Descriptive Epidemiological study of COVID-19 in Maghreb and European countries

An outbreak of 2019 novel coronavirus diseases (COVID-19) has spread quickly world wide. We performed a descriptive epidemiological study of COVID-19 in Mediterranean North African countries and South European countries. Cases data were collected through May 3, 2020 from WHO. Data analysis included: 1) geo-temporal analysis of viral spread in 6 countries (Morocco, Algeria, Tunisia, Spain, France and Italy), 2) epidemiological curve construction, 3)mortality and cured rates, 4) study  factors that led to differences of the spread of the virus in these 6 countries, and 5) comparison between Morocco and three European countries. The number of infected cases between North African and Southern European countries were different, which might be related to restriction conditions, age, geographic location, and lifestyle. We observed that The COVID-19 epidemic has spread very quickly in Southern European compared to North African countrie

Brocchia cinerea (Delile) Vis. Essential Oil Antimicrobial Activity and Crop Protection against Cowpea Weevil Callosobruchus maculatus (Fab.)

Antibiotics and synthetic pesticides are now playing a role in the spread of resistant pathogens. They continue to have negative consequences for animal and plant health. The goal of this work is to identify the chemical composition of Brocchia cinerea (Delile) Vis. essential oil (EO) using GC-MS(Gas Chromatography-Mass Spectrometer), evaluate its antimicrobial properties, and investigate its insecticidal and repellent effectiveness against Callosobruchus maculatus (C. maculatus). The GC-MS indicated the presence of 21 chemicals, with thujone (24.9%), lyratyl acetate (24.32%), camphor (13.55%), and 1,8-cineole (10.81%) being the most prominent. For the antimicrobial assay, the yeast Candida albicans was very sensitive to the EO with a growth inhibition diameter of (42.33 mm), followed by Staphylococcus aureus (31.33 mm). Fusarium oxysporum is the mycelia strain that appeared to be extremely sensitive to the utilized EO (88.44%) compared to the two species of Aspergillus (A. flavus (48.44%); A. niger (36.55%)). The results obtained in the microdilution method show that Pseudomonas aeruginosa was very sensitive to the EO, inhibited by a very low dose (0.0018 mg/mL). The minimum inhibitory concentration (MIC) results were between 0.0149 and 0.06 mg/mL. B. cinerea EO also demonstrated a potent insecticidal effect and a medium repulsive effect against C. maculatus. Thus, the LC50 value in the contact test was 0.61 μL/L of air, lower than that observed in the inhalation test (0.72 μL/L of air). The present study reveals that B. cinerea EO has the potential to be an antimicrobial and insecticidal agent with a better performance against several pathogenic microorganisms

Brocchia cinerea (Delile) Vis. Essential Oil Antimicrobial Activity and Crop Protection against Cowpea Weevil Callosobruchus maculatus (Fab.)

Antibiotics and synthetic pesticides are now playing a role in the spread of resistant pathogens. They continue to have negative consequences for animal and plant health. The goal of this work is to identify the chemical composition of Brocchia cinerea (Delile) Vis. essential oil (EO) using GC-MS(Gas Chromatography-Mass Spectrometer), evaluate its antimicrobial properties, and investigate its insecticidal and repellent effectiveness against Callosobruchus maculatus (C. maculatus). The GC-MS indicated the presence of 21 chemicals, with thujone (24.9%), lyratyl acetate (24.32%), camphor (13.55%), and 1,8-cineole (10.81%) being the most prominent. For the antimicrobial assay, the yeast Candida albicans was very sensitive to the EO with a growth inhibition diameter of (42.33 mm), followed by Staphylococcus aureus (31.33 mm). Fusarium oxysporum is the mycelia strain that appeared to be extremely sensitive to the utilized EO (88.44%) compared to the two species of Aspergillus (A. flavus (48.44%); A. niger (36.55%)). The results obtained in the microdilution method show that Pseudomonas aeruginosa was very sensitive to the EO, inhibited by a very low dose (0.0018 mg/mL). The minimum inhibitory concentration (MIC) results were between 0.0149 and 0.06 mg/mL. B. cinerea EO also demonstrated a potent insecticidal effect and a medium repulsive effect against C. maculatus. Thus, the LC50 value in the contact test was 0.61 μL/L of air, lower than that observed in the inhalation test (0.72 μL/L of air). The present study reveals that B. cinerea EO has the potential to be an antimicrobial and insecticidal agent with a better performance against several pathogenic microorganisms

Correction to: Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

An amendment to this paper has been published and can be accessed via the original article

Host and microbiome genome-wide association studies : current state and challenges

CITATION: Awany, D., et al. 2019. Host and microbiome genome-wide association studies : current state and challenges. Frontiers in Genetics, 9:637, doi:10.3389/fgene.2018.00637.The original publication is available at https://www.frontiersin.orgThe involvement of the microbiome in health and disease is well established. Microbiome genome-wide association studies (mGWAS) are used to elucidate the interaction of host genetic variation with the microbiome. The emergence of this relatively new field has been facilitated by the advent of next generation sequencing technologies that enable the investigation of the complex interaction between host genetics and microbial communities. In this paper, we review recent studies investigating host–microbiome interactions using mGWAS. Additionally, we highlight the marked disparity in the sampling population of mGWAS carried out to date and draw attention to the critical need for inclusion of diverse populations.https://www.frontiersin.org/articles/10.3389/fgene.2018.00637/fullPublisher's versio

A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome

Abstract Background Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Results Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. Conclusions The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies

Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery

Understanding how the gut microbiota is affected by diarrhea episodes may help explain alterations in intestinal function among children in low-income settings. This study examined the composition of the gut microbiome of Nicaraguan children both during diarrhea episodes and while free of diarrhea for at least 2 months. Relative abundances of bacterial taxa, phylogenetic diversity, and species richness were determined by 16S amplicon sequencing and compared between paired diarrhea and recovery samples. A total of 66 stools were provided by 25 children enrolled in a 1-year cohort study of diarrhea etiologies. Children in our cohort had a mean age of 21.9 months; 64% were breast-fed, and 10% had received an antibiotic during the diarrhea episode. Overall, phylogenetic diversity and species richness did not differ significantly between diarrhea and recovery stools. However, of children who had a bacterial enteropathogen detected in any diarrhea stool, none experienced an increase in phylogenetic diversity in recovery, whereas of those in whom no bacterial enteropathogens were detected in their diarrhea stool(s), 59% experienced an increase in phylogenetic diversity in recovery (P = 0.008). This preliminary study suggests that recovery of the gut microbiota after a diarrhea episode may take longer time than previously thought and may be pathogen specific

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support