title: PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria.
abstract: This study assessed the relative contributions of host genetics and diet in shaping the gut microbiota of rainbow trout. Full sibling fish from four unrelated families, each consisting of individuals derived from the mating of one male and one female belonging to a breeding program, were fed diets containing either vegetable proteins or vegetable oils for two months in comparison to a control diet consisting of only fish protein and fish oil. Two parallel approaches were applied on the same samples: transcriptionally active bacterial populations were examined based on RNA analysis and were compared with bacterial populations obtained from DNA analysis. Comparison of temporal temperature gradient gel electrophoresis (TTGE) profiles from DNA and RNA showed important differences, indicating that active bacterial populations were better described by RNA analysis. Results showed that some bacterial groups were significantly (P<0.05) associated with specific families, indicating that microbiota composition may be influenced by the host. In addition, the effect of diet on microbiota composition was dependent on the trout family.
authors.affiliation: Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Región Metropolitana, Chile. pnavarre@inta.cl
authors.forename: Paola
authors.initials: P
authors.lastname: Navarrete
authors.forename: Fabien
authors.initials: F
authors.lastname: Magne
authors.forename: Cristian
authors.initials: C
authors.lastname: Araneda
authors.forename: Pamela
authors.initials: P
authors.lastname: Fuentes
authors.forename: Luis
authors.initials: L
authors.lastname: Barros
authors.forename: Rafael
authors.initials: R
authors.lastname: Opazo
authors.forename: Romilio
authors.initials: R
authors.lastname: Espejo
authors.forename: Jaime
authors.initials: J
authors.lastname: Romero
mesh_terms: D000821:Animal Feed; D000818:Animals; D004269:DNA, Bacterial / Q000378:metabolism; D058645:Denaturing Gradient Gel Electrophoresis / Q000379:methods*; D004463:Ecology; D004751:Enteritis / Q000382:microbiology; D007422:Intestines / Q000382:microbiology*; D054892:Metagenome; D008856:Microscopy, Fluorescence / Q000379:methods; D017686:Oncorhynchus mykiss; D010802:Phylogeny; D010938:Plant Oils / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D012313:RNA / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D014675:Vegetables / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D010938:Plant Oils; D012336:RNA, Ribosomal, 16S; D012313:RNA