Identification of the microbiota in sugar extraction juices by sequencing-based techniques

The importance of microorganisms in the beet sugar industry came up in 1930. Since then, several approaches have been made to describe these bacteria. For this purpose, mainly cultivation-based methods were applied. However, the majority of the microorganisms cannot be cultivated or are in the viable-but-non-culturable state. In addition, these methods are time-consuming and costly. Progress in molecular biology allows a cheaper, faster and more precise identification of the microbiota. This study evaluates the application of an 16S rDNA-based metagenomic sequencing approach based on Illumina MiSeq technology to identify the microbiota in raw juice and juice of mid-tower in a beet sugar production plant and compares the results with those obtained by cultivation-based techniques. All bacteria orders detected with cultivation-based methods could be also found with the applied metagenomic approach. In raw juice, mainly mesophilic bacteria such as Lactobacillus spp. and Leuconostoc spp. species were identified. Additionally, a partly large proportion of gram-negative bacteria belonging to the order Enterobacterales were detected by the metagenomic approach. The diversity in juice of mid-tower was much lower and predominated by mainly thermophilic genera such as Geobacillus, Caldanaerobius and Thermoanaerobacter. The last two mentioned genera belong to the class of Clostridia. Surprisingly, in the juice of mid-tower Lactobacillus species could be verified by cultivation-based methods as well as by the metagenomic approach. As a consequence, it can be presumed that lactobacilli can survive in this very specific environment at 70 °C occurring in the central part of the extraction tower.