title: Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations.
abstract: BACKGROUND
  Dietary fibers contribute to health and physiology primarily via the fermentative actions of the host's gut microbiome. Physicochemical properties such as solubility, fermentability, viscosity, and gel-forming ability differ among fiber types and are known to affect metabolism. However, few studies have focused on how they influence the gut microbiome and how these interactions influence host health. The aim of this study is to investigate how the gut microbiome of growing pigs responds to diets containing gel-forming alginate and fermentable resistant starch and to predict important interactions and functional changes within the microbiota.
  
  
  RESULTS
  Nine growing pigs (3-month-old), divided into three groups, were fed with either a control, alginate-, or resistant starch-containing diet (CON, ALG, or RS), and fecal samples were collected over a 12-week period. SSU (small subunit) rDNA amplicon sequencing data was annotated to assess the gut microbiome, whereas comprehensive microarray polymer profiling (CoMPP) of digested material was employed to evaluate feed degradation. Gut microbiome structure variation was greatest in pigs fed with resistant starch, where notable changes included the decrease in alpha diversity and increase in relative abundance of Lachnospiraceae- and Ruminococcus-affiliated phylotypes. Imputed function was predicted to vary significantly in pigs fed with resistant starch and to a much lesser extent with alginate; however, the key pathways involving degradation of starch and other plant polysaccharides were predicted to be unaffected. The change in relative abundance levels of basal dietary components (plant cell wall polysaccharides and proteins) over time was also consistent irrespective of diet; however, correlations between the dietary components and phylotypes varied considerably in the different diets.
  
  
  CONCLUSIONS
  Resistant starch-containing diet exhibited the strongest structural variation compared to the alginate-containing diet. This variation gave rise to a microbiome that contains phylotypes affiliated with metabolically reputable taxonomic lineages. Despite the significant microbiome structural shifts that occurred from resistant starch-containing diet, functional redundancy is seemingly apparent with respect to the microbiome's capacity to degrade starch and other dietary polysaccharides, one of the key stages in digestion.
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr. Magnus Falsens Vei 1, P.O. Box 5003, N-1432 Ås Akershus, Norway.
authors.forename: Özgün C O
authors.initials: ÖC
authors.lastname: Umu
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr. Magnus Falsens Vei 1, P.O. Box 5003, N-1432 Ås Akershus, Norway.
authors.forename: Jeremy A
authors.initials: JA
authors.lastname: Frank
authors.affiliation: Department of Plant Biology and Biotechnology, University of Copenhagen, Copenhagen, DK-1871 Denmark.
authors.forename: Jonatan U
authors.initials: JU
authors.lastname: Fangel
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr. Magnus Falsens Vei 1, P.O. Box 5003, N-1432 Ås Akershus, Norway.
authors.forename: Marije
authors.initials: M
authors.lastname: Oostindjer
authors.affiliation: Adaptation Physiology Group, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands ; Animal Nutrition Group, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands.
authors.forename: Carol Souza
authors.initials: CS
authors.lastname: da Silva
authors.affiliation: Adaptation Physiology Group, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Bolhuis
authors.affiliation: Animal Nutrition Group, Wageningen University, PO Box 338, 6700 AH Wageningen, The Netherlands.
authors.forename: Guido
authors.initials: G
authors.lastname: Bosch
authors.affiliation: Department of Plant Biology and Biotechnology, University of Copenhagen, Copenhagen, DK-1871 Denmark.
authors.forename: William G T
authors.initials: WG
authors.lastname: Willats
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr. Magnus Falsens Vei 1, P.O. Box 5003, N-1432 Ås Akershus, Norway.
authors.forename: Phillip B
authors.initials: PB
authors.lastname: Pope
authors.affiliation: Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Chr. Magnus Falsens Vei 1, P.O. Box 5003, N-1432 Ås Akershus, Norway.
authors.forename: Dzung B
authors.initials: DB
authors.lastname: Diep
keywords: 16S rRNA gene; Alginate; Bacterial community; Growing pigs; Gut microbiota; Resistant starch