Dynamic interactions of lactic acid bacteria in Korean sourdough during back-slopping process

Water chlorination increases the relative abundance of an antibiotic resistance marker in developing sourdough starters

Multiple factors explain the proper development of sourdough starters. Although the role of raw ingredients and geography, among other things, have been widely studied recently, the possible effect of air quality and water chlorination on the overall bacterial communities associated with sourdough remains to be explored. Here, using 16S rRNA amplicon sequencing, we show that clean, filtered-air severely limited the presence of lactic acid bacteria in sourdough starters, suggesting that surrounding air is an important source of microorganisms necessary for the development of sourdough starters. We also show that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, using targeted sequencing, which offers a higher resolution, we found that the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic-resistance genes in spoilage and pathogenic bacteria, increased significantly with the level of water chlorination. Although our results suggest that water chlorination might not impact sourdough starters at a deep phylogenetic level, they indicate that it can favor the spread of genetic elements associated with spoilage bacteria.

IMPORTANCE

Proper development of sourdough starters is critical for making tasty and healthy bread. Although many factors contributing to sourdough development have been studied, the effect of water chlorination on the bacterial communities in sourdough has been largely ignored. Researchers used sequencing techniques to investigate this effect and found that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, they discovered that water chlorination could increase the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic resistance genes in spoilage and pathogenic bacteria. This suggests that water chlorination could favor the growth of key spoilage bacteria and compromise the quality and safety of the bread. These findings emphasize the importance of considering water quality when developing sourdough starters for the best possible bread.

Comparative Genomics Reveals Genetic Diversity and Variation in Metabolic Traits in Fructilactobacillus sanfranciscensis Strains

Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified. In this research, 14 F. sanfranciscensis strains were isolated from sourdough samples to evaluate the genetic diversity and variation in metabolic traits. These 14 and 31 other strains (obtained from the NCBI database) genomes were compared. The values for genome size and GC content, on average, turned out to 1.31 Mbp and 34.25%, respectively. In 45 F. sanfranciscensis strains, there were 162 core genes and 0 to 51 unique genes present in each strain. The primary functions of core genes were related to nucleotide, lipid transport, and amino acid, as well as carbohydrate metabolism. The size of core genes accounted for 41.18% of the pan-genome size in 14 F. sanfranciscensis strains, i.e., 0.70 Mbp of 1.70 Mbp. There were genetic variations among the 14 strains involved in carbohydrate utilization and antibiotic resistance. Moreover, exopolysaccharides biosynthesis-related genes were annotated, including epsABD, wxz, wzy. The Type IIA & IE CRISPR-Cas systems, pediocin PA-1 and Lacticin_3147_A1 bacteriocins operons were also discovered in F. sanfranciscensis. These findings can help to select desirable F. sanfranciscensis strains to develop standardized starter culture for sourdough fermentation, and expect to provide traditional fermented pasta with a higher quality and nutritional value for the consumers.

Identification of Key Parameters Inducing Microbial Modulation during Backslopped Kombucha Fermentation

The aim of this study was to assess the impact of production parameters on the reproducibility of kombucha fermentation over several production cycles based on backslopping. Six conditions with varying oxygen accessibility (specific interface surface) and initial acidity (through the inoculation rate) of the cultures were carried out and compared to an original kombucha consortium and a synthetic consortium assembled from yeasts and bacteria isolated from the original culture. Output parameters monitored were microbial populations, biofilm weight, key physico-chemical parameters and metabolites. Results highlighted the existence of phases in microbial dynamics as backslopping cycles progressed. The transitions between phases occurred faster for the synthetic consortium compared to the original kombucha. This led to microbial dynamics and fermentative kinetics that were reproducible over several cycles but that could also deviate and shift abruptly to different behaviors. These changes were mainly induced by an increase in the Saccharomyces cerevisiae population, associated with an intensification of sucrose hydrolysis, sugar consumption and an increase in ethanol content, without any significant acceleration in the rate of acidification. The study suggests that the reproducibility of kombucha fermentations relies on high biodiversity to slow down the modulations of microbial dynamics induced by the sustained rhythm of backslopping cycles.

