Metagenomic analysis of bacterial community associated with postharvest Irvingia species fruit wastes

Abstract

The use of culture-dependent methods in studying bacterial community has been proven to be inadequate, and often give misleading results. In this work, metagenomic analysis targeting the 16S ribosomal RNA genes was used to study the diversity and community structure of bacteria associated with postharvest Irvingia fruits. Results showed that Simpson’s diversity indices and number of Operational Taxonomic Units were dependent on the storage period (days after harvest, DAH) of fruits. Fresh fruits assessed on the day of harvest (DAH = 0) had a Simpson’s diversity index of 0.82, while fruits assessed on the 3rd and 6th DAH had diversity indices of 0.69 and 0.72, respectively. Whilst fruits assessed on the day of harvest had 64 OTUs spanning across 7 phyla, 11 classes, 32 genera with total reads of 23,776, fruits assessed on the 3rd and 6th days after harvest had 58 OTUs spanning across 6 phyla, 9 classes, 30 genera with 20,949 reads and 66 OTUs spanning across 4 phyla, 6 classes, 33 genera with 30,722 reads, respectively. Results further showed that majority of the OTUs belonged to two phyla – Proteobacteria and Firmicutes, mostly represented by members of Alphaproteobacteria and Bacilli subdivisions respectively. Predominant among these OTUs were sequences belonging to Acetobacter ghanensis (11.94%), A. okinawensis (15.36%), Lactobacillus species (14.90%), L. collinoides (12.35%), L. plantarum (7.11%) and L. vaccinostercus (2.89%). The relative abundance of these microorganisms indicates that fleshy pericarp of Irvingia fruits hitherto treated as wastes could potentially be used as a substrate in food and pharmaceutical industries.

Keywords: Metagenomics, operational taxonomic units, 16S rRNA, Irvingia, bacteria.