Metagenomic profiling of gut microbiota of diarrhoeic children in Southwest Nigeria

Background: Globally, around 63% of all diarrhoea cases occur in children that are below five years of age. accurate and timely detection of the aetiology of these diseases is very crucial but some of the current methods apart from being laborious and timeconsuming, often fail to identify difficult to culture pathogens. Here we investigated the impact of diarrhoea on the gut microbiome of children under 5 y of age in Southwest Nigeria using metagenomic approach. Methods and materials: Amplicon-based metagenomics analysis was carried out on 8 human DNA samples obtained from stool samples of diarrhoeic children and a control group. Phylogenetic diversity, species richness and relative abundance of bacterial taxa were determined using the CLC Genomics Workbench v12.0 and the implemented Microbial Genomics Module version 4.0 (Qiagen). Results: Six bacterial phyla comprising 78 genera were identified. The gut microbiome profile revealed Firmicutes (61%), Bacteroidetes (17%), Proteobacteria (15%), Actinobacteria (5%), Fusobacteria (1%) and Verrucomicrobia (1%). Among the diarrhoeic samples, the relative abundance of phyla shows decreasing order of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria, except phylum Verrucomicrobia which was not identified. There was a remarkably decreased abundance of Proteobacteria among the control samples when compared to the diarrhoeic samples (38%). Escherichia coli, Shigella, Staphylococcus and Klebsiella had increased species richness among the diarrhoeic samples, whereas, Bifidobacterium, Faeacalibacterium, Lactobacillus, Clostridium (sensu stricto), and Bacteroides were significantly increased among the control samples. Conclusion: An understanding of the impact of diarrhoea on the gut microbiota may help elucidate the role of the gut microbiome in the health and disease status of children in a Sub-Saharan setting, however, this can only be made easy with the application of metagenomics techniques

Risk Factors of Diarrhoea among Children Under Five Years in Southwest Nigeria

Diarrhoea is the passage of three or more loose or liquid stools per day or more frequent passage than is normal for an individual. Diarrhoea alters the microbiome, thus the immune system, and is a significant cause of morbidity and mortality in young children. )is study evaluated the association between the risk factors and diarrhoea prevalence among children under five years in Lagos and Ogun States, located in Southwest Nigeria. Participants included 280 women aged 15–49 years and children aged 0–59 months. )e study used quantitative data, which were assessed by a structured questionnaire. Data obtained were analyzed using the Statistical Package for the Social Sciences Software Version 25.0 and Microsoft Excel 2013.)erelationships and/or association between variables were evaluated using Pearson’s Chi Square and logistic regression tests. One hundred and eighteen (42%) of the children were male, and 162 (58%) were female. )e majority of the children belonged to the age group 0–11 months (166). Age (p � 0.113) and gender (p � 0.366) showed no significant association with diarrhoea among the children. )e majority of the mothers belonged to the age group 30–34. Multivariate analysis showed that the mother’s level of education (95% CI for OR� 11.45; P � 0.0001) and family income (95% CI for OR� 7.61, P � 0.0001) were the most significant risk factors for diarrhoea among children. Mother’s educational status, mother’s employment, and family income were the factors significantly associated with diarrhoea in Southwest Nigeria.)estudy recommends that female education should be encouraged by the right government policy to enhance the achievement of the sustainable development goal three (SDG 3) for the possible reduction of neonates and infants’ deaths in Nigeria

Antimicrobial Importance of Medicinal Plants in Nigeria

Despite the success of antibiotic discovery, infectious diseases remain the second leading source of death worldwide, while the resistance to antibiotics is among the significant problems in the twenty-first century. Medicinal plants are very rich in phytochemicals which can be structurally optimized and processed into new drugs. Nigeria enjoys a diverse collection of medicinal plants, and joint research has ascertained the efficacy of these plants. Plants such as guava (Psidium guajava), ginger (Zingiber officinale), neem (Azadirachta indica), and moringa (Moringa oleifera) have been found to exhibit broad range of antimicrobial activities. Studies on Nigerian plants have shown that they contain alkaloids, polyphenols, terpenes, glycosides, and others with possible therapeutic potentials. +e antimicrobial activities of some new compounds such as alloeudesmenol, hanocokinoside, orosunol, and 8-demethylorosunol, identified from medicinal plants in Nigeria, are not yet explored. Further investigation and optimization of these compounds will facilitate the development of new sets of pharmacologically acceptable antimicrobial agents. +is review study revealed the efficacy of medicinal plants as an alternative therapy in combating and curtailing the development and survival of multidrug-resistant pathogens coupled with the toxic effects of some antibiotics. Due to enormous therapeutic possibilities buried in medicinal plants, there is a need for more research into unique fingerprints and novel compounds that can provide cure to the neglected tropical diseases (NTDs) of humans and animals facing Africa, especially Nigeria

Computational Study of 16S rRNA of Microbe Cluster Implicated in Diarrhoeal: Phylogeny, Docking, and Dynamics