Distribution, inducibility, and characteristics of Latilactobacillus curvatus temperate phages

Aim: Temperate phages are known to heavily impact the growth of their host, be it in a positive way, e.g., when beneficial genes are provided by the phage, or negatively when lysis occurs after prophage induction. This study provides an in-depth look into the distribution and variety of prophages in Latilactobacillus curvatus (L. curvatus). This species is found in a wide variety of ecological niches and is routinely used as a meat starter culture. Methods: Fourty five L. curvatus genomes were screened for prophages. The intact predicted prophages and their chromosomal integration loci were described. Six L. curvatus lysogens were analysed for phage-mediated lysis post induction via UV light and/or mitomycin C. Their lysates were analysed for phage particles via viral DNA sequencing and transmission electron microscopy. Results: Two hundred and six prophage sequences of any completeness were detected within L. curvatus genomes. The 50 as intact predicted prophages show high levels of genetic diversity on an intraspecies level with conserved regions mostly in the replication and head/tail gene clusters. Twelve chromosomal loci, mostly tRNA genes, were identified, where intact L. curvatus phages were integrated. The six analysed L. curvatus lysogens showed strain-dependent lysis in various degrees after induction, yet only four of their lysates appeared to contain fully assembled virions with the siphovirus morphotype. Conclusion: Our data demonstrate that L. curvatus is a (pro)phage-susceptible species, harbouring multiple intact prophages and remnant sequences thereof. This knowledge provides a basis to study phage-host interaction influencing microbial communities in food fermentations.

Taxonomic structure of bacterial communities in sourdoughs of spontaneous fermentation

The article is devoted to the study of the microbiome of spontaneously fermented sourdoughs. The aim of the work was to study the inf luence of the technological parameters of sourdough propagations on the taxonomic structure of the microbiome of spontaneously fermented sourdoughs. Two spontaneously fermented sourdoughs were studied: dense rye sourdough and liquid rye sourdough, both prepared using the same batch of peeled rye f lour. To study the taxonomic structure of the sourdough microbiome in dynamics, the method of high-throughput sequencing of 16S rRNA gene fragments of microorganisms was used. It was shown that the technological parameters of sourdough (humidity, temperature) do not affect the taxonomic composition of the microbiome of dense rye or liquid rye sourdough at the phylum/class/genus level. It was found that during the f irst three days of propagations, bacteria from the phyla Proteobacteria and Firmicutes dominated in the microbial community. In the phylum Proteobacteria, microorganisms from the order Enterobacterales took a large share, which persisted for three days of backslopping. The phylum Firmicutes was represented by lactic acid bacteria of the genera Weissella, Lactobacillus, Leuconostoc, Pediococcus, Lactococcus. It was established by classical microbiological methods that after a day of fermentation, the number of lactic acid bacteria cells was signif icantly higher in liquid rye sourdough compared to dense one. However, with further propagation of sourdoughs, the number of cells was comparable, while signif icant changes occurred at the level of genera and species. It was shown that as the relative number of lactic acid bacteria of the genus Lactobacillus increased, a gradual displacement of the coccal forms of Lactococcus, Leuconostoc, Weissella, Pediococcus happened. With further propagation of sourdough after 10 days, the position of the dominant groups of bacteria was occupied by representatives of the phylum Firmicutes, lactic acid bacteria of the genus Lactobacillus. The inf luence of the mode and parameters of the sourdough on the species composition of lactobacilli, which demonstrated a low bacterial diversity, is shown. In the f irst three days of propagations, lactobacilli L. curvatus, L. brevis, and Lactiplantibacil- lus sp. dominated in both sourdoughs. After a month of backslopping, Fructilactobacillus sanfranciscensis and Companilactobacillus sp. dominated in dense rye sourdough, and L. pontis dominated in liquid rye sourdough