Characterization of Antibiotic-producing Actinomycetes Isolated from River Tana and Lake Elementaita in Kenya

The rise of antibiotic-resistant bacteria has become a global health concern, necessitating the search for novel sources of antibiotics. Actinomycetes, a group of microorganisms, have been known for their ability to produce bioactive compounds with antimicrobial properties. This study aimed to isolate, identify, and characterize antibiotic-producing Actinomycetes from River Tana and Lake Elementaita. Samples were collected from the study sites, and Actinomycetes were isolated using serial dilution and spread plate techniques. The isolates were characterized based on their morphological and biochemical properties. Furthermore, their antibacterial activity against Escherichia coli, Staphylococcus aureus, and Salmonella typhi was evaluated using the agar well diffusion method. The zones of inhibition were measured (mm), and analysis was done to compare the activity of the isolates using Kruskal Wallis test and medians compared using Wilcoxon with Bonferroni correction at alpha = 0.05 in SAS version 9.4. Analysis of DNA sequences was done using the BLAST program and a phylogenetic tree was constructed using MEGA X version 11. Biochemical tests revealed positive results for catalase, indole, oxidase, and citrate utilization, while coagulase and methyl red tests were negative. In terms of antibacterial activity, 54.5% of the isolates showed activity against E. coli, 45.5% against S. aureus, and 45.5% against S. typhi. Isolate LEL2201 had significant (p < 0.05) higher zone of inhibition against S. aureus (inhibition zone of 25.0mm), while isolate RT2201 exhibited the highest activity against E. coli and S. typhi (inhibition zone of 8.5 mm and 8.6 mm, respectively). Molecular characterization through 16S rRNA gene sequencing identified the isolates as belonging to the Actinobacterium order. Phylogenetic analysis revealed their similarity to known Actinomycetes species including Actinomycetales bacterium, Streptomyces intermedius and Streptomyces flavomacrosporus from various countries. The findings of this study demonstrate the presence of antibiotic-producing Actinomycetes in River Tana and Lake Elementaita. Thus, further investigations are warranted to identify and characterize the specific antibacterial compounds produced by these isolates.