In this study, 16S rRNA of diarrhoea microbial cluster was investigated computationally. The phylogeny, two- and three-dimensional structures, molecular docking and dynamics simulations were carried out. The result showed that Escherichia coli, Campylobacter jejuni, Campylobacter upsaliensis, Streptococcus lutetiensis 033, Streptococcus infantarius, Enterococcus ratti, Helicobacter sp. 'feline isolate, Helicobacter canadensis, Anaerobiospirillum sp. B0101, Anaerobiospirillum sp. 3J102 as well as uncultured bacterium (Prevotella) and unidentified bacterium (Lactobacillus) were involved in diarrhoea infection. Optimal secondary structure alignment from ClustalO has a minimum free energy (MFE) of -764.31 kcal/mol while that Aligner has MFE of -592.43 kcal/mol. The free energies from molecular docking reveal possible efficacy in the order of doxycycline > metacycline > streptomycin > rolitetracycline > tetracycline > tigecycline. Out of 17 antibiotics used in this study, chlortetracycline and minocycline have high affinity for methyltransferase KsgA (PDB ID: 3TPZ), kanamycin has almost equal affinity for both enzymes, while the remaining 14 antibiotic compounds have high affinity for pseudouridine synthase RsuA (PDB ID: 1KSV). The modelled three-dimensional structure of 16S rRNA bind to 1KSV and 3TPZ with free energy of -367.52 kcal/mol and-371.55 kcal/mol respectively. Moreover, the active site nucleotide residues were found to have direct interaction with amino acid residues in the active site of the enzymes. This study provides insight on the mechanism of action of antibiotics that targeted 16S rRNA by inhibition of key enzymes that involve in protein synthesis

Suitability of spectrophotometric assay for determination of honey microbial inhibition

Commonly used methods for determination of antibacterial potency of honey are usually the disc, agar well diffusion and dilution plate assay which had shown various demerit of inaccuracies and impreciseness. Therefore, the suitability of spectrophotometric assay for determination of honey inhibitory activity is evaluated in this study. Honeys from different sources in southwest states in Nigeria were assayed for antibacterial activity using 96-well micro-titre plate spectrophotometric methods to determine the minimum inhibitory concentration (MIC) against enteric bacteria strains. The honey inhibition assay of Nigerian honeys tested against enteric bacilli showed more than 90% inhibitory activity. Among all the honeys sample assayed, only two honeys reveal a very low MIC of 31.25 and 125mg/mL. The use of spectrophotometry is a precise method to determine honey inhibitory rate and it is proven to be suitable highly sensitive, reproducible, specific, reduced cost, fewer amounts of sample and reagent are require

Significance of African Diets in Biotherapeutic Modulation of the Gut Microbiome

Diet plays an essential role in human development and growth, contributing to health and well-being. The socio-economic values, cultural perspectives, and dietary formulation in sub-Saharan Africa can influence gut health and disease prevention. The vast microbial ecosystems in the human gut frequently interrelate to maintain a healthy, well-coordinated cellular and humoral immune signalling to prevent metabolic dysfunction, pathogen dominance, and induction of systemic diseases. The diverse indigenous diets could differentially act as biotherapeutics to modulate microbial abundance and population characteristics. Such modulation could prevent stunted growth, malnutrition, induction of bowel diseases, attenuated immune responses, and mortality, particularly among infants. Understanding the associations between specific indigenous African diets and the predictability of the dynamics of gut bacteria genera promises potential biotherapeutics towards improving the prevention, control, and treatment of microbiome-associated diseases such as cancer, inflammatory bowel disease, obesity, type 2 diabetes, and cardiovascular disease. The dietary influence of many African diets (especially grain-base such as millet, maize, brown rice, sorghum, soya, and tapioca) promotes gut lining integrity, immune tolerance towards the microbiota, and its associated immune and inflammatory responses. A fibre-rich diet is a promising biotherapeutic candidate that could effectively modulate inflammatory mediators’ expression associated with immune cell migration, lymphoid tissue maturation, and signalling pathways. It could also modulate the stimulation of cytokines and chemokines involved in ensuring balance for long-term microbiome programming. The interplay between host and gut microbial digestion is complex; microbes using and competing for dietary and endogenous proteins are often attributable to variances in the comparative abundances of Enterobacteriaceae taxa. Many auto-inducers could initiate the process of quorum sensing and mammalian epinephrine host cell signalling system. It could also downregulate inflammatory signals with microbiota tumour taxa that could trigger colorectal cancer initiation, metabolic type 2 diabetes, and inflammatory bowel diseases. The exploitation of essential biotherapeutic molecules derived from fibre-rich indigenous diet promises food substances for the downregulation of inflammatory signalling that could be harmful to gut microbiota ecological balance and improved immune response modulation

Microbial Assessment of Herbal Cleansers (Bitters) Sold in Ota, Ogun State, Nigeria

