Background: The ability to promptly sequence whole genomes at a relatively low cost has revolutionized how we study the microbiome. Analyzing whole genome sequencing (WGS) data enables metagenomics at scale. Still, it is a complex process that involves multiple moving parts and can be unintuitive for scientists that do not typically work with this type of data. Methods: Thus, to help lower the barrier for less computationally inclined individuals, TAXAPRO, a metagenomics pipeline that accurately assembles organelle genomes from WGS, data was developed. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents information on microorganisms’ diversity and relative abundance. Results: TAXAPRO was evaluated using gut microbiome data from COVID-19 patients. Analysis performed by TAXAPRO demonstrated a relatively high abundance of Clostridia and Bacteroides genera and a low abundance of Proteobacteria were detected in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings results derived using a different analysis methodology. Conclusion: Our results provide evidence that the TAXAPRO workflow dispenses quick and automated microorganism diversity and relative abundance information without the hassle of manually performing the analysis.

The relationship between gut microbiota and obesity has been investigated in numerous studies. However, inter-individual heterogeneity influenced by multiple factors may explain the inconsistent findings in human studies. Our primary aim was to identify the specific gut microbial composition that distinguishes obese male and female children from normal-weight children based on their body mass index (BMI) and to compare the results with previous analyses. Methods: Gut microbiome 16S rRNA sequences data from participants divided into three groups based on age (6–16 years), gender, and weight status: 13 obese female and 6 normal-weight female children, 13 obese male and 5 normal-weight male children, and a combined group of 13 obese male and 13 obese female children, has been analyzed using he EZBiocloud public data and analytics portal. Results: Gut microbiome composition of obese female and male children groups showed significant differences in terms of their alpha and beta diversity indices. Obese female children had significantly higher alpha diversity indices than male children with obesity. The increase in alpha diversity indices observed among female children with obesity indicates higher microbial diversity within their gut microbiota. Moreover, the analysis of beta diversity uncovered notable distinctions in the gut microbiota composition among subgroups of obese male and female children. We propose that bacterial microbiota, such as Bifidobacterium lactis and Lactobacillus rhamnosus, could potentially function as health indicators in obese children of both sexes. These microbial genera might be useful in aiding obese children to manage weight problems and alleviating metabolic disorders associated with obesity. Conclusions: Gender plays a crucial role in the composition of the gut microbiota of obese children. This finding emphasizes the necessity of considering gender-specific factors in both obesity research and management. Furthermore, using prebiotic and probiotic supplements in childhood obesity treatments could act as useful adjuncts to regulate gut microbiota composition and improve metabolic health. This approach aims to modify relative microbial abundance.

Cystic fibrosis (CF) is an inherited disorder caused by a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. While previous studies have examined the gut microbiome of children with CF, there remains a significant knowledge gap regarding the influence of sex on disease outcomes. Notably, emerging evidence suggests that females with CF tend to experience worse outcomes than males. Therefore, our study aimed to investigate the composition of the gut microbiome in children with CF and delve deeply into the potential correlation between sex and microbiome composition. We analyzed raw amplicon sequences of the V3-V5 region of the 16S rRNA gene of DNA extracted from stool samples collected from males with CF (n = 10) and females with CF (n = 10). Gut bacterial communities were characterized through measurements of diversity and taxa abundance. The study findings revealed the presence of opportunistic pathogens, such as Escherichia, with a higher prevalence in the male group (16

