https://doi.org/10.17113/ftb.61.01.23.7796

Supplement

Identification of Bulgarian Sourdough Microbiota by Metagenomic Approach Using Three Commercially Available DNA Extraction Protocols

Ivelina Vassileva¹, Vesselin Baev², Galina Yahubyan², Elena Apostolova-Kuzova², Angel Angelov³ and Miglena Koprinarova^1,4*

¹Institute of Molecular Biology “Acad. Roumen Tsanev”, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. bl. 21, 1113 Sofia, Bulgaria

²Department of Plant Physiology and Molecular Biology, Tzar Assen 24, University of Plovdiv, 4000 Plovdiv, Bulgaria

³Department of Biotechnology, University of Food Technologies, 26 Maritza Blvd., 4002 Plovdiv, Bulgaria

⁴Department of Catering and Nutrition, University of Food Technologies, 26 Maritza Blvd., 4002 Plovdiv, Bulgaria

Article history:

Received: 24 May 2022

Accepted: 6 February 2023

Keywords:

sourdough; DNA extraction methods; V1-V3 16S rRNA; next-generation sequencing; metagenomics; microbiota

Summary:

Research background. Sourdough is a spontaneously formed, complex microbial ecosystem of various lactic acid bacteria (LAB) and yeast which, by producing specific metabolites, determines the quality of the baked products. In order to design and control the sourdough with preferred nutritional characteristics, it is crucial that the LAB diversity ofthe product of interest be elucidated.

Experimental approach. Using the opportunities of next-generation sequencing (NGS) of the V1–V3 hypervariable gene region of 16S rRNA, we studied the microbial ecosystem of a whole grain sourdough made of Triticum monococcum, originating from Southwestern Bulgaria. Since the DNA extraction method is considered crucial for the accuracy of the sequencing results, as it can introduce significant differences in the examined microbiota, we used three different commercial kits for DNA isolation and analyzed their impact on the observed bacterial diversity.

Results and conclusions. All three DNA extraction kits provided bacterial DNA which passed quality control and was successfully sequenced on Illumina MiSeq platform. The results received from the different DNA protocols showed variations in the microbial profiles. Alpha diversity indices (ACE, Chao1, Shannon, and Simpson) were also different among the three groups of results. Nevertheless, a strong dominance of phylum Firmicutes, class Bacilli, order Lactobacillales, represented mostly by family Lactobacillaceae, genus Lactobacillus (relative abundance of 63.11–82.28 %) and family Leuconostocaceae, genus Weissella (relative abundance of 3.67–36.31 %) was observed. Lactiplantibacillus plantarum and Levilactobacillus brevis with relative abundance of 16.15–31.24 % and 6.21−16.29 % respectively, were the two dominant species identified in all three DNA isolates.

Novelty and scientific contribution. The presented results give insight into the taxonomic composition of bacterial community of a specific Bulgarian sourdough. Having in mind that the sourdough is a difficult matrix for DNA isolation on the one hand, and that there is no standardized DNA extraction protocol for this matrix on the other hand, this pilot study aims to give a small contribution to the future establishment and validation of such a protocol, which will allow accurate assessment of the specific microbiota of sourdough samples.