title: Starch and starch hydrolysates are favorable carbon sources for bifidobacteria in the human gut.
abstract: BACKGROUND
  Bifidobacteria are key commensals in human gut, and their abundance is associated with the health of their hosts. Although they are dominant in infant gut, their number becomes lower in adult gut. The changes of the diet are considered to be main reason for this difference. Large amounts of whole-genomic sequence data of bifidobacteria make it possible to elucidate the genetic interpretation of their adaptation to the nutrient environment. Among the nutrients in human gut, starch is a highly fermentable substrate and can exert beneficial effects by increasing bifidobacteria and/or being fermented to short chain fatty acids.
  
  
  RESULTS
  In order to determine the potential substrate preference of bifidobacteria, we compared the glycoside hydrolase (GH) profiles of a pooled-bifidobacterial genome (PBG) with a representative microbiome (RM) of the human gut. In bifidobacterial genomes, only 15% of GHs contained signal peptides, suggesting their weakness in utilization of complex carbohydrate, such as plant cell wall polysaccharides. However, compared with other intestinal bacteria, bifidobacteiral genomes encoded more GH genes for degrading starch and starch hydrolysates, indicating that they have genetic advantages in utilizing these substrates. Bifidobacterium longum subsp. longum BBMN68 isolated from centenarian's faeces was used as a model strain to further investigate the carbohydrate utilization. The pathway for degrading starch and starch hydrolysates was the only complete pathway for complex carbohydrates in human gut. It is noteworthy that all of the GH genes for degrading starch and starch hydrolysates in the BBMN68 genome were conserved in all studied bifidobacterial strains. The in silico analyses of BBMN68 were further confirmed by growth experiments, proteomic and real-time quantitative PCR (RT-PCR) analyses.
  
  
  CONCLUSIONS
  Our results demonstrated that starch and starch hydrolysates were the most universal and favorable carbon sources for bifidobacteria. The low amount of these carbon sources in adult intestine was speculated to contribute to the low relative abundance of bifidobacteria.
authors.affiliation: Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. 876910384@qq.com.
authors.forename: Songling
authors.initials: S
authors.lastname: Liu
authors.affiliation: Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. renfazheng@263.net.
authors.forename: Fazheng
authors.initials: F
authors.lastname: Ren
authors.affiliation: Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. 27782053@qq.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. lujiang_edu@163.com.|Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China. lujiang_edu@163.com.
authors.forename: Lu
authors.initials: L
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. h04024@cau.edu.cn.
authors.forename: Yanling
authors.initials: Y
authors.lastname: Hao
authors.affiliation: Beijing Laboratory for Food Quality and Safety, Beijing, 10083, China. 104110241@qq.com.
authors.forename: Junhua
authors.initials: J
authors.lastname: Jin
authors.affiliation: Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China. 36103805@qq.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Functional Dairy, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China. 5133323@qq.com.|Beijing Laboratory for Food Quality and Safety, Beijing, 10083, China. 5133323@qq.com.
authors.forename: Huiyuan
authors.initials: H
authors.lastname: Guo
authors.affiliation: Department of Animal Science, Cornell University, Ithaca, NY, 14853, USA. XL20@cornell.edu.
authors.forename: Xingen
authors.initials: X
authors.lastname: Lei
authors.affiliation: Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China. erna_sun@163.com.
authors.forename: Erna
authors.initials: E
authors.lastname: Sun
authors.affiliation: Higher Institution Engineering Research Center of Animal Product, Beijing, 10083, China. 15810152784@163.com.
authors.forename: Hongna
authors.initials: H
authors.lastname: Liu
mesh_terms: D001644:Bifidobacterium / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D050260:Carbohydrate Metabolism; D002244:Carbon / Q000378:metabolism*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D006868:Hydrolysis; D053858:Metabolic Networks and Pathways / Q000235:genetics; D013213:Starch / Q000378:metabolism*
chemical_list: D002244:Carbon; D013213:Starch