Background: Necrotizing enterocolitis (NEC) is a devastating intestinal disease that affects preterm infants and remains a leading cause of morbidity and mortality in this population. The gut microbiome has been implicated in the pathogenesis of NEC, and the taxonomic composition can vary depending on several factors, including geography. This study aims to compare the gut microbiome composition and abundance in preterm infants with NEC from the United States and Brazil to explore the impact of geography and ethnicity. Methods: This cohort study included forty-three (43) fecal samples from twenty- one (21) preterm infants with NEC from the United States USA and Brazil. A 16S rRNA amplicon profiling approach was conducted on extracted fecal DNA to characterize the gut microbiome composition and abundance of those NEC infants. The inclusion criteria were preterm infants with a confirmed diagnosis of NEC, birth weight between 440 g and 2101 g, gestational age under 34 weeks, and neonatal antibiotic exposure. The exclusion criteria were children with complex congenital cardiopathy or spontaneous intestinal perforation without radiological evidence of NEC. Taxonomic and statistical analyses were conducted via the EzBioCloud platform to identify the differences in gut microbiome composition and abundance between the infants from these 2 countries. Results: Differences in gut microbiome composition and abundance between NEC-preterm infants in the United States and Brazil has been demonstrated. The USA group had a higher abundance of Pseudomonadota and a lower abundance of Actinobacteria and Bacteroidetes, while the Brazil group had a higher abundance of Firmicutes and a lower abundance of Proteobacteria. At the genus level, Staphylococcus was most predominant in the USA group, while Bacteroides and Prevotella were most predominant in Brazil. Conclusion: The study findings revealed significant compositional and abundance differences in the gut microbiome of NEC-preterm infants between the USA and Brazil, suggesting geographical and ethnicity variations impact on the gut microbiome of NEC infants. This study will help improve our understanding of NEC pathogenesis and the development of targeted interventions, taking in consideration the geographical and ethnic specificities of the subjects.

Background: Methadone, a synthetic opioid, is frequently employed as an alternative treatment for opioid use disorder (OUD) and the management of chronic pain. However, its prolonged usage comes with a notable drawback: adverse effects on the gut microbiome. The utilization of methadone has been associated with substantial modifications in both the composition and functionality of the gut microbiome. These alterations encompass shifts in bacterial diversity and abundance, which can potentially exert significant influences on gut health and the intricate gut-brain axis. This article undertakes a meticulous examination, conducting a comparative analysis of findings from two distinct studies conducted in the United States and China. Through this approach, it sheds light on the multifaceted impact of methadone on the gut microbiome, elucidating the potential ramifications of these effects on addiction and overall health. The overarching objective is to provide readers with a comprehensive understanding of how methadone influences the gut microbiome, underscoring the imperative necessity for further exploration in this promising yet understudied realm. Methods: We obtained gut microbiome data from two sources: the study conducted by Li et al. (2020), accessible under accession number PRJEB36803, and the study by Cruz- Lebrón et al. (2021). These datasets were used to examine two distinct cohorts of individuals undergoing methadone maintenance treatment (MMT) for opioid use disorder (OUD). The first cohort included 24 patients from the Cleveland Treatment Center and Case Western Reserve University in USA. The second cohort comprised 16 MMT patients from Honghe Prefecture, Yunnan Province, China, with ages ranging from 29 to 58 years. To analyze the raw 16S rRNA amplicon sequence data, we employed the EzBioCloud metagenomics platform. Results: Both studies demonstrated that methadone use can lead to alterations in gut microbiome composition and potentially impact metabolic pathways within the gut microbiome, affecting nutrient metabolism and overall health. These alterations were observed in both American and Chinese populations, with differences in the abundance of specific bacterial taxa, including a reduction in beneficial Bacteroidetes and an increase in Firmicutes, noted in the American study compared to China MP. Conclusion: Methadone use can modulate the gut microbiome, which can have implications for addiction and health. These findings emphasize the need for further research into the relationship between methadone use, gut microbiome composition, and its implications for human health, especially in the context of different populations and their unique microbiome profiles.

Background: The gut microbiome has been shown to play a crucial role in modulating the immune system and protecting against infections. Studies have reported gender differences in the gut microbiome composition, but little is known about how these differences may be affected by COVID-19 infection. In this study, we aimed to compare the gut microbiome composition of male and female patients with COVID-19. Methods: We obtained gut microbiome data from the study by Zuo et al. (2020) available in the NCBI BioProject database under accession number PRJEB56080. We created two cohorts, one consisting of male patients and the other consisting of female patients. We used the SRA Toolkit to download the gut microbiome data and performed taxonomic classification and diversity analysis using the EZBioCloud server. Results: Our results showed that the gut microbiome composition of male and female patients with COVID-19 differed significantly in terms of alpha diversity indices, with male patients having higher species richness and diversity than female patients. However, no significant differences were observed in beta diversity indices between the two cohorts. Conclusion: Our findings suggest that sex may play a role in modulating the gut microbiome composition in COVID-19 patients. Future studies are needed to explore the underlying mechanisms behind this gender difference and its potential implications for COVID-19 pathogenesis and treatment.