The use of herbal medicines is on an increasing trend globally. Herbal medicines may be beneficial but are not completely harmless due to deficient quality control in certain cases. This study evaluated the microbial content of some herbal cleansers (bitters). Eight herbal cleansers obtained from pharmacies in Ota were evaluated for their microbial content. Bacterial and fungal isolates identified from the samples include Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermidis, Lactobacillus spp., Proteus spp., Pseudomonas spp., Shigella spp., Aspergillus niger, Rhizopus spp., Geotrichum spp., Fusarium spp., Alternaria spp., Penicillium spp., Mucor spp., Diplosporium spp. and Trichothecium spp. The mean total aerobic plate count values of the herbal cleansers were in the range of 1.0x104 and 3.0x105 cfu/ml. The results of this study revealed the presence of certain pathogenic organisms in these formulations and this emphasizes the importance of having stringent quality control measures in the manufacture of herbal preparations

Microbial Assessment of Herbal Cleansers (Bitters) Sold in Ota, Ogun State, Nigeria

The use of herbal medicines is on an increasing trend globally. Herbal medicines may be beneficial but are not completely harmless due to deficient quality control in certain cases. This study evaluated the microbial content of some herbal cleansers (bitters). Eight herbal cleansers obtained from pharmacies in Ota were evaluated for their microbial content. Bacterial and fungal isolates identified from the samples include Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermidis, Lactobacillus spp., Proteus spp., Pseudomonas spp., Shigella spp., Aspergillus niger, Rhizopus spp., Geotrichum spp., Fusarium spp., Alternaria spp., Penicillium spp., Mucor spp., Diplosporium spp. and Trichothecium spp. The mean total aerobic plate count values of the herbal cleansers were in the range of 1.0x104 and 3.0x105 cfu/ml. The results of this study revealed the presence of certain pathogenic organisms in these formulations and this emphasizes the importance of having stringent quality control measures in the manufacture of herbal preparations

Antimicrobial Importance of Medicinal Plants in Nigeria

Despite the success of antibiotic discovery, infectious diseases remain the second leading source of death worldwide, while the resistance to antibiotics is among the significant problems in the twenty-first century. Medicinal plants are very rich in phytochemicals which can be structurally optimized and processed into new drugs. Nigeria enjoys a diverse collection of medicinal plants, and joint research has ascertained the efficacy of these plants. Plants such as guava (Psidium guajava), ginger (Zingiber officinale), neem (Azadirachta indica), and moringa (Moringa oleifera) have been found to exhibit broad range of antimicrobial activities. Studies on Nigerian plants have shown that they contain alkaloids, polyphenols, terpenes, glycosides, and others with possible therapeutic potentials. The antimicrobial activities of some new compounds such as alloeudesmenol, hanocokinoside, orosunol, and 8-demethylorosunol, identified from medicinal plants in Nigeria, are not yet explored. Further investigation and optimization of these compounds will facilitate the development of new sets of pharmacologically acceptable antimicrobial agents. This review study revealed the efficacy of medicinal plants as an alternative therapy in combating and curtailing the development and survival of multidrug-resistant pathogens coupled with the toxic effects of some antibiotics. Due to enormous therapeutic possibilities buried in medicinal plants, there is a need for more research into unique fingerprints and novel compounds that can provide cure to the neglected tropical diseases (NTDs) of humans and animals facing Africa, especially Nigeria

Emerging vancomycin-non susceptible coagulase negative Staphylococci associated with skin and soft tissue infections

Backgrounds: Observable emergence of Vancomycin-Non susceptible Coagulase-negative Staphylococci (VNSCoNS) associated with skin and soft tissue infections spreading among the urban and rural populace is gradually intensifying severe complications. The isolated VNS-CoNS were evaluated with Matrix-assisted Laser Desorption/ioni‑ zation Time of Flight Mass Spectrometry (MALDI ToF MS) for species characterization and pan-antimicrobial resistance pattern. Methods: Out of 256 clinical samples collected including pus, abscess, ear swabs, eye swabs, and aspirates, 91 CoNS isolates were biotyped and further characterized with MALDI-TOF MS. Staphylococci marker genes, Vancomycin sus‑ ceptibility, and bioflm assays were performed. Results: Of 91 CoNS isolates, S.cohnii (2.3%), S.condimentii (3.4%), S. saprophyticus (6.7%), and S.scuri (21.1%) were characterized with MALDI-TOF with signifcant detection rate (99.4%; CI 95, 0.775–0.997, positive predictive values, 90.2%) compared to lower biotyping detection rate (p=0.001). Hemolytic VNS-CoNS lacked nuc, pvl and spa genes from wound, ear, and aspirates of more 0.83 MARI clustered into a separate phylo-diverse group and were widely distributed in urban and peri-urban locations. MALDI TOF–MS yielded a high discriminatory potential of AUC-ROC score of 0.963 with true-positivity prediction. VNS-CoNS of MIC≥16 µg/mL were observed among all the ages with signifcant resistance at 25th and 75th quartiles. More than 10.5% of CoNS expressed multi-antibiotic resistance with more than 8 µg/mL vancomycin cut-of values (p<0.05). Conclusion: Antibiotic resistant CoNS should be considered signifcant pathogens rather than contaminant. Bioflm producing VNS-S. sciuri and S. condimentii are potential strains with high pathological tropism for skin, soft tissues and wound infections, and these strains require urgent surveillance in peri-urban and rural communities