Full Length Research Paper

Use of the RAPD-PCR fingerprinting and API system for clustering lactic acid bacteria isolated from traditional Sudanese sour milk (Roab)

Abdelhalim A. Hamza¹, Eisa I. El Gaali^1* and Ahmed A. Mahdi²

¹Commission for Biotechnology and Genetic Engineering, National Centre for Research, Khartoum, Sudan. P. O. Box 2404.

²Unversity of Khartoum faculty of Agriculture, Sudan.

*Corresponding author. E-mail: elgaali@hotmail.com. Tel.: 00249-912297863.

Accepted 20 July, 2009

   Abstract

One hundred and sixty isolates of lactic acid bacteria (LAB) were isolated from ten samples of traditional soured milk (Roab) obtained from different Sudanese localities using Lactobacillus-selective medium. Forty-two representative single colonies were randomly picked (14 rods and 28 cocci).  Randomly amplified polymorphic DNA (RAPD) analysis was used for rapid investigation of the genetic diversity of the isolates through un-weighted clustering group method with arithmetic averages. The fourteen rod-shaped isolates formed five clusters based on numerical analysis of the RAPD-PCR profiles. Representative strains from these clusters were identified by the API 50 CHL STREP identification system. These were Lactobacillus delbreuckii supsp bulgaricus (one strain), Lactobacillus rhamnosus (nine strains), and lactobacillus plantarum (two strains), Lactobacillus casei (one strain) and Lactobacillus pentosus (one strain). The 28 coccal isolates were separated into nine clusters, the representative strains of which were identified by the API 20 STREP system as Aerococcus viridians (four strains), Enterococcus faecium (two strains), Enterococcus gallinarum (two strains), lactococcus lactis subsp lactis (five strains), Leuconostoc sp. (five strains), Streptococcus acidominimus (eight strains) and Streptococcus bovis (two strains). Some of the isolates produced exopolysaccharides from sucrose (Leuconostoc sp., Lactobacillus delbreuckii supsp. bulgaricus, and Lactobacillus plantarum and Lactobacillus pentosus).

Key words:  Lactic acid, Lactobacillus, molecular markers, RAPD-PCR.