Background: While a substantial body of research has been dedicated to exploring the influence of alterations in the brain-gut-microbiome axis on conditions like depression and other mental disorders, there has been comparatively less focus on understanding how the oral microbiome affects brain function, particularly in response to smoking. Depression has been found to have a potential connection with oral dysbiosis, a condition that has shown associations with various disorders. Methods: We conducted an analysis of the oral saliva microbiome data (accession number: PRJEB44565) from a cohort of 44 adult participants to explore the link between oral microbiome composition and depression, with a particular focus on distinguishing between smokers and nonsmokers. Our study involved a comparison of salivary microbiome data between individuals with depression (n = 22) and a matched control group (n = 22). Within the depressed cohort, we further stratified participants into two subgroups: smokers (n = 11) and nonsmokers (n = 11). To analyze the microbiome data, we employed the SRA Toolkit for gut microbiome data retrieval and conducted taxonomic classification and diversity assessments using the EZBioCloud server. Results: We observed significant disparities in both the abundance and diversity of the oral microbiome when comparing smokers to nonsmokers. In the salivary microbiome of smokers who were part of the depressed cohort, the predominant phyla were Bacteroidetes (37.91

Argania spinosa (L.) Skeels, an endemic Moroccan plant species from the Sapotaceae family, holds significant ecological, pharmaceutical, and socioeconomic value in the arid mid-western region. However, it is facing rapid degradation. Therefore, understanding its genetic diversity is critical for preserving this national heritage. We sequenced, assembled, and annotated the mitochondrial genome of A. spinosa and compared it to other plants in the Ericales order. Mitochondrial-like sequences from the A. spinosa genome were assembled using GetOrganelle, resulting in a 707,441 base pair mitochondrial genome with 45.75% GC content. Annotation identified 32 protein-coding genes, 16 transfer RNAs, and 2 ribosomal RNA genes. Phylogenetic analysis of 15 Ericales species affirms that A. spinosa is closely related to the Theaceae family, which is in accordance with results from the chloroplast genome.

Mitochondria play an important role in cellular energy provision. Contain their own genome that have been described in a variety of birds, but the mechanisms leading to their appearance and maintenance are not precise, and their effect on the evolution of the sequence has not been explored. Herein, we analyzed the complete mitochondrial genome sequence of Agapornis roseicollis, extracted using the Getorgannelle pipeline, and annotated using Mitos, then Blastx for CDS genes and tRNAscan for tRNA genes. The sequence analysis revealed a circular genome with 18,807 bp as the size of its mitogenome (mt). The annotation predicted the presence of 13 protein-coding sequences, 20 tRNA genes, and two rRNA genes. The comparison between Agapornis roseicollis newly analyzed with the same species from New Zealand published in 2009 showed different genome sizes and gene numbers. The maximum-likelihood tree was reconstructed with 6 species of Psittacidae obtained from GenBank, indicating that A. roseicollis published in 2009 and our species is most closely related,and Eremias dzungarica as an outcast of the group. These results may provide molecular information for species evolution. In addition to offering insight into the evolution of Psittacidae, the results of this work provide important molecular resources for further studies of identification, genetics conservation, and other phylogenetic evolution of Psittacidae.

The rapid and global spread of the novel coronavirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has raised serious public health concerns, including in Mauritania. We sequenced and analyzed the entire genome of 13 SARS-CoV-2 virus strains isolated from polymerase chain reaction (PCR)-positive symptomatic patients sampled from March 3 to May 31, 2021 to better understand SARS-CoV-2 introduction, propagation, and evolution in Mauritania. A phylogenetic tree using available data from the EpiCoV GISAID database and a variant network with non-Mauritanian sequences were constructed. Variant analysis of the 13 Mauritanian SARS-CoV-2 genome sequences indicated an average mutational percentage of 0.39, which is similar to that in other countries. Phylogenetic analysis revealed multiple spatiotemporal introductions, mainly from Europe (France, Belgium) and Africa (Senegal, Côte d'Ivoire), which also provided evidence of early community transmission. A total of 2 unique mutations, namely, NSP6_Q208K and NSP15_S273T, were detected in the NSP6 and NSP15 genes, respectively, confirming the aforementioned introduction of SARS-CoV-2 in Mauritania. These findings highlight the relevance of continuous genomic monitoring strategies for understanding virus transmission dynamics and acquiring knowledge to address forthcoming sources of infection in Africa.

