Deciphering bacterial community structure in Cola lepidota (K.) Schum fruits using Illumina next-generation sequencing

Abstract

Cola lepidota cultivation is hampered by pathogenic microorganisms which affect the quality and quantity of produce after harvest. Bacterial organisms cause softening of tissues which may lead to the spoilage of the whole fruit. This study aimed to detect the bacterial organisms and the bacterial community structure associated with monkey cola (Cola lepidota K. Schum) fruits using Illumina next-generation sequencing (NGS). Amplification of the v4 regions of the 16S rDNA gene was performed through Polymerase chain reaction (PCR) using the primers, 515F and 806R. Picking of the Operational Taxonomic Units (OTUs) and assignment of the OTUs into different taxonomic levels were performed on GREENGENES database. The most abundant phyla obtained from Cola lepidota mesocarp and seeds were Proteobacteria (40.83 %), Bacteroidetes (31.01 %) and Firmicutes (24.52 %). The abundance of Bacteroides, which was the predominant genus in the majority of the samples, was between 31 and 72 % among the total bacteria identified in most samples. Other relatively high abundant genera obtained across the total bacterial community of C. lepidota were Pseudomonas (19.20 %), Tepidimonas (13.76 %) and Acinetobacter (13.33 %). We obtained potentially beneficial, human and phytopathogenic microorganisms which play important roles in evolutionary and ecological processes. Among these genera include Acinetobacter and Staphylococcus which are opportunistic human pathogens. This study revealed the bacterial organisms associated with monkey cola fruits and indicates that Illumina next generation sequencing can be used to determine the bacterial community structure and bacterial organisms in fruits.