Mwendwa, Peter K.2025-04-022025-04-022024-11https://ir-library.ku.ac.ke/handle/123456789/29887A Thesis Submitted in Partial Fulfilment of the Requirements for the Award of the Degree of Master of Science (Medical Microbiology) in the School of Pure and Applied Sciences of Kenyatta University, November, 2024 Supervisors: 1.Anncarol Karanja 2.John MaingiAzadirachta indicahas been used in treatment of diseases such as skin inflammations, Chikungunya, Measles and fungal infections. Aloe secundiflora has been shown to inhibit Staphylococcus aureusand Cryptococcus neoformans. Medicinal plants have been shown to contain microbialendophytes that live and feed within the plantsand play a role in protection against pathogens, either by triggering their defense mechanisms or directly acting on the pathogens. The current antimicrobial resistance has led to the need to explore alternative sources for new generation antibiotics. These alternative sources include endophytes of Azadirachta indicaand Aloe secundiflora which have the potential to produce new generation antibiotics. The current industrial catalysts are expensive, toxic and difficult to remove from reaction mixtures. Endophytes are potential sources of the desired enzymes. These endophytes have not been comprehensively researched. The objectives of this study wereto isolate and identify endophytes from young and mature leaves of Az. indica and A. secundiflora in Kitui and Kiambu Counties, determine the antimicrobial activity of the endophytes against selected pathogens, screen for phytochemicals produced by the endophytes and quantify the cellulase enzymes produced by the endophytes. The endophytes were isolated on sterile growth media and identified by gene sequencingand using the NCBI genomesequence database. The agar diffusion and dual culture techniques were used to determine antimicrobial activity for bacteria and fungi respectively. For phytochemical screening, the endophytic isolates were transferred from solid culture media to broth media for fermentation and the phytochemicals extracted by solvent extraction method, using ethyl acetate. For enzyme production, the endophytes were subjected to SSF and their enzymes extracted and quantified. Bacterial isolates obtained belonged to Bacillus sp., Alcaligenes faecalis, Providencia vermicola, and Priestia megaterium. Fungal isolates belonged to Colletotrichum sp., Trichoderma lixii, Galactomyces candidum, Penicillium sp., Fusarium luffae, Cladosporium cladosporioides and Candida sp. Endophytic isolates with antimicrobial activity were Bacillus subtilis, Priestia megaterium, Bacillus aerophilus and Penicillium sp. The isolates were positive for terpenoids, saponins, alkaloids and flavonoids. All fungal isolates produced cellulase enzymes across all assays (p ≤ 0.05). This study showed that Azadirachta indica and Aloe secundiflora contain fungal and bacterial endophytes which are potential sources forproducing bioactive compounds and cellulose enzymes. Thus the recommendation is that the endophytes of these plants can be used in developing new antibiotics and more research need to be done to quantify the bioactive compounds present in the isolates.enThesis