Sexual and reproductive health (SRH) concerns physical, mental, and social well-being as related to sexual and reproductive systems. Self-care, which is the ability to promote health without the support of a health-care provider, can advance SRH, especially for fragile populations. Mobile health (mHealth) solutions can be used to raise awareness about SRH. We performed a structured literature review and analysis of mHealth-based approaches for delivering self-SRH services and interventions in the WHO Eastern Mediterranean Region (EMR). A fuzzy-based framework for assessing those mHealth apps was proposed. We identified 6 out of 737 papers, and 23 (5.7%) out of 400 mHealth apps retrieved from app-stores, describing mHealth use for self SRH with only 10 apps developed in EMR countries, namely Morocco, Pakistan, Egypt, Iran, and Jordan. Our fuzzy-based framework proposes guidelines regarding the implementation of self-care interventions to help project leaders promote their adoption in the SRH systems.

We explored the gut microbiome composition in four Moroccan patients with coronavirus disease 2019 (COVID-19) during hospitalization and treatment, using 16S rRNA gene amplicon metataxonomic profiling, and compared it with that in four healthy severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-free control subjects.

The emergence of a novel coronavirus that later on rendered a global pandemic, caused desperation within the communities and drove increased interest in exploring medicinal plant–based therapeutics to treat and prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections. Many medicinal plants have been reported to have antiviral, anti-inflammatory, and immunomodulatory effects that hinder, cure, or ease the symptoms of COVID-19 infection. This exploratory study seeks to dock the active components of Cannabis sativa, a natural plant with several pharmacological and biological properties, with the angiotensin-converting enzyme II (ACE2) receptor. A total of 3 C. sativa active components have been found to bind to the ACE2 protein active site and could inhibit spike binding, although they do not compete directly with the receptor-binding domain (RBD) of SARS-CoV-2. 6-Prenylapigenin, cannabivarin (CBN-C3), and Δ8-tetrahydrocannabinolic acid-A (Δ8-THCA) have a greater affinity (−8.3, −8.3, and −8.0 kcal/mol, respectively) and satisfactory interaction with ACE2 than its inhibitor MLN-4760 (−7.1 kcal/mol). These potential drugs with higher affinity for the ACE2 receptor and adequate absorption, distribution, metabolism, excretion, and toxicity (ADMET) values are candidates for treating or preventing SARS-CoV-2 infections. In vitro and in vivo investigations are needed to evaluate further the efficacy and toxicity of these hit compounds.

Androctonus mauritanicus is a large scorpion indigenous to North Africa. Notable for its extremely potent venom, it is responsible for several human deaths a year. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single wild-caught individual. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR10738938) and Assembly (GCA_011317285).

The emergence of a novel coronavirus that later on rendered a global pandemic, caused desperation within the communities and drove increased interest in exploring medicinal plant–based therapeutics to treat and prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections. Many medicinal plants have been reported to have antiviral, anti-inflammatory, and immunomodulatory effects that hinder, cure, or ease the symptoms of COVID-19 infection. This exploratory study seeks to dock the active components of Cannabis sativa , a natural plant with several pharmacological and biological properties, with the angiotensin-converting enzyme II (ACE2) receptor. A total of 3 C. sativa active components have been found to bind to the ACE2 protein active site and could inhibit spike binding, although they do not compete directly with the receptor-binding domain (RBD) of SARS-CoV-2. 6-Prenylapigenin, cannabivarin (CBN-C3), and Δ8-tetrahydrocannabinolic acid-A (Δ8-THCA) have a greater affinity (−8.3, −8.3, and −8.0 kcal/mol, respectively) and satisfactory interaction with ACE2 than its inhibitor MLN-4760 (−7.1 kcal/mol). These potential drugs with higher affinity for the ACE2 receptor and adequate absorption, distribution, metabolism, excretion, and toxicity (ADMET) values are candidates for treating or preventing SARS-CoV-2 infections. In vitro and in vivo investigations are needed to evaluate further the efficacy and toxicity of these hit compounds. Keywords Medicinal plant , , , COVID-19 , SARS-CoV-2 , ACE2 , spike , drug discovery , molecular docking , ADMET

