Complete and Annotated Genome Sequence of the Sourdough Lactic Acid Bacterium Lactobacillus fermentum IMDO 130101

Various cold storage-backslopping cycles show the robustness of Limosilactobacillus fermentum IMDO 130101 as starter culture for Type 3 sourdough production

Type 3 sourdoughs, which are starter culture-initiated and subsequently backslopped, are less studied than other sourdough types. Yet, they can serve as a model to assess how competitive starter culture strains for sourdough production are and how the microbial composition of such sourdoughs may evolve over time. In the present study, Limosilactobacillus fermentum IMDO 130101 was used to produce Type 3 sourdoughs, prepared from wheat and wholemeal wheat flours. Therefore, an initial fermentation of the flour-water mixture was performed at 30 °C for 48 h. This was followed by cold storage-backslopping cycles, consisting of refreshments (50 %, v/v), fermentation steps of 16 h, and storage at 4 °C each week, every three weeks, and every six weeks. The microbial dynamics (culture-dependent and -independent approaches) and metabolite dynamics were measured. In all sourdoughs produced, starter culture strain monitoring, following an amplicon sequence variant approach, showed that Liml. fermentum IMDO 130101 prevailed during one month when the sourdoughs were refreshed each week, during 24 weeks when the sourdoughs were refreshed every three weeks, and during 12 weeks when the sourdoughs were refreshed every six weeks. This suggested the competitiveness and robustness of Liml. fermentum IMDO 130101 for a considerable duration but also showed that the strain is prone to microbial interference. For instance, Levilactobacillus brevis and Pediococcus spp. prevailed upon further cold storage and backslopping. Also, although no yeasts were inoculated into the flour-water mixtures, Kazachstania unispora, Torulaspora delbrueckii, and Wickerhamomyces anomalus were the main yeast species found. They appeared after several weeks of storage and backslopping, which however indicated the importance of an interplay between LAB and yeast species in sourdoughs. The main differences among the mature sourdoughs obtained could be explained by the different flours used, the refreshment conditions applied, and the sampling time (before and after backslopping). Finally, the metabolite quantifications revealed continued metabolite production during the cold storage periods, which may impact the sourdough properties and those of the breads made thereof.

Microbial ecology and metabolite dynamics of backslopped triticale sourdough productions and the impact of scale

Triticale (X Triticosecale Wittmack) is a hybrid of wheat (Triticum aestivum L.) and rye (Secale cereale L.), combining the positive attributes of both cereals. However, it has not been exploited for sourdough production yet. Further, the effect of scale on sourdough production has not been investigated systematically up to now. The aims of the present study were to assess the microbial ecology and metabolomic output of eleven spontaneously fermented, backslopped sourdough productions made with triticale flour on a scale of 100, 200, 500, and 1000 g. The acidification profile [pH and total titratable acidity (TTA)], microbial diversity (culture-dependent and culture-independent), metabolite dynamics, and appropriate correlations were determined. After ten fermentation steps, different species of Lactobacillaceae were prevalent in the mature sourdoughs, in particular Latilactobacillus curvatus, Limosilactobacillus fermentum, and Pediococcus pentosaceus. The microbial diversity could be traced back to the grains and was also present in the milling fractions (flour, bran, and shorts). Furthermore, thanks to the use of Illumina-based high-throughput sequencing and an amplicon sequence variant (ASV) approach, the presence of undesirable bacterial groups (bacilli, clostridia, and enterobacteria) during the initial steps of the backslopping cycle was revealed, as well as a finetuned taxonomic diversity of the LAB genera involved. Small sourdough productions (100 and 200 g) selected for a lower species diversity and reached a stable consortium faster than large ones (500 and 1000 g). Although a comparable final pH of 3.6-4.0 was obtained, the TTA of small sourdoughs was lower than that of large ones. Regarding the metabolic output, the simultaneous production of mannitol and erythritol, beyond ethanol and glycerol, could be linked to sourdoughs in which Liml. fermentum was the sole LAB species present. Further, the use of the arginine deiminase pathway by P. pentosaceus and Liml. fermentum was obvious. An appropriate extraction method followed by liquid injection gas chromatography coupled to triple quadrupole tandem mass spectrometry allowed the quantification of interesting volatile organic compounds, such as ethyl lactate. These findings support the inclusion of triticale as a viable alternative to wheat or rye for the production of sourdoughs that can be integrated into bread-making production schemes.

Comparative genomics of Lactobacillus fermentum suggests a free-living lifestyle of this lactic acid bacterial species

Lactobacillus fermentum is a lactic acid bacterium frequently isolated from mammal tissues, milk, and plant material fermentations, such as sourdough. A comparative genomics analysis of 28 L. fermentum strains enabled the investigation of the core and accessory genes of this species. The core protein phylogenomic tree of the strains examined, consisting of five clades, did not exhibit clear clustering of strains based on isolation source, suggesting a free-living lifestyle. Based on the presence/absence of orthogroups, the largest clade, containing most of the human-related strains, was separated from the rest. The extended core genome included genes necessary for the heterolactic fermentation. Many traits were found to be strain-dependent, for instance utilisation of xylose and arabinose. Compared to other strains, the genome of L. fermentum IMDO 130101, a candidate starter culture strain capable of dominating sourdough fermentations, contained unique genes related to the metabolism of starch degradation products, which could be advantageous for growth in sourdough matrices. This study explained the traits that were previously demonstrated for L. fermentum IMDO 130101 at the genetic level and provided future avenues of research regarding L. fermentum strains isolated from sourdough.