Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs

Abstract

Sourdough has played a significant role in human nutrition and culture for thousands of years and is still of eminent importance for human diet and the bakery industry. Lactobacillus sanfranciscensis is the predominant key bacterium in traditionally fermented sourdoughs.The genome of L. sanfranciscensis TMW 1.1304 isolated from an industrial sourdough fermentation was sequenced with a combined Sanger/454-pyrosequencing approach followed by gap closing by walking on fosmids. The sequencing data revealed a circular chromosomal sequence of 1,298,316 bp and two additional plasmids, pLS1 and pLS2, with sizes of 58,739 bp and 18,715 bp, which are predicted to encode 1,437, 63 and 19 orfs, respectively. The overall GC content of the chromosome is 34.71%. Several specific features appear to contribute to the ability of L. sanfranciscensis to outcompete other bacteria in the fermentation. L. sanfranciscensis contains the smallest genome within the lactobacilli and the highest density of ribosomal RNA operons per Mbp genome among all known genomes of free-living bacteria, which is important for the rapid growth characteristics of the organism. A high frequency of gene inactivation and elimination indicates a process of reductive evolution. The biosynthetic capacity for amino acids scarcely availably in cereals and exopolysaccharides reveal the molecular basis for an autochtonous sourdough organism with potential for further exploitation in functional foods. The presence of two CRISPR/cas loci versus a high number of transposable elements suggests recalcitrance to gene intrusion and high intrinsic genome plasticity.

Genomics of Weissella cibaria with an examination of its metabolic traits

“…However, the low number of transposases in these strains of W. cibaria is in stark contrast to the 111 found in another sourdough LAB, Lactobacillus sanfranciscensis TMW 1.1304, in which it was suggested that their high number facilitated niche adaptation of this strain (Vogel et al, 2011).…”

“…Oxygen tolerance. Tolerance of oxygen in LAB generally requires the presence of NADH oxidase or several thiol-active enzyme systems, including the glutathioneglutathione reductase system, the thioredoxin-thioredoxin reductase couple and cysteine uptake and metabolism capability (Vogel et al, 2011). In the genome of W. cibaria MG1 putative homologues of functional proteins in these systems were identified, including an NADH oxidase, three glutathione reductase genes, a glutathione peroxidase and thioredoxin reductase.…”

“…None of these W. cibaria bacteriophages was isolated from sourdough, and very few phages have been isolated from this niche. It is thought that phage infections and spread in sourdough may be hampered by the dough's solid nature and texture (Vogel et al, 2011).…”

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“…In most cases, genome assembly was done using different versions of Newbler assembler 33,39 except in a few cases where gsAssembler 36,37 or CLC Genomics Workbench 37 Phred-Phrap-Consed software package 41 . Genome annotation was done using the Rapid Assembly using Subsystems Technology (RAST) server 38 -40 , often combined with Glimmer 38 , tRNAscan-SE 38 , RNAmmer 38 , EDGAR 36 , PEDANT 41 , GeneMark 41 , and NCBI Prokaryotic Genome Automated Annotation Pipeline (PGAAP) analysis 33,36 .…”

“…Genome annotation was done using the Rapid Assembly using Subsystems Technology (RAST) server 38 -40 , often combined with Glimmer 38 , tRNAscan-SE 38 , RNAmmer 38 , EDGAR 36 , PEDANT 41 , GeneMark 41 , and NCBI Prokaryotic Genome Automated Annotation Pipeline (PGAAP) analysis 33,36 .…”