Early infancy is critical for the development of an infant's gut flora. Many factors can influence microbiota development during the pre- and postnatal periods, including maternal factors, antibiotic exposure, mode of delivery, dietary patterns, and feeding type. Therefore, investigating the connection between these variables and host and microbiome interactions in neonatal development would be of great interest. As the "unculturable" era of microbiome research gives way to an intrinsically multidisciplinary field, microbiome research has reaped the advantages of technological advancements in next-generation sequencing, particularly 16S rRNA gene amplicon and shotgun sequencing, which have considerably expanded our knowledge about gut microbiota development during early life. Using omics approaches to explore the neonatal microbiome may help to better understand the link between the microbiome and newborn diseases. Herein, we summarized the metagenomics methods and tools used to advance knowledge on the neonatal microbiome origin and evolution and how the microbiome shapes early and late individuals' lives for health and disease. The way to overcome limitations in neonatal microbiome studies will be discussed.

Over the last decade, it has become increasingly apparent that the microbiome is a central component in human well-being and illness. However, to establish innovative therapeutic methods, it is crucial to learn more about the microbiota. Thereby, the area of metagenomics and associated bioinformatics methods and tools has become considerable in the study of the human microbiome biodiversity. The application of these metagenomics approaches to studying the gut microbiome in COVID-19 patients could be one of the promising areas of research in the fight against the SARS-CoV-2 infection and disparity. Therefore, understanding how the gut microbiome is affected by or could affect the SARS-CoV-2 is very important. Herein, we present an overview of approaches and methods used in the current published studies on COVID-19 patients and the gut microbiome. The accuracy of these researches depends on the appropriate choice and the optimal use of the metagenomics bioinformatics platforms and tools. Interestingly, most studies reported that COVID-19 patients' microbiota are enriched with opportunistic microorganisms. The choice and use of appropriate computational tools and techniques to accurately investigate the gut microbiota is therefore critical in determining the appropriate microbiome profile for diagnosis and the most reliable antiviral or preventive microbial composition.

Introduction SARS-Cov-2 first appeared in Wuhan, China, in December 2019 and spread all over the world soon after that. Given the infectious nature ofSARS-CoV-2, fast and accurate diagnosis tools are important to detect the virus. In this review, we discuss the different diagnostic tests that are currently being implemented in laboratories and provide a description of various COVID-19 kits. Areas covered We summarize molecular techniques that target the viral load, serological methods used for SARS-CoV-2 specific antibodies detection as well as newly developed faster assays for the detection of SARS-COV 2 in various biological samples. Expert opinion In the light of the widespread pandemic, the massive diagnosis of COVID-19, using various detection techniques, appears to be the most effective strategy for monitoring and containing its propagation.

Plants are the world's most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population's increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving next-generation sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine.

During the last century, cancer biology has been arguably one of the most investigated research ?elds. To gain deeper insight into cancer mechanisms, scientists have been attempting to integrate multi omics data in cancer research. Cancer genomics, transcriptomics, metabolomics, proteomics, and metagenomics are the main multi omics strategies used currently in the diagnosis, prognosis, treatment, and biomarker discovery in cancer. In this review, we describe the use of different multi omics strategies in cancer research in the African continent and discuss the main challenges facing the implementation of these approaches in African countries such as the lack of training programs in bioinformatics in general and omics strategies in particular and suggest paths to address deficiencies. As a way forward, we advocate for the establishment of an "African Cancer Genomics Consortium" to promote intracontinental collaborative projects and enhance engagement in research activities that address indigenous aspects for cancer precision medicine.