bbc 2015

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015
Abstract ID: P
Poster
10th Benelux Bioinformatics Conference bbc 2015
P64. THE COMPLETE GENOME SEQUENCE OF LACTOBACILLUS
FERMENTUM IMDO 130101 AND ITS METABOLIC TRAITS RELATED TO
THE SOURDOUGH FERMENTATION PROCESS
Marko Verce, Koen Illeghems, Luc De Vuyst & Stefan Weckx * .
Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering
Sciences, Vrije Universiteit Brussel, Brussels, Belgium. * stefan.weckx@vub.ac.be
The genome of the lactic acid bacterium species Lactobacillus fermentum IMDO 130101, capable of dominating
sourdough fermentation processes, was sequenced, annotated, and curated. Further, this genome sequence of 2.09 Mbp
was compared to other complete genomes of different strains of L. fermentum to elucidate the potential of L. fermentum
IMDO 130101 as a sourdough starter culture strain. As opposed to the other strains, L. fermentum IMDO 130101
contained unique genes related to carbohydrate import and metabolism as well as a gene coding for a phenolic acid
decarboxylase and a gene encoding a 4,6- -glucanotransferase. The latter enzyme activity may result in the production
of isomalto/malto-polysaccharides. All these features make L. fermentum IMDO 130101 attractive for further study as a
candidate sourdough starter culture strain.
INTRODUCTION
Lactobacillus fermentum is a heterofermentative lactic
acid bacterium often found in fermented food products,
including sourdough. Strain L. fermentum IMDO 130101,
a dominant sourdough strain originally isolated from a rye
sourdough (Weckx et al., 2010) and extensively described
previously (e.g., Vrancken et al., 2008), was sequenced
and compared to other L. fermentum strains with
completed genomes to elucidate unique adaptations of the
strain studied to the sourdough environment.
METHODS
High-quality genomic DNA was used to construct an 8-kb
paired-end library for 454 pyrosequencing. The
pyrosequencing reads were assembled using the GS De
Novo Assembler version 2.5.3 with default parameters.
Primers for gap closure were designed using CONSED
23.0, the gaps amplified with polymerase chain reaction
(PCR) assays and the amplicons sequenced using Sanger
sequencing. The sequences were imported into CONSED
23.0 and used to close the gaps. The genome was
annotated using the automated genome annotation
platform GenDB v2.2 (Meyer et al., 2003), followed by
extensive manual curation. Publicly available genome
sequences of L. fermentum F-6 (Sun et al., 2015), L.
fermentum IFO 3956 (Morita et al., 2008), and L.
fermentum CECT 5716 (Jiménez et al., 2010) were
acquired from RefSeq. Whole-genome comparisons with
the other three L. fermentum strains and ortholog findings
were performed using the progressiveMauve algorithm
(Darling et al., 2010).
RESULTS & DISCUSSION
The 2.09 Mbp genome was assembled from 403,466 reads,
resulting in 74 contigs. No plasmids were found. The
comparative genome analysis with other strains showed
that 477 coding sequences were found in L. fermentum
IMDO 130101 solely (Figure 1).
L. fermentum IMDO 130101 was predicted to be able to
import and utilise glucose, fructose, xylose, mannose, N-
acetylglucosamine, maltose, sucrose, lactose and gluconic
acid via the heterolactic fermentation pathway. Also, the
ability to degrade raffinose and arabinose was predicted.
Consumption of glucose, fructose, maltose and sucrose
was shown in previous research, although growth with
sucrose as the sole energy source was impaired (Vrancken
et al., 2008). The strain possibly imports isomaltose and
maltodextrins, hence elaborating glucose subunits. The
-glucosidase-encoding gene was not found in the
genomes of the other three strains considered, and neither
were the putative maltodextrin import-related genes, the
trehalose-6-phosphate phosphorylase-encoding gene and a
putative -glucanase-encoding gene, which all may be
adaptations of L. fermentum IMDO 130101 to the
sourdough environment. The presence of the arginine
deiminase gene cluster was confirmed. Also, L. fermentum
IMDO 130101 contained a gene for a phenolic acid
decarboxylase, which may have an impact on sourdough
aroma. Further, a 4,6- -glucanotransferase-encoding gene
was present in strain IMDO 130101 solely, which could
result in isomalto/malto-polysaccharide production, a
soluble dietary fibre with prebiotic properties.
Overall, comparative genome analysis revealed metabolic
traits that are of interest for the use of L. fermentum IMDO
130101 as a functional starter culture for sourdough
fermentation processes.
FIGURE 1. Venn diagram of shared coding sequences between four
different strains of Lactobacillus fermentum.
REFERENCES
Darling et al. PLoS ONE 5, e11147 (2010).
Jiménez E. et al. J. Bacteriol. 192, 4800-4800 (2010).
Meyer et al. Nucleic Acids Res. 31, 2187-2195 (2003).
Morita et al. DNA Res. 15: 151-161 (2008).
Sun et al. J. Biotechnol. 194, 110-111 (2015).
Vrancken et al. Int. J. Food Microbiol. 128, 58-66 (2008).
Weckx et al. Food Microbiol. 27, 1000-1008 (2010).
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