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Background   Fructobacillus  spp. in fructose-rich niches belong to the family  Leuconostocaceae . They were originally classified as  Leuconostoc  spp., but were later grouped into a novel genus,  Fructobacillus , based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of  Fructobacillus  spp. and compared their metabolic properties against those of  Leuconostoc  spp.    Results   Fructobacillus  species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The  adhE  gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in  Fructobacillus  spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position.    Conclusion  The present genome characteristics in  Fructobacillus  spp. suggest reductive evolution that took place to adapt to specific niches.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2339-x) contains supplementary material, which is available to authorized users.

Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.