Applied Biology and Biochemistry Publications

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    Comparison of oxidative stress biomarkers in Oreochromis mossambicus in minimally and highly disturbed aquatic environments in the Matabeleland region, Zimbabwe
    (African Journal of Aquatic Science, 2022-09-06) Makuvara, Z.; Marumure, J.; Chapungu, L.; Machingura, J.; Siwela, A.H.
    Owing to their ability to provide a functional measure of organismal response to chemical stressors, oxidative biomarkers are useful in ecotoxicological studies to assess disturbance in aquatic environments. This study assessed the use of oxidative stress biomarkers in Oreochromis mossambicus (Peters, 1852) (Perciformes: Cichlidae) to distinguish between minimally and highly disturbed aquatic environments. A water quality index (WQI) and overall index of pollution (OIP) were used to characterize the target sites, namely the Mananda Dam (control, reference site) and Lower Mguza Dam (disturbed site). Forty male O. mossambicus samples were collected from each dam between April and August 2013. Values for the WQI and OIP indices were significantly higher for the Lower Mguza Dam than for the Mananda Dam (p < 0.05). Oxidative stress biomarker evaluation results showed that the activities of glutathione peroxidase (GPx), superoxide dismutase (SOD) and glutathione S-transferase (GST) as well as the malondialdehyde (MDA) concentration in the liver of O. mossambicus were significantly higher in fish collected from Lower Mguza Dam than those collected from Mananda Dam (p < 0.05). The activities of DT-diaphorase (DTD) and catalase (CAT) were significantly inhibited in fish from the Lower Mguza Dam, when compared to those collected from the Mananda Dam (p < 0.05). From these findings, it is evident that oxidative stress biomarkers, such as antioxidant enzyme activity and MDA accumulation, can be used to differentiate minimally and highly disturbed aquatic environments.
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    Genomic characterization of multi drug resistant ESBL-producing Escherichia coli isolates from patients and patient environments in a teaching hospital in Ghana.
    (BMC Microbiology, 2025-07-08) Asare Yeboah, E.E.; Agyepong, N.; Mbanga, J.; Amoako, D.G.; Abia, A.L.K.; Ismail, A.; Owusu-Ofori, A.; Essack, S.Y.
    Background ESBL-producing Escherichia coli pose a growing health risk in community and healthcare settings. We investigated the resistome, virulome, mobilome, and genetic relatedness of multidrug-resistant (MDR) E. coli isolates from patients and their environment in a Ghanaian teaching hospital. Materials and methods Twenty-three MDR ESBL-producing or carbapenem-resistant E. coli isolates from a collection of MDR Gram-negative bacteria (GNB) from patients and environments were selected for genomic analyses. Whole genome sequencing and bioinformatics tools were used to analyze genomic characteristics and phylogeny. Results The prevalence and incidence of rectal carriage of ESBL E. coli among patients were 13.65% and 11.32% respectively. The β-lactamase genes, blaTEM−1B (10 isolates) and blaCTX−M−15 (12 isolates) were commonly associated with IncFIB plasmid replicons and co-occurred with aminoglycoside, macrolide, and sulfamethoxazole/trimethoprim resistance. Insertion sequences, transposons, and class I integrons were found with blaCTX−M−15. Carriage and environmental isolates carried multiple virulence genes, with terC being the most prevalent in 21 isolates. Seventeen sequence types (STs) were identified, including a novel ST (ST13846). Phylogenetic analysis grouped the isolates into four main clusters, with one outlier. High genetic relatedness was observed between two carriage isolates of ST940 and between a carriage isolate and an environmental isolate of ST648. Isolates with different STs, collected at different times and locations, also showed genetic similarities. Conclusion We identified ESBL-producing E. coli with diverse genomic characteristics circulating in different hospital directorates. Clonal relatedness was observed among isolates from patients and the environment, as well as between different patients, suggesting transmission within and between sources.
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    Mycofltration of Aqueous Iron (III) and Imidacloprid Solutions, and the Efects of the Filtrates on Selected Biomarkers of the Freshwater Snail Helisoma duryi
    (Archives of Environmental Contamination and Toxicology, 2024-02-08) Mnkandla, S.M.; Mosoabisane, M.F.T.; Basopo, N.; Otomo, P.V.
