title: Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage.
abstract: BACKGROUND
  The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community (microbiome) in newly weaned (35 days of age) piglets. The piglets were fed a cereal-based diet without (B) and with inclusion (80 and 160 g/kg air-dry forage) of vegetative shoots of chicory (C) and leaves of ribwort (R) forage in a 35-day growth trial. Fecal samples were collected at the start (D0), 17 (D17) and 35 (D35) days after weaning and profiles of the microbial consortia were generated using terminal restriction fragment length polymorphism (T-RFLP). 454-FLX pyrosequencing of 16S rRNA gene amplicons was used to analyze the microbial composition in a subset of the samples already analyzed with T-RFLP.
  
  
  RESULTS
  The microbial clustering pattern was primarily dependent on age of the pigs, but diet effects could also be observed. Lactobacilli and enterobacteria were more abundant at D0, whereas the genera Streptococcus, Treponema, Clostridium, Clostridiaceae1 and Coprococcus were present in higher abundances at D35. Pigs fed ribwort had an increased abundance of sequences classified as Treponema and a reduction in lactobacilli. However, the abundance of Prevotellaceae increased with age in on both the chicory and the ribwort diet. Moreover, there were significant correlations between the abundance of Bacteroides and the digested amount of galactose, uronic acids and total non-starch polysaccharides, and between the abundance of Bacteroidales and the digested amount of xylose.
  
  
  CONCLUSIONS
  This study demonstrated that both chicory and ribwort inclusion in the diet of newly weaned pigs influenced the composition of the fecal microbiota and that digestion of specific dietary components was correlated with species composition of the microbiota. Moreover, this study showed that the gut will be exposed to a dramatic shift in the microbial community structure several weeks after weaning.
authors.affiliation: Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, P.O. Box 7024, SE75007 Uppsala, Sweden ; Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, SE75007 Uppsala, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Dicksved
authors.affiliation: Division of Biology Earth and Biological Sciences, Pacific Northwest National Laboratories, P.O. Box 999, MSIN J4-18, WA99352 Richland, WA USA.
authors.forename: Janet K
authors.initials: JK
authors.lastname: Jansson
authors.affiliation: Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, P.O. Box 7024, SE75007 Uppsala, Sweden.
authors.forename: Jan Erik
authors.initials: JE
authors.lastname: Lindberg
keywords: 16S; Amplicon sequencing; Chicory; Microbiome; Ribwort; Uronic acid; Weaning