title: Comparative genomics of Fructobacillus spp. and Leuconostoc spp. reveals niche-specific evolution of Fructobacillus spp.
abstract: 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.
  
  
  CONCLUSIONS
  The present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specific niches.
authors.affiliation: Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido, 099-2493, Japan. a3endou@bioindustry.nodai.ac.jp.
authors.forename: Akihito
authors.initials: A
authors.lastname: Endo
authors.affiliation: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan. ytanizaw@nig.ac.jp.|Center for Information Biology, National Institute of Genetics, Mishima, Japan. ytanizaw@nig.ac.jp.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Tanizawa
authors.affiliation: NODAI Culture Collection Centre, Tokyo University of Agriculture, Tokyo, Japan. n3tanaka@nodai.ac.jp.
authors.forename: Naoto
authors.initials: N
authors.lastname: Tanaka
authors.affiliation: Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido, 099-2493, Japan. 47715003@bioindustry.nodai.ac.jp.
authors.forename: Shintaro
authors.initials: S
authors.lastname: Maeno
authors.affiliation: Functional Foods Forum, University of Turku, Turku, Finland. kumar.himanshu@utu.fi.
authors.forename: Himanshu
authors.initials: H
authors.lastname: Kumar
authors.affiliation: Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan. y3shiwa@icloud.com.
authors.forename: Yuh
authors.initials: Y
authors.lastname: Shiwa
authors.affiliation: NODAI Culture Collection Centre, Tokyo University of Agriculture, Tokyo, Japan. sokada@nodai.ac.jp.
authors.forename: Sanae
authors.initials: S
authors.lastname: Okada
authors.affiliation: Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan. hiyoshik@nodai.ac.jp.|Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan. hiyoshik@nodai.ac.jp.
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Yoshikawa
authors.affiliation: Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa. lmtd@sun.ac.za.
authors.forename: Leon
authors.initials: L
authors.lastname: Dicks
authors.affiliation: Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido, 099-2493, Japan. j3nakaga@bioindustry.nodai.ac.jp.
authors.forename: Junichi
authors.initials: J
authors.lastname: Nakagawa
authors.affiliation: Center for Information Biology, National Institute of Genetics, Mishima, Japan. arita@nig.ac.jp.|RIKEN Center for Sustainable Resource Science, Yokohama, Japan. arita@nig.ac.jp.
authors.forename: Masanori
authors.initials: M
authors.lastname: Arita
mesh_terms: D001482:Base Composition / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D056584:Leuconostocaceae / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial