Disparity in Phenotypic and Genetic Characterization of Lactic Acid Microorganisms Isolated from Spontaneous Fermentation of Yam (Dioscorea rotundata)

Abstract

Aim: In order to ensure the accurate taxonomic identification of the lactic acid organisms that were previously isolated from spontaneously fermented yam for safety assessment and quality assurance purposes, phenotypic and genetic identification data were compared. Study Design: Using the purposive sampling method, four microorganisms were characterized using molecular methods. Place and Duration of Study:  Isolates of lactic acid microorganisms (2 bacterial and 2 fungal organisms) from spontaneously fermented yam in a previous study carried out in May 2016 were genetically identified using molecular methods.  Methodology: Genomic DNA extracted from the test lactic acid microorganisms were used as templates in a PCR reaction, then, 16s rRNA and nuclear ribosomal internal transcribed spacer (ITS) genes were amplified for the bacterial and fungal isolates respectively. The polymerase chain reaction (PCR) products were electrophoresed on 2% agarose gel prepared with Tris Borate Ethylenediamintetraacetate (TBE) buffers stained with ethidium bromide. Subsequently, the ladder was used in order to determine the sizes of the corresponding amplicons captured on gel images in comparisons. Moreover, sequences of the PCR products were analyzed and the chromatograms subjected to BLAST (Basic Local Alignment Search Tool) analyses to identify the lactic acid organisms. Results: The 2 bacterial isolates were identified as Bacillus subtilis (MK448227) and Bacillus pumilus (MK446418), on the other hand, the fungal isolates were identified as Aspergillus flavus (MK433604) and Aspergillus niger (MK430926). Discrepancies were observed when phenotypic identification data in an earlier report were compared with the molecular data from the present study.  Conclusion: The present results underscore the limitations of phenotypic (biochemical) methods in characterizing organisms, particularly, organisms that may end up being used in food processing. Moreover, this is the first report of the novel organisms reported in the present study and makes further work into the development of starter organisms for the production of amala possible in the near future. In addition, proper identification helps in benchmarking the quality assurance and safety assessment of foods prepared using these organisms.