title: Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function.
abstract: Bifidobacteria, often associated with the gastrointestinal tract of animals, are well known for their roles as probiotics. Among the dozens of Bifidobacterium species, Bifidobacterium bifidum, B. breve, and B. longum are the ones most frequently isolated from the feces of infants and known to help the digestion of human milk oligosaccharides. To investigate the correlation between the metabolic properties of bifidobacteria and their phylogeny, we performed a phylogenomic analysis based on 452 core genes of forty-four completely sequenced Bifidobacterium species. Results show that a major evolutionary event leading to the clade of the infant-adapted species is linked to carbohydrate metabolism, but it is not the only factor responsible for the adaptation of bifidobacteria to the gut. The genome of B. longum subsp. infantis, a typical bifidobacterium in the gut of breast-fed infants, encodes proteins associated with several kinds of species-specific metabolic pathways, including urea metabolism and biosynthesis of riboflavin and lantibiotics. Our results demonstrate that these metabolic features, which are associated with the probiotic function of bifidobacteria, are species-specific and highly correlate with their phylogeny.
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
authors.forename: Min-Jung
authors.initials: MJ
authors.lastname: Kwak
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
authors.forename: Soon-Kyeong
authors.initials: SK
authors.lastname: Kwon
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
authors.forename: Jae-Kyung
authors.initials: JK
authors.lastname: Yoon
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
authors.forename: Ju Yeon
authors.initials: JY
authors.lastname: Song
authors.affiliation: R&D Center, Cell Biotech Co., Ltd., 50, Aegibong-ro 409 beon-gil, Wolgot-myeon, Gimpo-si, Gyeonggi-do 10003, Republic of Korea.
authors.forename: Jae-Gu
authors.initials: JG
authors.lastname: Seo
authors.affiliation: R&D Center, Cell Biotech Co., Ltd., 50, Aegibong-ro 409 beon-gil, Wolgot-myeon, Gimpo-si, Gyeonggi-do 10003, Republic of Korea.
authors.forename: Myung Jun
authors.initials: MJ
authors.lastname: Chung
authors.affiliation: Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul 03722, Republic of Korea. Electronic address: jfk1@yonsei.ac.kr.
authors.forename: Jihyun F
authors.initials: JF
authors.lastname: Kim
mesh_terms: D001430:Bacteriocins / Q000096:biosynthesis; D001483:Base Sequence; D001644:Bifidobacterium / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D001942:Breast Feeding; D004063:Digestion; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D007223:Infant; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008895:Milk, Human / Q000378:metabolism*; D010802:Phylogeny; D019936:Probiotics; D012256:Riboflavin / Q000096:biosynthesis; D017422:Sequence Analysis, DNA; D014508:Urea / Q000378:metabolism
chemical_list: D001430:Bacteriocins; D014508:Urea; D012256:Riboflavin
keywords: Gut microbiota; Orthologous genes; Phylogenetic tree; Probiotics