AUTHOR=Tlou Matsobane , Ndou Benedict , Mabona Nokufa , Khwathisi Adivhaho , Ateba Collins , Madala Ntakadzeni , Serepa-Dlamini Mahloro Hope 

TITLE=Next generation sequencing-aided screening, isolation, molecular identification, and antimicrobial potential for bacterial endophytes from the medicinal plant, Elephantorrhiza elephantina

JOURNAL=Frontiers in Microbiology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1383854

DOI=10.3389/fmicb.2024.1383854

ISSN=1664-302X

ABSTRACT=<p><italic>Elephantorrhiza elephantina</italic>, a wild plant in southern Africa, is utilized in traditional medicine for various ailments, leading to its endangerment and listing on the Red List of South African Plants. To date, there have been no reports on bacterial endophytes from this plant, their classes of secondary metabolites, and potential medicinal properties. This study presents (i) taxonomic characterization of bacterial endophytes in leaf and root tissues using 16S rRNA, (ii) bacterial isolation, morphological, and phylogenetic characterization, (iii) bacterial growth, metabolite extraction, and LC–MS-based metabolite fingerprinting, and (iv) antimicrobial testing of bacterial crude extracts. Next-generation sequencing yielded 693 and 2,459 DNA read counts for the rhizomes and leaves, respectively, detecting phyla including Proteobacteria, Bacteroidota, Gemmatimonadota, Actinobacteriota, Verrucomicrobiota, Dependentiae, Firmicutes, and Armatimonodata. At the genus level, <italic>Novosphingobium</italic>, <italic>Mesorhizobium</italic>, <italic>Methylobacterium</italic>, and Ralstonia were the most dominant in both leaves and rhizomes. From root tissues, four bacterial isolates were selected, and 16S rRNA-based phylogenetic characterization identified two closely related <italic>Pseudomonas</italic> sp. (strain BNWU4 and 5), <italic>Microbacterium oxydans</italic> BNWU2, and <italic>Stenotrophomonas maltophilia</italic> BNWU1. The ethyl acetate:chloroform (1:1 v/v) organic extract from each isolate exhibited antimicrobial activity against all selected bacterial pathogens. Strain BNWU5 displayed the highest activity, with minimum inhibitory concentrations ranging from 62.5 μg/mL to 250 μg/mL against diarrhoeagenic <italic>Escherichia coli</italic>, <italic>Escherichia coli O157:H7</italic>, <italic>Salmonella enterica</italic>, antibiotic-resistant <italic>Vibrio cholerae</italic>, <italic>Staphylococcus aureus</italic>, <italic>Bacillus cereus</italic>, and <italic>Enterococcus durans</italic>. LC–MS analysis of the crude extract revealed common antimicrobial metabolites produced by all isolates, including Phenoxomethylpenicilloyl (penicilloyl V), cis-11-Eicosenamide, 3-Hydroxy-3-phenacyloxindole, and 9-Octadecenamide.</p>