (Hordeum maritimum) are relatively well understood, its recovery after salt stress remains poorly characterized. In this pot experiment, plants were exposed to 200 mM NaCl for 0, 15, 30, 45, or 60 days to evaluate changes in growth and water status. Wild barley exhibited high tolerance during the early stages of salt exposure, maintaining normal growth and water balance for up to 30 days. However, longer exposure reduced plant growth and leaf water content, indicating that prolonged salinity eventually compromises plant performance. To cope with salt stress, plants accumulate soluble sugars, proline, and mineral ions, helping maintain water uptake and cell hydration. Mineral ions, particularly sodium (Na

Cystic echinococcosis, caused by the tapeworm Echinococcus granulosus sensu stricto (ss), is a globally distributed, zoonotic disease that is recognised by WHO as a neglected tropical disease. Despite its clinical and economic importance, nuclear genomic variation in this parasite has not been systematically characterised across global populations. In this study, we aimed to characterise the genome-wide nuclear genetic diversity and population structure of E granulosus ss across globally distributed populations. We conducted a genomic study of 137 E granulosus ss samples from endemic regions across five continents, derived from previously collected parasite material from livestock, wildlife, and human infections. Using a chromosome-scale reference genome, we applied population genomic approaches to investigate genome-wide nuclear genetic diversity, population structure, and patterns of evolutionary constraint. We identified 1 071 085 nuclear single-nucleotide polymorphisms across 137 samples, with heterozygosity ranging from 46% to 93% per sample. Genome-wide analyses identified two major clades associated with geographical origin. Distinct regions of genetic differentiation were observed, particularly on chromosome 9. Conserved genes under purifying selection included those involved in glycan biosynthesis and core cellular functions, whereas variable genes were enriched in pathways such as ribosome biogenesis. Mitochondrial genotypes (G1 and G3) did not align with the nuclear genomic structure. To the best of our knowledge, this study provides the first broad atlas of nuclear genomic diversity in E granulosus ss, uncovering genetic diversity and population structure. The findings have important implications for molecular epidemiology, genomic surveillance, and translational development of diagnostics and vaccines. Incorporating genomic data into cystic echinococcosis control programmes could enhance WHO-aligned efforts to reduce the burden of this neglected tropical disease. Australian Research Council and the Estonian Ministry of Education and Research.

Aeromonas spp. are critical aquatic pathogens affecting global aquaculture and human health, yet their taxonomy is frequently confounded by persistent horizontal gene transfer and high recombination rates. While whole-genome sequencing offers definitive resolution, many laboratories remain dependent on biochemical profiling or multi-locus sequence typing (MLST) due to cost and infrastructure constraints. To address this diagnostic gap, a two-phase phylogenomic study to identify a robust single locus genetic marker was conducted. In the discovery phase, we analyzed 22 high-quality complete Aeromonas type strain genomes to quantify the evolutionary impact of recombination and selection of new marker candidate, followed by a validation phase involving high-quality 374 genus-wide assemblies. Our results indicate that an elevated recombination-to-mutation ratio (r/m ≈ 1.70) is associated with reduced phylogenetic congruence of standard MLST loci, including gyrB, groL, and recA. In contrast, the prc gene exhibited the highest congruence with the recombination-filtered clonal genealogy (score = 0.94). Within the 95-96% ANI species boundary, the prc gene identity consistently remained more than 97%. This observed prc stability may be associated with functional constraints related to its predicted role in the periplasm. We therefore propose that a prc gene phylogeny and sequence identity threshold of > 97% could serve as a rapid and cost-effective marker for preliminary species-level assignment and epidemiological surveillance of Aeromonas spp., particularly in settings where a whole-genome sequencing is not readily available.

Aminoglycosides remain clinically valuable against Staphylococcus aureus. Aminoglycoside resistance in S. aureus represents a critical One Health concern and is primarily driven by aminoglycoside-modifying enzymes (AMEs), which are frequently plasmid-encoded. Although regional studies have provided valuable insights, the global epidemiology of aminoglycoside resistance determinants remains poorly characterized because comprehensive data integrating human, animal, and environmental reservoirs are still lacking. This study addresses this gap by analyzing over 110,000 S. aureus genomes (2000-2025) to map the global resistome, quantify temporal and host-specific trends, and assess the association between genetic determinants and phenotypic resistance. We performed a retrospective One Health meta-analysis of 110,309 S. aureus genomes collected between 2000 and 2025 from 128 countries. Genomes were quality-filtered and aminoglycoside resistance determinants were identified using NCBI AMRFinderPlus (v4.0.23). Multilocus sequence typing and host-source harmonization (Human, Animal, Environment, Unknown) enabled clonal and reservoir stratification. Temporal trends in gene prevalence and resistance burden were modeled with robust regression. Geographic and host-associated structuring of key genes was assessed via χ Aminoglycoside resistance-associated genes were dominated by modifying enzyme determinants, with ant(6)-Ia, ant(9)-Ia, aph(3')-IIIa, sat4, aadD1, and aac(6')-Ie/aph(2'')-Ia occurring in 14-22% of isolates worldwide. Temporal analysis revealed significant declines in several major determinants, most notably ant(9)-Ia (-2.22 percentage points per year, p < 0.001), whereas apmA exhibited a non-significant decreasing trend in animal isolates. Host structuring was marked: human clinical isolates concentrated common determinants, while animal and environmental isolates harbored rare alleles (apmA, spw, str, spd). Geographic mapping confirmed near-universal distribution of common genes but focal restriction of rare ones. Publicly available phenotypic data indicated strong activity of amikacin, whereas gentamicin showed a distinct resistant subpopulation that closely corresponded with AME gene carriage. Genotype-phenotype analyses demonstrated strong concordance, with gene-rich complements predicting resistant MIC strata and absence of determinants predicting susceptibility. Analysis across different gene classes revealed frequent co-occurrence of aminoglycoside resistance genes with determinants from other classes, such as mecA, blaZ, and MLS_B, embedding them within multidrug-resistant (MDR) genomic contexts. Over 25 years, the prevalence of aminoglycoside resistance-associated genes in S. aureus has declined for several common determinants, while rare veterinary-linked alleles are emerging in animal isolates. Strong genotype-phenotype concordance supports genomic prediction for gentamicin and amikacin, where MIC data are available, although phenotypic confirmation remains essential. The frequent co-occurrence of aminoglycoside resistance genes with other antimicrobial resistance determinants indicates their integration within co-occurrence patterns of MDR genes, defined here as clusters of co-occurring resistance genes often carried on shared mobile genetic elements. These patterns highlight the need for integrated One Health surveillance combining clinical, veterinary, and environmental monitoring with plasmid-context resolution to anticipate emerging threats.

Induction chemotherapy outcomes in acute myeloid leukemia (AML) remain suboptimal in many low- and middle-income countries due to delayed diagnosis, limited supportive care resources, and treatment-related complications. Data regarding predictors of induction outcomes in resource-limited settings remain scarce. This study aimed to evaluate day-28 induction outcomes and identify clinical, laboratory, infectious, comorbidity-related, and diagnostic factors associated with unfavorable induction outcomes in adult AML patients. This observational cohort study included 90 adult patients with newly diagnosed non-acute promyelocytic leukemia (non-APL) AML who received induction chemotherapy between January 2020 and December 2024 at Al-Azhar University Hospitals, Cairo, Egypt. Day-28 induction outcomes were categorized as complete remission (CR), refractory disease (R), or induction-related death (IID). Unfavorable induction outcome was defined as refractory disease or IID. Baseline demographic, clinical, laboratory, infectious, comorbidity, immunophenotypic, and cytogenetic variables were analyzed using univariate and multivariate logistic regression models. Among the 90 patients, 53 (58.9%) achieved CR, 20 (22.2%) had refractory disease, and 17 (18.9%) experienced IID. Poor ECOG performance status (≥2) was significantly associated with unfavorable induction outcomes in both univariate (OR = 4.58, 95% CI: 1.74 - 12.08, P = 0.002) and multivariate analyses (OR = 3.96, 95% CI: 1.39 - 11.27, P = 0.010). Severe thrombocytopenia (<50 ×10³/μL) and higher peripheral blood blast burden were also associated with poorer induction outcomes on univariate analysis. Patients with comorbidities demonstrated lower CR rates compared with patients without comorbidities, although this association did not reach statistical significance. Hypovolemic/hemorrhagic shock and sepsis were the leading causes of IID. Day-28 induction outcomes in AML patients from this resource-limited setting were strongly influenced by baseline functional status and disease burden. Poor ECOG performance status was the strongest independent predictor of unfavorable induction outcome. The findings highlight the importance of early risk stratification, optimized supportive care, and individualized induction strategies to improve AML outcomes in low-resource healthcare environments.

Fishes host a diverse microbiome in their gills, but a broad characterization of this microbiome at the metagenomic level is lacking. Here, we apply genome-resolved metagenomics to the gills of the hamlets (Hypoplectrus spp), a group of reef fishes from the Greater Caribbean. The analysis of 353 gill samples from 15 hamlet species collected at eight locations over 13 years revealed a stark contrast between the gill microbiota and reef water microbial communities, indicating a distinct and specific gill microbiome. A total of 70 gill-associated metagenome-assembled genomes (MAGs) were recovered. These MAGs belong to 17 lineages, most of which are novel. They relate to known fish gill pathogens, fish gut microbes, free-living and biofilm-associated taxa, indicating that the gill microbiome was assembled from a collection of distinct eco-evolutionary trajectories. The MAGs harbor diverse metabolic modules, involved notably in nitrogen cycling, antibiotic production and biofilm formation, revealing a highly dynamic microbial ecosystem. One lineage in the Burkholderiaceae family was outstandingly prevalent across fish host species, sampling locations and years. Its genome encoded complete metabolic modules for carbon fixation and sulfur oxidation, indicating chemosynthetic potential. To the best of our knowledge, this is the first line of evidence that fishes may host sulfur-oxidizing chemosynthetic bacteria in their gills. The functional significance of this chemosynthetic potential for the fish host or other members of the gill microbiome remains to be established. The high prevalence of this lineage allowed to build a pangenome. It revealed large-scale geographic structure (western Caribbean, eastern Caribbean and Gulf of Mexico), which parallels the phylogenomic pattern observed in the hamlets. Overall, our findings point to complex fish host-microbe and microbe-microbe eco-evolutionary interactions in the gills that may influence fish physiology, homeostasis and immune response.