    To alleviate the burden of water contamination, a newly developed form of bioremediation known as mycofiltration can be employed. Mycofiltration is an environment-friendly technology involving the treatment of contaminated water by passing it through a network of saprophytic fungal mycelium. A mycofilter made of Pleurotus ostreatus was used for the removal of iron (III) and imidacloprid from aqueous solutions. Batch mycofiltration, at a dosage of 1 g of mycofilter per 50 mL, was performed on iron (III) solutions of different concentrations (0.99, 10.7, 22.9, and 27.72 mg/L) and pH (3.3, 7 and 11). For column mycofiltration, the mycofilter was packed into pyrex columns (3.3 × 15 cm) to desired bed heights. Iron (III) and imidacloprid solutions of 18.99 mg/L and 234.70 ng/L, respectively, were filtered at a constant flow rate. Thereafter, Helisoma duryi snails were exposed for 96 h to the respective filtrates, and their catalase and acetylcholinesterase activities were assessed. Batch mycofiltration showed iron (III) removal rates as high as 85%. Column mycofiltration showed removal rates of 94 and 31% for iron (III) and imidacloprid, respectively. Catalase activity was significantly reduced (p < 0.05) in the snails exposed to iron (III) or imidacloprid filtrates, compared to the snails exposed to the non-mycofiltered media. A significantly higher acetylcholinesterase activity was induced by iron (III) filtrates in comparison with the non-mycofiltered media (p < 0.05). There were no significant differences in acetylcholinesterase activity (p > 0.05) in the snails exposed to mycofiltered and non-mycofiltered imidacloprid media. Mycofilter characterisation using Fourier Transform Infrared Spectrophotometry revealed significant changes in transmittance intensity in the mycofilters used for the iron (III) vs the ones used for the imidacloprid solutions. Mycofiltration was found to improve water quality although iron (III) was removed more effectively than imidacloprid.
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    Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe
    (PLoS ONE, 2024-12-02) Mangoma, N.; Zhou, N.; Ncube, T.
    The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.
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    Bifidobacterium species viability in dairy-based probiotic foods: challenges and innovative approaches for accurate viability determination and monitoring of probiotic functionality
    (Frontiers in Microbiology, 2024-02-02) Sibanda, T.; Marole, T.A; Thomashoff, U.L.; Thantsha, M.S.; Buys, E.M.
    Bifidobacterium species are essential members of a healthy human gut microbiota. Their presence in the gut is associated with numerous health outcomes such as protection against gastrointestinal tract infections, inflammation, and metabolic diseases. Regular intake of Bifidobacterium in foods is a sustainable way of maintaining the health benefits associated with its use as a probiotic. Owing to their global acceptance, fermented dairy products (particularly yogurt) are considered the ideal probiotic carrier foods. As envisioned in the definition of probiotics as “live organisms,” the therapeutic functionalities of Bifidobacterium spp. depend on maintaining their viability in the foods up to the point of consumption. However, sustaining Bifidobacterium spp. viability during the manufacture and shelf-life of fermented dairy products remains challenging. Hence, this paper discusses the significance of viability as a prerequisite for Bifidobacterium spp. probiotic functionality. The paper focuses on the stress factors that influence Bifidobacterium spp. viability during the manufacture and shelf life of yogurt as an archetypical fermented dairy product that is widely accepted as a delivery vehicle for probiotics. It further expounds the Bifidobacterium spp. physiological and genetic stress response mechanisms as well as the methods for viability retention in yogurt, such as microencapsulation, use of oxygen scavenging lactic acid bacterial strains, and stress-protective agents. The report also explores the topic of viability determination as a critical factor in probiotic quality assurance, wherein, the limitations of culture-based enumeration methods, the challenges of species and strain resolution in the presence of lactic acid bacterial starter and probiotic species are discussed. Finally, new developments and potential applications of next-generation viability determination methods such as flow cytometry, propidium monoazide–quantitative polymerase chain reaction (PMA-qPCR), next-generation sequencing, and single-cell Raman spectroscopy (SCRS) methods are examined.