title: Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.
abstract: BACKGROUND
  In our published randomized, double-blind, placebo-controlled, 3-period crossover trial, healthy adult men (n = 21) consumed bars containing no supplemental fiber (placebo; NFC), polydextrose (21 g/d), and soluble corn fiber (SCF; 21 g/d) for 21 d each. Fecal specimens were collected between days 16 and 21 for fermentative end-product analysis and 16S ribosomal RNA bacterial gene amplification for bacterial taxa identification. Fiber supplementation decreased fecal putrefaction compounds and shifted abundances of several bacterial taxa.
  
  
  OBJECTIVE
  The objective was to perform whole-genome shotgun 454 pyrosequencing on the same fecal specimens collected in that clinical trial to obtain comprehensive fecal bacterial genome sequencing coverage and explore the full range of bacterial genetic information in the fecal microbiome, thereby using a systematic approach to study the impact of dietary fiber supplementation on fecal metabolites, bacterial taxa, and bacterial metagenomes.
  
  
  METHODS
  Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing to identify both fecal bacterial populations present and their functional genetic capacity.
  
  
  RESULTS
  Whole-genome shotgun sequencing results revealed that fiber consumption shifted the Bacteroidetes:Firmicutes ratio, increasing the relative abundance of Bacteroidetes 12 ± 2% and 13 ± 2% with polydextrose and SCF, respectively, compared with NFC. Bivariate correlations showed a positive correlation between the Bacteroidetes:Firmicutes ratio and total dietary fiber intake but not body mass index. Principal coordinates analysis of Bray-Curtis distances indicated that bacterial gene composition was more similar in participants consuming fibers (polydextrose and SCF combined) in comparison with NFC. Shifts in bacterial gene abundances after polydextrose and SCF supplementation included genes associated with carbohydrate, amino acid, and lipid metabolism, as well as metabolism of cofactors and vitamins.
  
  
  CONCLUSIONS
  This study conveys novel information about the impact of dietary fiber supplementation on the phylogenetic structure and functional capacity of the fecal microbiome of healthy adults.
authors.affiliation: From the Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL (HDH, SH, GCF, and KSS); the Department of Biological Sciences and Computer Sciences, Northern Arizona University, Flagstaff, AZ (JGC); and General Mills Inc., Bell Institute of Health and Nutrition, Minneapolis, MN (JMB).
authors.forename: Hannah D
authors.initials: HD
authors.lastname: Holscher
authors.affiliation: From the Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL (HDH, SH, GCF, and KSS); the Department of Biological Sciences and Computer Sciences, Northern Arizona University, Flagstaff, AZ (JGC); and General Mills Inc., Bell Institute of Health and Nutrition, Minneapolis, MN (JMB).
authors.forename: J Gregory
authors.initials: JG
authors.lastname: Caporaso
authors.affiliation: From the Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL (HDH, SH, GCF, and KSS); the Department of Biological Sciences and Computer Sciences, Northern Arizona University, Flagstaff, AZ (JGC); and General Mills Inc., Bell Institute of Health and Nutrition, Minneapolis, MN (JMB).
authors.forename: Seema
authors.initials: S
authors.lastname: Hooda
authors.affiliation: From the Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL (HDH, SH, GCF, and KSS); the Department of Biological Sciences and Computer Sciences, Northern Arizona University, Flagstaff, AZ (JGC); and General Mills Inc., Bell Institute of Health and Nutrition, Minneapolis, MN (JMB).
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Brulc
authors.affiliation: From the Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL (HDH, SH, GCF, and KSS); the Department of Biological Sciences and Computer Sciences, Northern Arizona University, Flagstaff, AZ (JGC); and General Mills Inc., Bell Institute of Health and Nutrition, Minneapolis, MN (JMB).
authors.forename: George C
authors.initials: GC
authors.lastname: Fahey
authors.affiliation: From the Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL (HDH, SH, GCF, and KSS); the Department of Biological Sciences and Computer Sciences, Northern Arizona University, Flagstaff, AZ (JGC); and General Mills Inc., Bell Institute of Health and Nutrition, Minneapolis, MN (JMB).
authors.forename: Kelly S
authors.initials: KS
authors.lastname: Swanson
mesh_terms: D000328:Adult; D041963:Bacteroidetes / Q000145:classification / Q000254:growth & development* / Q000302:isolation & purification / Q000378:metabolism; D018592:Cross-Over Studies; D004068:Digestive System Physiological Phenomena; D004311:Double-Blind Method; D005243:Feces / Q000382:microbiology; D005285:Fermentation; D005500:Follow-Up Studies; D005936:Glucans / Q000008:administration & dosage / Q000009:adverse effects / Q000737:chemistry; D006094:Gram-Positive Bacteria / Q000145:classification / Q000254:growth & development* / Q000302:isolation & purification / Q000378:metabolism; D006801:Humans; D007087:Illinois; D007422:Intestines / Q000382:microbiology* / Q000502:physiology; D008297:Male; D064307:Microbiota; D058889:Molecular Typing; D010802:Phylogeny; D056692:Prebiotics / Q000009:adverse effects; D025341:Principal Component Analysis; D012995:Solubility; D055815:Young Adult; D003313:Zea mays / Q000009:adverse effects / Q000737:chemistry
chemical_list: D005936:Glucans; D056692:Prebiotics; C033375:polydextrose
keywords: fiber; gastrointestinal microbiota; metagenome; microbiome; prebiotic