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. 2019 May 23;20(1):416.
doi: 10.1186/s12864-019-5783-1.

Comparative genome analysis of the Lactobacillus brevis species

Marine Feyereisen  1 , Jennifer Mahony  1   2 , Philip Kelleher  1 , Richard John Roberts  3 , Tadhg O'Sullivan  4 , Jan-Maarten A Geertman  4 , Douwe van Sinderen  5   6
Affiliations

Comparative genome analysis of the Lactobacillus brevis species

Marine Feyereisen et al. BMC Genomics. .

Abstract

Background: Lactobacillus brevis is a member of the lactic acid bacteria (LAB), and strains of L. brevis have been isolated from silage, as well as from fermented cabbage and other fermented foods. However, this bacterium is also commonly associated with bacterial spoilage of beer.

Results: In the current study, complete genome sequences of six isolated L. brevis strains were determined. Five of these L. brevis strains were isolated from beer (three isolates) or the brewing environment (two isolates), and were characterized as beer-spoilers or non-beer spoilers, respectively, while the sixth isolate had previously been isolated from silage. The genomic features of 19 L. brevis strains, encompassing the six L. brevis strains described in this study and thirteen L. brevis strains for which complete genome sequences were available in public databases, were analyzed with particular attention to evolutionary aspects and adaptation to beer.

Conclusions: Comparative genomic analysis highlighted evolution of the taxon allowing niche colonization, notably adaptation to the beer environment, with approximately 50 chromosomal genes acquired by L. brevis beer-spoiler strains representing approximately 2% of their total chromosomal genetic content. These genes primarily encode proteins that are putatively involved in oxidation-reduction reactions, transcription regulation or membrane transport, functions that may be crucial to survive the harsh conditions associated with beer. The study emphasized the role of plasmids in beer spoilage with a number of unique genes identified among L. brevis beer-spoiler strains.

Keywords: Beer adaptation; Beer spoilage; Genomics; Lactobacillus brevis; Pan-genome; SMRT sequencing.

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Conflict of interest statement

The authors declare that TOS and JG are employees of Heineken and supplied Lb. brevis strains UCCLB521, UCCLB556, UCCLB95, UCCLBBS124 and UCCLBBS449.

Figures

Fig. 1
Fig. 1
Growth profile of L. brevis strains sequenced in this study. Growth profile of L. brevis strains UCCLBBS124, UCCLBBS449, UCCLB95, UCCLB521, UCCLB556 and SA-C12 in (a) MRS broth or (b) beer. Growth curves were performed in triplicate and the average of those measurements is displayed in the graph above
Fig. 2
Fig. 2
Phylogenetic analysis of L. brevis species. a 16S ribosomal tree obtained from the alignment of the 16S rRNA-encoding genes of 19 L. brevis strains, bootstrapped × 1000 replicates, values > 250 are indicated. The 16S rRNA sequence of Enterococcus faecalis V583 (noted EF on the figure) was used as an outgroup. b Phylogenetic supertree obtained from the alignment of 631 orthologous genes among the 19 L. brevis strains used in this study as well as in Enterococcus faecalis V583 (noted EF on the figure) which was used as an outgroup, bootstrapped × 1000 replicates, values > 250 are indicated. Source of isolation for the different L. brevis strains are also indicated
Fig. 3
Fig. 3
Pan- and core-genome of L. brevis. Accumulated number of new genes in the L. brevis pan-genome plotted against the number of new genomes added as well as accumulated number of genes attributed to the core-genome plotted against the number of genomes added. Deduced mathematical functions are also displayed on the graph
Fig. 4
Fig. 4
Comparative genomics of chromosomal orthologous proteins in L. brevis. Panel a: Venn diagram representing the orthologous and unique gene families of 19 L. brevis strains obtained by MCL clustering. Panel b: Cluster of Orthologous Groups (COG) classification of L. brevis. Histograms represent COG predictions for each of the following 16 L. brevis isolates: L. brevis 100D8, L. brevis ATCC 367, L. brevis BDGP6, L. brevis KB290, L. brevis NCTC13768, L. brevis NPS-QW-145, L. brevis SA-C12, L. brevis SRCM101106, L. brevis SRCM101174, L. brevis TMW 1.2108, L. brevis TMW 1.2111, L. brevis TMW 1.2112, L. brevis TMW 1.2113, L. brevis UCCLB521, L. brevis UCCLB556, L. brevis UCCLB95, L. brevis UCCLBBS124, L. brevis UCCLBBS449, L. brevis ZLB004
Fig. 5
Fig. 5
Association between chromosome size and CDS number in nineteen L. brevis complete chromosomal sequences
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